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t

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

☑ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2025

or

☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from to

Commission file number: 001-35969

PTC Therapeutics, Inc.

(Exact name of registrant as specified in its charter)

​

​ | ​ | ​
Delaware |  | 04-3416587
(State or other jurisdiction of incorporation or organization) | ​ | (I.R.S. Employer Identification No.)

​

​ | ​ | ​
500 Warren Corporate Center Drive |  | ​
Warren, NJ | ​ | 07059
(Address of principal executive offices) | ​ | (Zip Code)

​

(908) 222-7000

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

​

​ | ​ | ​ | ​ | ​
Title of each class |  | Trading Symbol(s) |  | Name of each exchange on which registered
Common Stock, $0.001 par value per share | ​ | PTCT | ​ | Nasdaq Global Select Market

​

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes þ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer”, “accelerated filer,” “smaller reporting company,” and "emerging growth company" in Rule 12b-2 of the Exchange Act.

​

​ | ​ | ​ | ​
Large accelerated filer | þ | Accelerated filer | ☐
​ | ​ | ​ | ​
Non-accelerated filer | ☐ | Smaller reporting company | ☐
​ | ​ | ​ | ​
​ | ​ | Emerging growth company | ☐

​

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

​

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No þ

​

As of November 3, 2025, there were 80,288,305 shares of Common Stock, $0.001 par value per share, outstanding.

​

​

​

Table of Contents

TABLE OF CONTENTS

PTC Therapeutics, Inc.

​ | ​
​ | Page No.
PART I—FINANCIAL INFORMATION | ​
| ​
Item 1. Financial Statements (unaudited) | 4
| ​
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations | 41
| ​
Item 3. Quantitative and Qualitative Disclosures About Market Risk | 61
| ​
Item 4. Controls and Procedures | 61
| ​
PART II—OTHER INFORMATION | ​
| ​
Item 1. Legal Proceedings | 62
​ | ​
Item 1A. Risk Factors | 62
​ | ​
Item 5. Other Information | 62
​ | ​
Item 6. Exhibits | 64

​

​

​

​

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FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements that involve substantial risks and uncertainties. All statements, other than statements of historical facts, contained in this Quarterly Report on Form 10-Q, including statements regarding our strategy, future operations, future financial position, future revenues, projected costs, prospects, plans and objectives of management, are forward-looking statements. The words “anticipate,” “believe,” “estimate,” “expect,” “intend,” “may,” “might,” “plan,” “predict,” “project,” “target,” “potential,” “will,” “would,” “could,” “should,” “continue,” “aim,” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

The forward-looking statements in this Quarterly Report on Form 10-Q include, among other things, statements about:

| ● | the outcome of pricing, coverage and reimbursement negotiations with third-party payors for our products or product candidates that we commercialize or may commercialize in the future;

| ● | expectations with respect to Sephience for the treatment of phenylketonuria, including timing of commercialization and of any regulatory submissions and potential approvals, and the potential achievement of regulatory and sales milestones and contingent payments that we may be obligated to make;

| ● | our ability to maintain our marketing authorization of Translarna for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in Brazil, Russia and other regions in which Translarna has been approved;

| ● | the effect of the European Commission’s adoption of the Committee for Medicinal Products for Human Use’s negative opinion not to renew the conditional marketing authorization for Translarna in the European Economic Area on other regulatory bodies;

| ● | our ability to use the results of Study 041, a randomized, 18-month, placebo-controlled clinical trial of Translarna for the treatment of nmDMD followed by an 18-month open-label extension, and from our international drug registry study to support a marketing approval for Translarna for the treatment of nmDMD in the United States;

| ● | whether investigators agree with our interpretation of the results of clinical trials and the totality of clinical data from our trials of Translarna;

| ● | expectations with respect to our license and collaboration agreement with Novartis Pharmaceuticals Corporation, or Novartis, for votoplam for the treatment of Huntington’s disease, including the design and expected timing of clinical trials and studies, the availability of data, and regulatory submissions and responses, including potential accelerated approval, and our right to receive any development, regulatory and sales milestones, and profit sharing and royalty payments from Novartis;

| ● | expectations with respect to vatiquinone for the treatment of Friedreich’s ataxia, including with respect to the design and expected timing of clinical trials and studies, the availability of data, and regulatory submissions and responses, meetings with regulatory agencies, and potential approvals and sales milestones and contingent payments that we may be obligated to make;

| ● | expectations with respect to Upstaza/Kebilidi, including commercialization, manufacturing capabilities, and the potential achievement of sales milestones and contingent payments that we may be obligated to make;

| ● | our expectations with respect to the commercial status of Evrysdi and our program directed against spinal muscular atrophy in collaboration with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. and the Spinal Muscular Atrophy Foundation and our estimates regarding future revenues from sales-based royalty payments or the achievement of milestones in that program;

| ● | our expectations and the potential financial impact and benefits related to our Collaboration and License Agreement with a subsidiary of Ionis Pharmaceuticals, Inc., including the commercialization of Tegsedi and

1

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|  | Waylivra, and our expectations with respect to royalty payments by us based on our potential achievement of certain net sales thresholds;

| ● | the timing and scope of our commercialization of our products and product candidates;

| ● | our estimates regarding the potential market opportunity for our products or product candidates, including the size of eligible patient populations and our ability to identify such patients;

| ● | our ability to obtain additional and maintain existing reimbursed named patient and cohort early access programs for our products on adequate terms, or at all;

| ● | our estimates regarding expenses, future revenues, third-party discounts and rebates, capital requirements and needs for additional financing, including our ability to maintain the level of our expenses consistent with our internal budgets and forecasts and to secure additional funds on favorable terms or at all;

| ● | our ability to realize the anticipated benefits of our acquisitions or other strategic transactions, including the possibility that the expected impact of benefits from the acquisitions or strategic transactions will not be realized or will not be realized within the expected time period, significant transaction costs, the integration of operations and employees into our business, our ability to obtain marketing approval of our product candidates we acquired from the acquisitions or other strategic transactions and unknown liabilities;

| ● | the rate and degree of market acceptance and clinical utility of any of our products or product candidates;

| ● | the ability and willingness of patients and healthcare professionals to access our products and product candidates through alternative means if pricing and reimbursement negotiations in the applicable territory do not have a positive outcome;

| ● | the timing of, and our ability to obtain additional marketing authorizations for our products and product candidates;

| ● | the ability of our products and our product candidates to meet existing or future regulatory standards;

| ● | the potential receipt of revenues from future sales of our products or product candidates;

| ● | the expected impact of our loss of market exclusivity for Emflaza for the treatment of Duchenne muscular dystrophy in the United States under the Orphan Drug Act of 1983;

| ● | our sales, marketing and distribution capabilities and strategy, including the ability of our third-party manufacturers to manufacture and deliver our products and product candidates in clinically and commercially sufficient quantities and the ability of distributors to process orders in a timely manner and satisfy their other obligations to us;

| ● | our ability to establish and maintain arrangements for the manufacture of our products and product candidates that are sufficient to meet clinical trial and commercial launch requirements;

| ● | our ability to complete any post-marketing requirements imposed by regulatory agencies with respect to our products;

| ● | our ability to satisfy our obligations under the terms of our lease agreements;

| ● | our ability to satisfy our obligations under the indenture governing our 1.50% convertible senior notes due September 15, 2026;

| ● | our regulatory submissions, including with respect to timing and outcome of regulatory review;

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| ● | the timing and conduct of our ongoing, planned and potential future clinical trials and studies for our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications, including the timing of initiation, enrollment and completion of the trials and the period during which the results of the trials will become available;

| ● | our plans to advance our earlier stage programs and pursue research and development of other product candidates, including our splicing and inflammation and ferroptosis programs;

| ● | whether we may pursue business development opportunities, including potential collaborations, alliances, and acquisition or licensing of assets and our ability to successfully develop or commercialize any assets to which we may gain rights pursuant to such business development opportunities;

| ● | the potential advantages of our products and any product candidate;

| ● | our intellectual property position;

| ● | the impact of government laws and regulations;

| ● | the impact of litigation that has been or may be brought against us or of litigation that we are pursuing against others; and

| ● | our competitive position.

We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. We have included important factors in the cautionary statements included in this Quarterly Report on Form 10-Q, particularly in Part II, Item 1A. Risk Factors as well as in Part I, Item 1A. Risk Factors in our Annual Report on Form 10-K for the year ended December 31, 2024, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make.

You should read this Quarterly Report on Form 10-Q and the documents that we have filed as exhibits to this Quarterly Report on Form 10-Q and our Annual Report on Form 10-K for the year ended December 31, 2024 completely and with the understanding that our actual future results may be materially different from what we expect. We do not assume any obligation to update any forward-looking statements whether as a result of new information, future events or otherwise, except as required by applicable law.

In this Quarterly Report on Form 10-Q, unless otherwise stated or the context otherwise requires, references to “PTC,” “PTC Therapeutics,” “the Company,” “we,” “us,” “our,” and similar references refer to PTC Therapeutics, Inc. and, where appropriate, its subsidiaries. The trademarks, trade names and service marks appearing in this Quarterly Report on Form 10-Q are the property of their respective owners.

All website addresses given in this Quarterly Report on Form 10-Q are for information only and are not intended to be an active link or to incorporate any website information into this document.

​

3

Table of Contents

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements.

PTC Therapeutics, Inc.

Consolidated Balance Sheets (unaudited)

In thousands (except shares)

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, | ​ | December 31, | ​
​ |  | 2025 |  | 2024 | ​
Assets | ​ | ​ | ​ | ​ | ​ | ​ | ​
Current assets: |  | ​ | ​ |  | ​ |  | ​
Cash and cash equivalents | ​ | $ | 672,617 | ​ | $ | 779,709 | ​
Marketable securities | ​ |  | 1,015,200 | ​ |  | 359,987 | ​
Trade and royalty receivables, net | ​ |  | 203,074 | ​ |  | 158,554 | ​
Inventory, net | ​ |  | 52,688 | ​ |  | 23,194 | ​
Prepaid expenses and other current assets | ​ |  | 64,224 | ​ |  | 44,087 | ​
Total current assets | ​ |  | 2,007,803 | ​ |  | 1,365,531 | ​
Fixed assets, net | ​ |  | 56,970 | ​ |  | 60,970 | ​
Intangible assets, net | ​ |  | 396,466 | ​ |  | 118,794 | ​
Goodwill | ​ |  | 82,341 | ​ |  | 82,341 | ​
Operating lease ROU assets | ​ | ​ | 80,682 | ​ | ​ | 56,685 | ​
Deposits and other assets | ​ |  | 19,438 | ​ |  | 20,703 | ​
Total assets | ​ | $ | 2,643,700 | ​ | $ | 1,705,024 | ​
Liabilities and stockholders’ deficit | ​ |  |  | ​ |  |  | ​
Current liabilities: | ​ |  | ​ | ​ |  |  | ​
Accounts payable and accrued expenses | ​ | $ | 303,141 | ​ | $ | 304,292 | ​
Current portion of long-term debt | ​ |  | 286,319 | ​ |  | — | ​
Deferred revenue | ​ |  | 1,691 | ​ |  | 5,505 | ​
Operating lease liabilities- current | ​ | ​ | 11,810 | ​ | ​ | 10,363 | ​
Finance lease liabilities- current | ​ | ​ | 2,676 | ​ | ​ | 3,000 | ​
Liability for sale of future royalties- current | ​ | ​ | 260,608 | ​ | ​ | 257,821 | ​
Total current liabilities | ​ |  | 866,245 | ​ |  | 580,981 | ​
Long-term debt | ​ |  | — | ​ |  | 285,412 | ​
Contingent consideration payable | ​ |  | — | ​ |  | 800 | ​
Operating lease liabilities- noncurrent | ​ | ​ | 95,488 | ​ | ​ | 74,947 | ​
Finance lease liabilities- noncurrent | ​ | ​ | 13,833 | ​ | ​ | 15,574 | ​
Liability for sale of future royalties- noncurrent | ​ | ​ | 1,821,313 | ​ | ​ | 1,823,955 | ​
Other long-term liabilities | ​ | ​ | 2,579 | ​ | ​ | 21,426 | ​
Total liabilities | ​ |  | 2,799,458 | ​ |  | 2,803,095 | ​
Stockholders’ deficit: | ​ |  |  | ​ |  |  | ​
Common stock, $0.001 par value. Authorized 250,000,000 shares; issued and outstanding 79,931,766 shares at September 30, 2025. Authorized 250,000,000 shares; issued and outstanding 77,704,188 shares at December 31, 2024. | ​ |  | 79 | ​ |  | 77 | ​
Additional paid-in capital | ​ |  | 2,667,497 | ​ |  | 2,574,611 | ​
Accumulated other comprehensive income (loss) | ​ |  | 5,930 | ​ |  | (25,886) | ​
Accumulated deficit | ​ |  | (2,829,264) | ​ |  | (3,646,873) | ​
Total stockholders’ deficit | ​ |  | (155,758) | ​ |  | (1,098,071) | ​
Total liabilities and stockholders’ deficit | ​ | $ | 2,643,700 | ​ | $ | 1,705,024 | ​

​

See accompanying unaudited notes.

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PTC Therapeutics, Inc.

Consolidated Statements of Operations (unaudited)

In thousands (except shares and per share amounts)

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024 | ​
Revenues: |  | ​ |  |  | ​ |  | ​ | ​ |  |  | ​ |  | ​
Net product revenue | ​ | $ | 130,956 | ​ | $ | 135,421 | ​ | $ | 402,711 | ​ | $ | 446,245 | ​
Collaboration and license revenue | ​ |  | 9,258 | ​ | ​ | — | ​ |  | 998,430 | ​ |  | — | ​
Royalty revenue | ​ | ​ | 70,793 | ​ | ​ | 61,365 | ​ | ​ | 164,837 | ​ | ​ | 145,702 | ​
Manufacturing revenue | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,661 | ​
Total revenues | ​ |  | 211,007 | ​ |  | 196,786 | ​ |  | 1,565,978 | ​ |  | 593,608 | ​
Operating expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets | ​ |  | 15,781 | ​ | ​ | 10,848 | ​ |  | 40,063 | ​ |  | 41,115 | ​
Amortization of acquired intangible assets | ​ |  | 7,534 | ​ | ​ | 3,036 | ​ |  | 15,393 | ​ |  | 57,431 | ​
Research and development | ​ |  | 100,158 | ​ | ​ | 161,412 | ​ |  | 322,121 | ​ |  | 409,710 | ​
Selling, general and administrative | ​ |  | 84,046 | ​ | ​ | 73,456 | ​ |  | 250,269 | ​ |  | 216,228 | ​
Change in the fair value of contingent consideration | ​ |  | — | ​ | ​ | 700 | ​ |  | (800) | ​ |  | 5,700 | ​
Tangible asset impairment and losses (gains) on transactions, net | ​ | ​ | 472 | ​ | ​ | 1,844 | ​ | ​ | 648 | ​ | ​ | 3,605 | ​
Total operating expenses | ​ |  | 207,991 | ​ |  | 251,296 | ​ |  | 627,694 | ​ |  | 733,789 | ​
Income (loss) from operations | ​ |  | 3,016 | ​ |  | (54,510) | ​ |  | 938,284 | ​ |  | (140,181) | ​
Interest expense, net | ​ |  | (32,592) | ​ | ​ | (41,609) | ​ |  | (97,042) | ​ |  | (125,933) | ​
Other income (expense), net | ​ |  | 6,502 | ​ | ​ | (1,872) | ​ |  | (5,540) | ​ |  | (2,306) | ​
(Loss) income before income tax benefit (expense) | ​ |  | (23,074) | ​ |  | (97,991) | ​ |  | 835,702 | ​ |  | (268,420) | ​
Income tax benefit (expense) | ​ |  | 38,970 | ​ | ​ | (8,663) | ​ |  | (18,093) | ​ |  | (28,989) | ​
Net income (loss) attributable to common stockholders | ​ | $ | 15,896 | ​ | $ | (106,654) | ​ | $ | 817,609 | ​ | $ | (297,409) | ​
Weighted-average shares outstanding: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Basic (in shares) | ​ |  | 78,471,119 | ​ | ​ | 76,925,523 | ​ | ​ | 78,642,478 | ​ | ​ | 76,716,340 | ​
Diluted (in shares) | ​ | ​ | 87,115,369 | ​ | ​ | 76,925,523 | ​ | ​ | 86,899,727 | ​ | ​ | 76,716,340 | ​
Net income (loss) per share—basic (in dollars per share) | ​ | $ | 0.20 | ​ | $ | (1.39) | ​ | $ | 10.40 | ​ | $ | (3.88) | ​
Net income (loss) per share—diluted (in dollars per share) | ​ | $ | 0.20 | ​ | $ | (1.39) | ​ | $ | 9.45 | ​ | $ | (3.88) | ​

​

See accompanying unaudited notes.

​

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PTC Therapeutics, Inc.

Consolidated Statements of Comprehensive Income (Loss) (unaudited)

In thousands

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024 | ​
Net income (loss) | ​ | $ | 15,896 | ​ | $ | (106,654) | ​ | $ | 817,609 | ​ | $ | (297,409) | ​
Other comprehensive income (loss): | ​ |  |  | ​ |  |  | ​ |  | ​ | ​ |  |  | ​
Unrealized gain on marketable securities, net of tax | ​ |  | 676 | ​ | ​ | 2,760 | ​ |  | 402 | ​ |  | 2,204 | ​
Foreign currency translation (loss) gain, net of tax | ​ |  | (2,102) | ​ | ​ | 9,395 | ​ |  | 31,414 | ​ |  | (5,262) | ​
Comprehensive income (loss) | ​ | $ | 14,470 | ​ | $ | (94,499) | ​ | $ | 849,425 | ​ | $ | (300,467) | ​

​

See accompanying unaudited notes.

​

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PTC Therapeutics, Inc.

Consolidated Statements of Stockholders’ Deficit (unaudited)

In thousands (except shares)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ |  | Accumulated |  | ​ | ​ |  | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | Additional |  | other | ​ | ​ | ​ |  | Total
Three months ended September 30, 2025 | ​ | Common stock | ​ | paid-in |  | comprehensive | ​ | Accumulated | ​ | stockholders’
​ |  | Shares |  | Amount |  | capital |  | income (loss) |  | deficit |  | deficit
Balance, June 30, 2025 | ​ | 79,378,145 | ​ | $ | 78 | ​ | $ | 2,631,180 | ​ | $ | 7,356 | ​ | $ | (2,845,160) | ​ | $ | (206,546)
Exercise of options |  | 486,129 | ​ | ​ | 1 | ​ | ​ | 16,829 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 16,830
Restricted stock vesting and issuance, net |  | 67,492 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Share-based compensation expense |  | — | ​ | ​ | — | ​ | ​ | 19,426 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 19,426
Receivable from investor | ​ | — | ​ | ​ | — | ​ | ​ | 62 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 62
Net income |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 15,896 | ​ | ​ | 15,896
Comprehensive loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (1,426) | ​ | ​ | — | ​ | ​ | (1,426)
Balance, September 30, 2025 |  | 79,931,766 | ​ | $ | 79 | ​ | $ | 2,667,497 | ​ | $ | 5,930 | ​ | $ | (2,829,264) | ​ | $ | (155,758)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ |  | Accumulated |  | ​ | ​ |  | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | Additional |  | other | ​ | ​ | ​ |  | Total
Three months ended September 30, 2024 | ​ | Common stock | ​ | paid-in |  | comprehensive | ​ | Accumulated | ​ | stockholders’
​ |  | Shares |  | Amount |  | capital |  | (loss) income |  | deficit |  | deficit
Balance, June 30, 2024 |  | 76,900,123 | ​ | $ | 76 | ​ | $ | 2,510,574 | ​ | $ | (16,498) | ​ | $ | (3,474,333) | ​ | $ | (980,181)
Retired Shares | ​ | (20) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Exercise of options |  | 19,483 | ​ | ​ | — | ​ | ​ | 573 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 573
Restricted stock vesting and issuance, net |  | 32,538 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Share-based compensation expense |  | — | ​ | ​ | — | ​ | ​ | 19,755 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 19,755
Net loss |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (106,654) | ​ |  | (106,654)
Comprehensive income |  | — | ​ |  | — | ​ |  | — | ​ |  | 12,155 | ​ | ​ | — | ​ |  | 12,155
Balance, September 30, 2024 |  | 76,952,124 | ​ | $ | 76 | ​ | $ | 2,530,902 | ​ | $ | (4,343) | ​ | $ | (3,580,987) | ​ | $ | (1,054,352)

​

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ |  | Accumulated |  | ​ | ​ |  | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | Additional |  | other | ​ | ​ | ​ |  | Total
Nine months ended September 30, 2025 | ​ | Common stock | ​ | paid-in |  | comprehensive | ​ | Accumulated | ​ | stockholders’
​ |  | Shares |  | Amount |  | capital |  | (loss) income |  | deficit |  | deficit
Balance, December 31, 2024 |  | 77,704,188 | ​ | $ | 77 | ​ | $ | 2,574,611 | ​ | $ | (25,886) | ​ | $ | (3,646,873) | ​ | $ | (1,098,071)
Exercise of options |  | 953,414 | ​ | ​ | 1 | ​ | ​ | 33,714 | ​ | ​ | — | ​ | ​ | — | ​ |  | 33,715
Restricted stock vesting and issuance, net |  | 1,201,681 | ​ | ​ | 1 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1
Issuance of common stock in connection with an employee stock purchase plan |  | 72,483 | ​ | ​ | — | ​ | ​ | 2,827 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,827
Share-based compensation expense |  | ​ | ​ | ​ | — | ​ | ​ | 56,029 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 56,029
Receivable from investor | ​ | — | ​ | ​ | — | ​ | ​ | 316 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 316
Net income |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 817,609 | ​ | ​ | 817,609
Comprehensive income |  | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 31,816 | ​ | ​ | — | ​ | ​ | 31,816
Balance, September 30, 2025 |  | 79,931,766 | ​ | $ | 79 | ​ | $ | 2,667,497 | ​ | $ | 5,930 | ​ | $ | (2,829,264) | ​ | $ | (155,758)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ |  | Accumulated |  | ​ | ​ |  | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ |  | Additional |  | other | ​ | ​ | ​ |  | Total
Nine months ended September 30, 2024 | ​ | Common stock | ​ | paid-in |  | comprehensive | ​ | Accumulated | ​ | stockholders’
​ |  | Shares |  | Amount |  | capital |  | loss |  | deficit |  | deficit
Balance, December 31, 2023 |  | 75,708,889 |  | $ | 75 |  | $ | 2,466,233 |  | $ | (1,285) |  | $ | (3,283,578) |  | $ | (818,555)
Retired shares | ​ | (20) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Exercise of options | ​ | 200,927 | ​ |  | — | ​ |  | 5,320 | ​ |  | — | ​ |  | — | ​ | ​ | 5,320
Restricted stock vesting and issuance, net | ​ | 935,183 | ​ |  | 1 | ​ |  | — | ​ |  | — | ​ |  | — | ​ | ​ | 1
Issuance of common stock in connection with an employee stock purchase plan |  | 107,145 | ​ |  | — | ​ |  | 1,973 | ​ |  | — | ​ |  | — | ​ |  | 1,973
Share-based compensation expense |  | — | ​ |  | — | ​ |  | 57,376 | ​ |  | — | ​ |  | — | ​ |  | 57,376
Net loss |  | — | ​ |  | — | ​ |  | — | ​ |  | — | ​ |  | (297,409) | ​ |  | (297,409)
Comprehensive loss |  | — | ​ |  | — | ​ |  | — | ​ |  | (3,058) | ​ |  | — | ​ |  | (3,058)
Balance, September 30, 2024 |  | 76,952,124 | ​ | $ | 76 | ​ | $ | 2,530,902 | ​ | $ | (4,343) | ​ | $ | (3,580,987) | ​ | $ | (1,054,352)

​

See accompanying unaudited notes.

​

​

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PTC Therapeutics, Inc.

Consolidated Statements of Cash Flows (unaudited)

In thousands

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 | ​
Cash flows from operating activities | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net income (loss) | ​ | $ | 817,609 | ​ | $ | (297,409) | ​
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities: | ​ |  | ​ | ​ | ​ |  | ​
Depreciation and amortization | ​ |  | 25,913 | ​ | ​ | 68,899 | ​
Non-cash operating lease expense | ​ |  | 5,635 | ​ | ​ | 6,272 | ​
Non-cash royalty revenue related to sale of future royalties | ​ | ​ | (149,160) | ​ | ​ | (128,877) | ​
Non-cash interest expense on liability related to sale of future royalties | ​ | ​ | 149,305 | ​ | ​ | 155,039 | ​
Change in valuation of contingent consideration | ​ |  | (800) | ​ | ​ | 5,700 | ​
Tangible asset impairment | ​ | ​ | 518 | ​ | ​ | 1,486 | ​
Loss on sale of fixed assets | ​ | ​ | 130 | ​ | ​ | 4,298 | ​
Gain on lease terminations | ​ | ​ | — | ​ | ​ | (2,179) | ​
Unrealized gain on ClearPoint Equity Investments | ​ |  | (5,734) | ​ | ​ | (3,954) | ​
Unrealized loss on ClearPoint convertible debt security | ​ | ​ | — | ​ | ​ | 1,931 | ​
Unrealized gain on marketable securities - equity investments | ​ | ​ | (3,160) | ​ | ​ | (1,923) | ​
Realized loss on ClearPoint convertible debt security | ​ | ​ | — | ​ | ​ | 622 | ​
Disposal of asset | ​ | ​ | 163 | ​ | ​ | 76 | ​
Deferred income taxes | ​ | ​ | (4) | ​ | ​ | (2) | ​
Amortization of discounts on investments, net | ​ |  | (12,972) | ​ | ​ | (9,947) | ​
Amortization of debt issuance costs | ​ |  | 906 | ​ | ​ | 891 | ​
Share-based compensation expense | ​ |  | 56,029 | ​ | ​ | 57,376 | ​
Unrealized foreign currency transaction losses (gains), net | ​ |  | 4,768 | ​ | ​ | (147) | ​
Changes in operating assets and liabilities: | ​ |  | ​ | ​ | ​ | ​ | ​
Inventory, net | ​ |  | (27,117) | ​ | ​ | (4,922) | ​
Prepaid expenses and other current assets | ​ |  | (13,876) | ​ | ​ | 107,957 | ​
Trade and royalty receivables, net | ​ |  | (32,365) | ​ | ​ | (39,029) | ​
Deposits and other assets | ​ |  | 1,501 | ​ | ​ | 7,909 | ​
Accounts payable and accrued expenses | ​ |  | (36,341) | ​ | ​ | (417) | ​
Other liabilities | ​ |  | (26,497) | ​ | ​ | (4,733) | ​
Deferred revenue | ​ |  | (4,298) | ​ | ​ | (801) | ​
Payments on contingent consideration | ​ | ​ | (4,684) | ​ | ​ | (1,800) | ​
Net cash provided by (used in) operating activities | ​ | $ | 745,469 | ​ | $ | (77,684) | ​
Cash flows from investing activities | ​ |  | ​ | ​ |  | ​ | ​
Purchases of fixed assets | ​ | $ | (6,486) | ​ | $ | (2,735) | ​
Proceeds from sale of fixed assets | ​ | ​ | 70 | ​ | ​ | 28,056 | ​
Purchases of marketable securities- available for sale | ​ | ​ | (1,051,267) | ​ | ​ | (476,680) | ​
Purchases of marketable securities- equity investments | ​ | ​ | (46,537) | ​ | ​ | (49,614) | ​
Sale and redemption of marketable securities- available for sale | ​ | ​ | 424,351 | ​ | ​ | 290,836 | ​
Sale and redemption of marketable securities- equity investments | ​ | ​ | 40,112 | ​ | ​ | 41,624 | ​
Proceeds from settlement of Clearpoint convertible debt security | ​ | ​ | — | ​ | ​ | 10,000 | ​
Acquisition of product rights and licenses | ​ | ​ | (256,235) | ​ | ​ | (65,017) | ​
Net cash used in investing activities | ​ | $ | (895,992) | ​ | $ | (223,530) | ​
Cash flows from financing activities | ​ |  | ​ | ​ |  | ​ | ​
Proceeds from exercise of options | ​ | $ | 33,715 | ​ | $ | 5,320 | ​
Proceeds from employee stock purchase plan | ​ | ​ | 2,827 | ​ | ​ | 1,973 | ​
Proceeds from sale of future royalties | ​ | ​ | — | ​ | ​ | 241,792 | ​
Payments on contingent consideration obligation | ​ | ​ | (6,341) | ​ | ​ | (18,200) | ​
Payment of finance lease principal | ​ | ​ | (1,611) | ​ | ​ | (1,490) | ​
Net cash provided by financing activities | ​ | $ | 28,590 | ​ | $ | 229,395 | ​
Effect of exchange rate changes on cash | ​ |  | 12,917 | ​ | ​ | 1,325 | ​
Net decrease in cash and cash equivalents | ​ |  | (109,016) | ​ |  | (70,494) | ​
Cash and cash equivalents, and restricted cash beginning of period | ​ |  | 795,316 | ​ | ​ | 610,284 | ​
Cash and cash equivalents, and restricted cash end of period | ​ | $ | 686,300 | ​ | $ | 539,790 | ​
Supplemental disclosure of cash information | ​ |  | ​ | ​ |  | ​ | ​
Cash paid for interest | ​ | $ | 5,702 | ​ | $ | 5,823 | ​
Cash paid for income taxes | ​ | ​ | 40,124 | ​ | ​ | 12,781 | ​
Supplemental disclosure of non-cash investing and financing activity | ​ |  | ​ | ​ |  |  | ​
Unrealized gain on marketable securities, net of tax | ​ | $ | 402 | ​ | $ | 2,204 | ​
Right-of-use assets obtained in exchange for operating lease obligations | ​ | ​ | 27,675 | ​ | ​ | 5,786 | ​
Acquisition of product rights and licenses | ​ | ​ | 2,221 | ​ | ​ | 2,346 | ​
Fixed asset additions through tenant improvement allowance | ​ | ​ | 766 | ​ | ​ | 18,675 | ​
Milestone payable | ​ | ​ | 32,500 | ​ | ​ | 50,000 | ​

​

See accompanying unaudited notes.

​

8

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PTC Therapeutics, Inc.

Notes to Consolidated Financial Statements (unaudited)

September 30, 2025

In thousands (except share and per share amounts unless otherwise noted)

1. The Company

PTC Therapeutics, Inc. (the “Company” or “PTC”) is a global biopharmaceutical company dedicated to the discovery, development and commercialization of clinically differentiated medicines for children and adults living with rare disorders. PTC is advancing a robust and diversified pipeline of transformative medicines as part of its mission to provide access to best-in-class treatments for patients with unmet medical needs. PTC’s strategy is to leverage its scientific expertise and global commercial infrastructure to optimize value for its patients and other stakeholders. PTC has a diversified therapeutic portfolio pipeline that includes several commercial products and product candidates in various stages of development, including clinical, pre-clinical and research and discovery stages, focused on the development of new treatments for multiple therapeutic areas for rare diseases relating to neurology and metabolism.

The Company has developed Sephience™ (sepiapterin), a product for the treatment of phenylketonuria (“PKU”), a rare inherited metabolic disease characterized by the body’s inability to break down an essential amino acid called phenylalanine, and which can result in neurological and other symptoms. On July 28, 2025, Sephience™ was approved by the U.S. Food and Drug Administration (“FDA”) for the treatment of pediatric and adult patients living with PKU in the United States age one month and above. On June 19, 2025, Sephience was granted marketing authorization by the European Commission (“EC”) for the treatment of children and adults living with PKU within the European Economic Area (“EEA”). The Company also made regulatory submissions for Sephience for the treatment of PKU in Brazil in the third quarter of 2024, and in Japan in the fourth quarter of 2024, with regulatory decisions expected in the fourth quarter of 2025.

The Company has two products, Translarna™ (ataluren) and Emflaza® (deflazacort), for the treatment of Duchenne muscular dystrophy (“DMD”), a rare, life-threatening disorder. Translarna has marketing authorization in Russia for the treatment of nonsense mutation Duchenne muscular dystrophy (“nmDMD”) in patients aged two years and older, and in Brazil for the treatment of nmDMD in ambulatory patients two years and older and for continued treatment of patients that become non-ambulatory, as well as in various other countries. Emflaza is approved in the United States for the treatment of DMD in patients two years and older.

The Company previously had a marketing authorization for Translarna in the EEA, which had been subject to annual review and renewal by the EC following reassessment by the European Medicines Agency (“EMA”) of the benefit-risk balance of the authorization. In September 2022, the Company submitted a Type II variation to the EMA to support conversion of the conditional marketing authorization for Translarna to a standard marketing authorization, which included a report on the placebo-controlled trial of Study 041 and data from the open-label extension. In February 2023, the Company also submitted an annual marketing authorization renewal request to the EMA. In September 2023, the Committee for Medicinal Products for Human Use (“CHMP”), gave a negative opinion on the conversion of the conditional marketing authorization to full marketing authorization of Translarna for the treatment of nmDMD and a negative opinion on the renewal of the existing conditional marketing authorization of Translarna for the treatment of nmDMD. In January 2024, the CHMP issued a negative opinion for the renewal of the conditional marketing authorization following a re-examination procedure. In May 2024, the EC decided not to adopt the CHMP’s negative opinion for the renewal of the conditional marketing authorization of Translarna and returned such opinion to the CHMP for re-evaluation. In June 2024, following the EC’s request for re-review, the CHMP issued a negative opinion on the renewal of the conditional marketing authorization of Translarna for the treatment of nmDMD. In October 2024, the CHMP maintained its negative opinion for the renewal of the conditional marketing authorization following the requested reexamination procedure. In March 2025, the EC adopted the opinion of the CHMP to not renew the authorization of Translarna for the treatment of nmDMD. However, the EC indicated that individual countries within the European Union (“EU”) can leverage Articles 117(3) and 5(1) of the EU Directive 2001/83 to allow continued commercial use of Translarna.

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Translarna is an investigational new drug in the United States. Following the Company’s announcement of top-line results from the placebo-controlled trial of Study 041 in June 2022, the Company submitted a meeting request to the FDA to gain clarity on the regulatory pathway for a potential resubmission of a New Drug Application (“NDA”) for Translarna. The FDA provided initial written feedback that Study 041 does not provide substantial evidence of effectiveness to support an NDA resubmission. The Company held a Type C meeting with the FDA in the fourth quarter of 2023 to discuss the totality of Translarna data. Based on feedback from the FDA, the Company resubmitted the NDA in July 2024, based on the results from Study 041 and from the Company’s international drug registry study for nmDMD patients receiving Translarna. In October 2024, the FDA accepted for review the resubmission of the NDA for Translarna for the treatment of nmDMD. As this was an NDA resubmission following a complete response letter to the NDA which was filed over protest in 2016, the FDA is not obligated to follow the review timelines under Prescription Drug User Fee Act guidelines, and an action date has not been provided.

The Company has developed Upstaza™ (eladocagene exuparvovec), a gene therapy for the treatment of Aromatic L-Amino Acid Decarboxylase (“AADC”) deficiency (“AADC deficiency”), a rare central nervous system (“CNS”) disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. In July 2022, the EC approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the EEA. In November 2022, the Medicines and Healthcare Products Regulatory Agency approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the United Kingdom. In November 2024, the FDA approved the Company’s gene therapy treatment of AADC deficiency, which is marketed under the brand name Kebilidi™ in the United States.

The Company holds the rights for the commercialization of Tegsedi® (inotersen) and Waylivra® (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to the Collaboration and License Agreement (the “Tegsedi-Waylivra Agreement”), dated August 1, 2018, by and between the Company and Akcea Therapeutics, Inc. (“Akcea”), a subsidiary of Ionis Pharmaceuticals, Inc. Tegsedi has received marketing authorization in the United States, the EU and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis (“hATTR amyloidosis”). In August 2021, ANVISA, the Brazilian health regulatory authority, approved Waylivra as the first treatment for familial chylomicronemia syndrome (“FCS”) in Brazil. In December 2022, ANVISA approved Waylivra for the treatment of familial partial lipodystrophy (“FPL”). Waylivra has also received marketing authorization in the EU for the treatment of FCS.

The Company also has a spinal muscular atrophy (“SMA”) collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc. (referred to collectively as “Roche”) and the Spinal Muscular Atrophy Foundation (“SMA Foundation”). The SMA program has one approved product, Evrysdi® (risdiplam), which was approved by the FDA in August 2020 for the treatment of SMA in adults and children two months and older and by the EC in March 2021 for the treatment of 5q SMA in patients two months and older with a clinical diagnosis of SMA Type 1, Type 2 or Type 3 or with one to four SMN2 copies. Evrysdi has also received marketing authorization for the treatment of SMA in over 100 countries. In May 2022, the FDA approved a label expansion for Evrysdi to include infants under two months old with SMA. In August 2023, the EC approved an extension of the Evrysdi marketing authorization to include infants under two months old in the EU.

In addition to the Company’s SMA program, the Company’s splicing platform also includes votoplam (PTC518), which is being developed for the treatment of Huntington’s disease (“HD”). The Company initiated a Phase 2 study of votoplam for the treatment of HD in the first quarter of 2022, which consisted of an initial 12-week placebo-controlled phase focused on safety, pharmacology and pharmacodynamic effects followed by a nine-month placebo-controlled phase focused on votoplam biomarker effect. In June 2024, the Company announced interim results from the full Phase 2 study of votoplam. At month 12, votoplam treatment demonstrated durable dose-dependent lowering of mutant HTT (“mHTT”) protein in the blood and dose-dependent lowering of mHTT protein in the cerebrospinal fluid in the interim cohort of stage 2 patients. In addition, favorable trends were demonstrated on several relevant HD clinical assessments. Furthermore, following 12 months of treatment, votoplam continued to be well tolerated. In September 2024, the FDA granted Fast Track designation to the votoplam program for the treatment of HD. In December 2024, the Company held a Type C meeting with the FDA to discuss whether huntingtin protein lowering could be considered a surrogate endpoint for accelerated approval of votoplam. The FDA was aligned on the scientific rationale and asked to see additional data supportive of an association between huntingtin protein lowering and changes in clinical outcome scores. In May 2025, the Company announced that the Phase 2 study of votoplam met its primary endpoints of blood HTT lowering and safety. The results on the full study

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population are consistent with the previously reported evidence of dose-dependent HTT lowering, favorable safety profile and early signals of dose-dependent clinical effect at 12 months in Stage 2 patients. In addition, at 24 months of treatment, there were continued trends of dose-dependent favorable clinical effect relative to a propensity-matched natural history cohort as well as dose-dependent NfL lowering. In November 2024, the Company entered into a License and Collaboration Agreement (the “Novartis Agreement”) with Novartis Pharmaceuticals Corporation (“Novartis”), relating to its votoplam HD program which included related molecules. This transaction closed in January 2025, triggering a $1.0 billion upfront cash payment to the Company. The Company continues to collaborate with Novartis on next steps for votoplam and aims to meet with FDA in the fourth quarter of 2025 to discuss Phase 3 clinical trial design and potential accelerated approval pathway.

The Company’s inflammation and ferroptosis platform consists of small molecule compounds that target key enzymes that regulate oxidative stress and inflammatory pathways central to the pathology of a number of CNS and non-CNS diseases. The most advanced molecule in the Company’s inflammation and ferroptosis platform is vatiquinone. The Company announced topline results from a registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich’s ataxia (“FA”), called MOVE-FA, in May 2023. While the study did not meet its primary endpoint, vatiquinone treatment did demonstrate significant benefit on key disease subscales, including the upright stability subscale, as well as on other disease relevant endpoints. In October 2024, the Company announced that the pre-specified endpoint for two different FA long-term extension studies was met, with statistically significant evidence of durable treatment benefit on disease progression. In December 2024, the Company submitted an NDA to the FDA for vatiquinone for the treatment of children and adults living with FA. In August 2025, the FDA issued a complete response letter related to the NDA stating that substantial evidence of efficacy was not demonstrated for vatiquinone and that an additional adequate and well-controlled study would be needed to support NDA resubmission. The Company plans to meet with the FDA in the fourth quarter to discuss the vatiquinone development program.

In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas for rare diseases.

As of September 30, 2025, the Company had an accumulated deficit of approximately $2,829.3 million. The Company has financed its operations to date primarily through the private offerings of convertible senior notes (see Note 9), public and “at the market offerings” of common stock, proceeds from royalty purchase agreements (see Note 9), private placements of its convertible preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates. The Company has also relied on revenue generated from net sales of its products. The Company has also relied on revenue associated with milestone and royalty payments from Roche pursuant to the License and Collaboration Agreement (the “SMA License Agreement”) dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation, under its SMA program. The Company also relies on revenues associated with the Novartis Agreement. The Company expects that cash flows from the sales of its products, royalty payments from Roche, and milestone payments from Novartis, together with the Company’s cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

2. Summary of significant accounting policies

The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2024 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on February 27, 2025 (the "2024 Form 10-K"). Selected significant accounting policies are discussed in further detail below.

Basis of presentation

The accompanying financial information as of September 30, 2025 and for the three and nine months ended September 30, 2025 and 2024 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance

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with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2024 and notes thereto included in the 2024 Form 10-K.

In the opinion of management, the unaudited financial information as of September 30, 2025 and for the three and nine months ended September 30, 2025 and 2024 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders’ deficit, and cash flows. The results of operations for the three and nine months ended September 30, 2025 are not necessarily indicative of the results to be expected for the year ended December 31, 2025 or for any other interim period or for any other future year.

Use of estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, royalty revenue, certain accruals related to the Company’s research and development expenses, valuation procedures for liability for sale of future royalties, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Restricted cash

Restricted cash included in deposits and other assets on the consolidated balance sheet contains an unconditional, irrevocable and transferable letter of credit of $3.0 million in connection with an amendment and restatement of the Company’s lease in Hopewell Township, New Jersey. Restricted cash also contains an unconditional, irrevocable and transferable letter of credit of $10.0 million in connection with obligations for the Company’s new facility lease in Warren, New Jersey. If after July 1, 2027, the Company is not in default of the lease agreement and meets certain creditworthiness guidelines, then the letter of credit will be reduced to $5.0 million. If after December 31, 2028, the Company is not in default of the lease agreement and meets certain creditworthiness guidelines, then the letter of credit will be further reduced to $2.5 million. Both letters of credit are classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letters of credit. Restricted cash also includes a bank guarantee of $0.7 million denominated in a foreign currency.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the consolidated statement of cash flows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | End of |  | Beginning of
​ |  | period- |  | period-
​ |  | September 30, |  | December 31,
​ |  | 2025 | ​ | 2024
Cash and cash equivalents | ​ | $ | 672,617 | ​ | $ | 779,709
Restricted cash included in deposits and other assets | ​ |  | 13,683 | ​ |  | 15,607
Total Cash, cash equivalents and restricted cash per consolidated statement of cash flows | ​ | $ | 686,300 | ​ | $ | 795,316

​

Segment information

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker (“CODM”), or decision-making group, in deciding how to allocate resources and in assessing performance. The Company’s CODM consists of the chief executive officer, the chief financial officer, and the chief business officer. The Company views its operations and manages its business in one operating and reporting segment: life science. The life science segment is focused on the discovery, development and commercialization of the Company’s clinically differentiated medicines that provide benefits to patients with rare disorders. The Company is managed on a consolidated basis, and accordingly, the CODM assesses performance for the life science segment based on net income (loss), with a focus on revenues, research and development expense, and selling general, and administrative expense. Net income is reported on the income statement as consolidated net income (loss).

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The measure of segment assets is reported on the balance sheet as total consolidated assets. The Company derives its revenues through its worldwide net sales of its commercial products, collaboration agreements and license agreements, and royalty revenues. Refer to Note 11 for further segment information on revenues.

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The Company expects to continue to incur significant expenses as it advances product candidates through all stages of development and clinical trials and, ultimately, seek regulatory approval. As such, the CODM uses cash forecast models in deciding how to invest into the life science segment. Such cash forecast models are reviewed to assess the entity-wide operating results and performance. Net income (loss) is used to monitor planned versus actual results. Monitoring planned versus actual results is used in assessing performance of the segment and in establishing management’s compensation, along with the cash forecast models. Refer to Note 13 for segment information on significant segment expenses.

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Marketable securities

The Company’s marketable securities consists of both debt securities and equity investments. The Company considers its investments in debt securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income (loss). The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three and nine months ended September 30, 2025 and 2024, no allowance was recorded for credit losses.

Marketable securities that are equity investments are measured at fair value, as it is readily available, and as such are classified as Level 1 assets. Unrealized holding gains and losses for these equity investments are components of other income (expense), net within the consolidated statement of operations.

Inventory and cost of product, collaboration and license sales

Inventory

Inventories are stated at the lower of cost and net realizable value, utilizing standard costing, which approximates average costs by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. Amounts related to clinical development programs and marketing efforts are immaterial.

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The following table summarizes the components of the Company’s inventory for the periods indicated:

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​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, 2025 |  | December 31, 2024
Raw materials | ​ | $ | 2,244 | ​ | $ | 2,538
Work in progress | ​ |  | 41,827 | ​ |  | 12,216
Finished goods | ​ |  | 8,617 | ​ |  | 8,440
Total inventory | ​ | $ | 52,688 | ​ | $ | 23,194

​

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. For the three and nine months ended September 30, 2025, the Company recorded inventory write-downs of $0.5 million and $4.8 million, respectively, primarily related to adjustments to inventory reserves and product approaching expiration. For the three months ended September 30, 2024, the inventory write-downs were immaterial. For the nine months ended September 30, 2024, the Company recorded inventory write-downs of $2.5 million, primarily related to adjustments to inventory reserves and product approaching expiration. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product, collaboration and license sales. For the three and nine months ended September 30, 2025 and 2024, these amounts were immaterial.

Cost of product, collaboration and license sales

Cost of product, collaboration and license sales consists of the cost of inventory sold, manufacturing and supply chain costs, storage costs, amortization of the acquired intangible asset, royalty payments associated with net product sales, royalty payments to collaborative partners associated with royalty revenues and collaboration revenue related to milestones, and costs related to performance of services associated with license agreement revenues. Production costs are expensed as cost of product, collaboration and license sales when the related products are sold or royalty revenues and collaboration revenue milestones are earned.

Revenue recognition

Net product revenue

The Company’s net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. Beginning in the three months ended September 30, 2025, net product revenues also includes Sephience for the treatment of PKU. The Company recognizes revenue when its performance obligations with its customers have been satisfied and if it is probable that a significant revenue reversal will not occur. The Company’s performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of the product, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to product sales. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.

The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors

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and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.

In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. The Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Collaboration, license, and royalty revenue

The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.

At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations.

For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance.

For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company’s control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes royalties from product sales at the later of when the related sales occur or when the performance obligation to which the royalty has been allocated has been satisfied. If it is probable that a significant revenue reversal will not occur, the Company will estimate the royalty payments using the most likely amount method.

The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.

Allowance for doubtful accounts

The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends. The Company also assesses whether an allowance for expected credit losses may be required which includes a review of the Company’s receivables portfolio, which are pooled on a customer basis or country basis. In making its assessment of whether an allowance for

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credit losses is required, the Company considers its historical experience with customers, current balances, levels of delinquency, regulatory and legal environments, and other relevant current and future forecasted economic conditions. For the three and nine months ended September 30, 2025 and 2024, no allowance was recorded for credit losses. The allowance for doubtful accounts was $11.6 million as of September 30, 2025 and $2.3 million as of December 31, 2024. For the three and nine months ended September 30, 2025, bad debt expense was $0.8 million and $8.6 million, respectively. For the three and nine months ended September 30, 2024, bad debt expense was $0.7 million and $0.5 million, respectively.

Liability for sale of future royalties

The Company has a royalty purchase agreement with Royalty Pharma Investments 2019 ICAV (“Royalty Pharma”) in which the Company sold its right to receive sales-based royalty payments on worldwide net sales of Evrysdi in exchange for upfront cash consideration from Royalty Pharma. In accordance with the guidance in ASC 470-10-25-2, the Company determined that cash consideration obtained pursuant to the royalty purchase agreement should be classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to Royalty Pharma. The liability is amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance, utilizing the prospective method to account for subsequent changes in the estimated future payments to be made to Royalty Pharma and the Company updates the effective interest rate on a quarterly basis. Refer to Note 9 for further details.

Goodwill

Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassesses its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount.

Income Taxes

On December 15, 2022, the EU Member States formally adopted the EU’s Pillar Two Directive, which generally provides for a minimum effective tax rate of 15%, as established by the Organization for Economic Co-operation and Development Pillar Two Framework that was supported by over 130 countries worldwide. The EU effective dates were January 1, 2024, and January 1, 2025, for different aspects of the directive. A significant number of other countries are also implementing similar legislation. As a result, the tax laws in the U.S. and other countries in which PTC and its affiliates do business could change on a prospective or retroactive basis and any such changes could materially adversely affect the Company’s business. The Company is continuing to evaluate the potential impact on future periods of the Pillar Two Framework, pending legislative adoption by additional individual countries, including those within the EU.

On December 22, 2017, the U.S. government enacted the 2017 Tax Cuts and Jobs Act (“TCJA”), which significantly revised U.S. tax law by, among other provisions, lowering the U.S. federal statutory corporate income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-Taxed Income (“GILTI”) provisions of the TCJA require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2025.

Since 2022, TCJA amendments to Internal Revenue Code (“IRC”) Section 174 have no longer permitted an immediate deduction for research and development expenditures in the tax year that such costs were incurred. Instead, these IRC Section 174 development costs have had to be capitalized and amortized over a 5-year or 15-year period for domestic and foreign expenditures, respectively. On July 4, 2025, the U.S. government enacted the One Big Beautiful Bill Act

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(“OBBBA”) which generally extended the tax provisions previously enacted by the TCJA that were set to expire, as well as made other changes to federal tax law for multinational corporations. Effective beginning with PTC’s 2025 tax year, the OBBBA restored immediate deductibility of domestic expenditures, while foreign expenditures will continue to be capitalized and amortized over 15 years. Additionally, IRC Section 174A, enacted as part of the OBBBA, allows for the immediate expensing of all remaining unamortized domestic costs either upfront in 2025, or ratably in 2025 and 2026.

Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized.

Leases

The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating and finance leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating and finance lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments.

Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases.

Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories.

A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates.

The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. Refer to Note 3 for further details.

Tangible asset impairment and losses (gains) on transactions, net

Tangible asset impairment and losses (gains) on transactions, net includes impairments identified on fixed assets, losses and gains on sales of fixed assets, and gains on lease terminations. For the three months ended September 30, 2025, these amounts consisted of a $0.1 million loss on sale of fixed assets and a $0.4 million loss related to fixed asset impairments. For the nine months ended September 30, 2025, these amounts consisted of a $0.1 million loss on sales of fixed assets and a $0.5 million loss related to fixed asset impairments. For the three months ended September 30, 2024, these amounts

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consisted of a $1.3 million loss for fixed asset impairments related to the South Plainfield, New Jersey office closure, as well as a $0.5 million loss on sales of fixed assets. For the nine months ended September 30, 2024, these amounts consisted of a $4.4 million loss primarily related to the sale of certain assets for gene therapy manufacturing, and a $1.5 million loss primarily related to fixed asset impairments related to the South Plainfield, New Jersey office closure. These amounts were partially offset by a gain of $2.2 million on lease terminations and a $0.1 million gain on sales of fixed assets.

Recently issued accounting standards

In December 2023, the FASB issued ASU 2023-09, Improvements to Income Tax Disclosures. ASU 2023-09 enhances the transparency about income tax information through improvements to income tax disclosures primarily related to the rate reconciliation and income taxes paid information. The guidance is effective for public business entities for annual periods beginning after December 15, 2024. For entities other than public business entities, the amendments are effective for annual periods beginning after December 15, 2025. Early adoption is permitted. The Company is currently planning to adopt this guidance when effective. The Company is assessing the impact of the adoption on the Company’s consolidated financial statements and accompanying footnotes, but expects the impact will be enhanced disclosures related to income taxes.

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In November 2024, the FASB issued ASU 2024-03, Income Statement-Reporting Comprehensive Income- Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses. ASU 2024-03 enhances financial reporting by requiring additional information about specific expense categories in the notes to financial statements at interim and annual reporting periods. The guidance is effective for public business entities for annual periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027. Early adoption is permitted. The Company is currently planning to adopt this guidance when effective. The Company is assessing the impact of the adoption on the Company’s consolidated financial statements and accompanying footnotes but expects the impact will be enhanced disclosures related to income statement expenses.

In July 2025, the FASB issued ASU 2025-05, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses for Accounts Receivable and Contract Assets. ASU 2025-05 addresses challenges encountered when applying the guidance in Topic 326, Financial Instruments—Credit Losses, to current accounts receivable and current contract assets arising from transactions accounted for under Topic 606, Revenue from Contracts with Customers. The guidance is effective for public business entities for annual periods beginning after December 15, 2025, and interim reporting periods within those annual reporting periods. Early adoption is permitted in both interim and annual reporting periods in which financial statements have not yet been issued or made available for issuance. In developing reasonable and supportable forecasts as part of estimating expected credit losses, the guidance provides that all entities may elect a practical expedient that assumes that current conditions as of the balance sheet date do not change for the remaining life of the asset. The Company is assessing the impact of the adoption on the Company’s consolidated financial statements and accompanying footnotes but expects the guidance will not have a material impact.

In September 2025, the FASB issued ASU 2025-06, Intangibles—Goodwill and Other— Internal-Use Software (Subtopic 350-40): Targeted Improvements to the Accounting for Internal-Use Software. ASU 2025-06 enhances accounting for software costs that are accounted for under Subtopic 350-40, Intangibles—Goodwill and Other—Internal-Use Software (referred to as “internal-use software”). The guidance is effective for public business entities for annual periods beginning after December 15, 2027, and interim reporting periods within those annual reporting periods. Entities have three transition options: prospective, retrospective, or modified prospective adoption. Early adoption is permitted as of the beginning of an annual reporting period. Instead of following prescriptive project stages for capitalization of internal-use software, entities will capitalize costs when management has authorized and committed funding for the software project and it is probable that the project will be completed and used as intended. The Company is assessing the impact of the adoption on the Company’s consolidated financial statements and accompanying footnotes.

3. Leases

The Company’s principal office space is a facility located in Warren, New Jersey, which is approximately 180,000 square feet. The Company also leases laboratory space in Bridgewater, New Jersey and other locations throughout the United States and office space in various countries for international employees primarily through workspace providers.

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On August 1, 2025, the Company commenced a lease for office and laboratory space at a facility located in Mountainview, CA. The initial term of the lease is twelve years and nine months with an aggregate base rent of approximately $42.6 million. The Company recorded an operating lease ROU asset of $26.8 million and an operating lease ROU liability of $26.7 million as of the commencement date of the lease.

The Company also has a finance lease related to its commercial manufacturing agreement with MassBiologics of the University of Massachusetts Medical School (“MassBio”). As of September 30, 2025, the balance of the finance lease liabilities-current and finance lease liabilities-noncurrent are $2.7 million and $13.8 million, respectively, and are directly related to the Company’s MassBio agreement. As of December 31, 2024, the balance of the finance lease liabilities-current and finance lease liabilities-noncurrent were $3.0 million and $15.6 million, respectively. Additionally, the Company recorded finance lease costs of $0.3 million and $0.9 million related to interest on the lease liability during the three and nine months ended September 30, 2025, respectively. The Company recorded finance lease costs of $0.4 million and $1.0 million related to interest on the lease liability during three and nine months ended September 30, 2024, respectively.

The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s leases have remaining operating lease terms ranging from 0.6 years to 13.7 years and certain of the leases include renewal options to extend the lease for up to 15 years. For the three months ended September 30, 2025 and 2024, rent expense was $5.5 million and $5.9 million, respectively. For the nine months ended September 30, 2025 and 2024, rent expense was $15.7 million and $19.5 million, respectively.

The components of operating lease expense were as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | Three Months Ended |  | Three Months Ended |  | Nine Months Ended |  | Nine Months Ended | ​
​ | ​ | September 30, 2025 | ​ | September 30, 2024 | ​ | September 30, 2025 | ​ | September 30, 2024 | ​
Operating Lease Cost |  | ​ |  | ​ | ​ |  | ​ | ​ |  | ​ | ​ |  | ​
Fixed lease cost | ​ | $ | 4,032 | ​ | $ | 4,049 | ​ | $ | 10,847 | ​ | $ | 15,173 | ​
Variable lease cost | ​ |  | 1,083 | ​ |  | 1,581 | ​ |  | 3,988 | ​ |  | 3,623 | ​
Short-term lease cost | ​ |  | 359 | ​ |  | 308 | ​ |  | 914 | ​ |  | 750 | ​
Total operating lease cost | ​ | $ | 5,474 | ​ | $ | 5,938 | ​ | $ | 15,749 | ​ | $ | 19,546 | ​

​

Total operating lease cost is a component of operating expenses on the consolidated statements of operations.

Supplemental lease term and discount rate information related to leases was as follows as of September 30, 2025 and December 31, 2024:

​

​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, 2025 |  | December 31, 2024 |
Weighted-average remaining lease terms - operating leases (years) |  | 11.63 | ​ | 11.62 | ​
Weighted-average discount rate - operating leases | ​ | 7.44 | % | 7.64 | %
Weighted-average remaining lease terms - finance lease (years) |  | 7.26 | ​ | 8.01 | ​
Weighted-average discount rate - finance lease |  | 7.80 | % | 7.80 | %

​

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Supplemental cash flow information related to leases was as follows as of September 30, 2025 and 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 | ​
Cash paid for amounts included in the measurement of lease liabilities: |  | ​ |  | ​ | ​ |  | ​
Operating cash flows from operating leases | ​ | $ | 12,248 | ​ | $ | 12,963 | ​
Financing cash flows from finance lease | ​ | ​ | 1,611 | ​ | ​ | 1,490 | ​
Operating cash flows from finance lease | ​ | ​ | 1,389 | ​ | ​ | 1,510 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Right-of-use assets obtained in exchange for lease obligations: | ​ |  | ​ | ​ |  |  | ​
Operating leases | ​ | $ | 27,675 | ​ | $ | 5,786 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Changes due to lease modification and termination: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net decrease in right-of-use assets | ​ | $ | — | ​ | $ | 31,763 | ​
Net decrease in operating lease liabilities | ​ | ​ | — | ​ | ​ | 33,908 | ​

​

Future minimum lease payments under non-cancelable leases as of September 30, 2025 were as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | Operating Leases |  | Finance Lease | ​
2025 (excludes the nine months ended September 30, 2025) | ​ | $ | 4,245 | ​ | $ | — | ​
2026 | ​ |  | 18,315 | ​ |  | 3,000 | ​
2027 | ​ |  | 16,493 | ​ |  | 3,000 | ​
2028 | ​ |  | 11,102 | ​ |  | 3,000 | ​
2029 and thereafter | ​ |  | 109,668 | ​ |  | 12,000 | ​
Total lease payments | ​ |  | 159,823 | ​ |  | 21,000 | ​
Less: Imputed Interest expense | ​ |  | 52,525 | ​ |  | 4,491 | ​
Total | ​ | $ | 107,298 | ​ | $ | 16,509 | ​

​

​

​

4. Fair value of financial instruments and marketable securities

The Company follows the fair value measurement rules, which provideguidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority).

| ● | Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date.

| ● | Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs).

| ● | Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available.

Cash equivalents and marketable securities are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments.

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The Company owns common stock in ClearPoint Neuro, Inc. (“ClearPoint”) (formerly MRI Interventions, Inc.), a publicly traded medical device company. The ClearPoint equity investments (collectively, the “ClearPoint Equity Investments”) represent financial instruments, and therefore, are recorded at fair value, which is readily determinable. The ClearPoint Equity Investments are components of prepaids and other current assets on the consolidated balance sheet as of September 30, 2025 and December 31, 2024. The Company classifies the ClearPoint Equity Investments as Level 1 assets within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted. Other than the ClearPoint Equity Investments, no other items included in prepaids and other current assets on the consolidated balance sheets are fair valued.

In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that was convertible into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, with a maturity date five years from the purchase date. In August 2024, the outstanding principal amount of the convertible note, together with any accrued and unpaid interest thereon, was repaid in full by ClearPoint and therefore the balance at September 30, 2025 was $0. The Company determined that the convertible note represented an available for sale debt security and the Company had elected to record it at fair value under ASC 825. The Company classified its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value was based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security was determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk-free rate and the estimated credit spread as of the valuation date as the discount rate. The convertible debt security was included as a component of deposits and other assets on the consolidated balance sheet.

The Company has an investment in mutual funds that is denominated in a foreign currency and is classified as marketable securities on the Company’s consolidated balance sheets. This equity investment is reported at fair value, as it is readily available, and as such is classified as a Level 1 asset. Unrealized holding gains and losses for this equity investment are included as components of interest expense, net within the consolidated statement of operations.

The tables presented below are a summary of changes in the fair value for the Company’s marketable securities – equity investments, ClearPoint Equity Investments, and ClearPoint convertible debt security for the three and nine months ended September 30, 2025 and September 30, 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Ending | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Ending
​ | ​ | Balance at | ​ | ​ | ​ | ​ | Currency | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Balance at
​ | ​ | June 30, | ​ | Unrealized | ​ | Unrealized | ​ | Investments | ​ | Redemptions/ | ​ | September 30,
​ |  | 2025 |  | Gain |  | Gain |  | Purchased |  | Sale |  | 2025
Marketable securities - equity investments | ​ | $ | 34,203 | ​ | ​ | 1,622 | ​ | ​ | 1,605 | ​ | ​ | 29,508 | ​ | ​ | (22,982) | ​ | ​ | 43,956
ClearPoint Equity Investments | ​ | ​ | 10,681 | ​ | ​ | 8,812 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 19,493
Total Fair Value | ​ | $ | 44,884 | ​ | $ | 10,434 | ​ | $ | 1,605 | ​ | $ | 29,508 | ​ | $ | (22,982) | ​ | $ | 63,449

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Ending | ​ | ​ | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | ​ | ​ | ​ | ​ | Ending
​ | ​ | Balance at | ​ | ​ | ​ | ​ | ​ | ​ | Currency | ​ | ​ | ​ | ​ | ​ | ​ | Balance at
​ | ​ | June 30, | ​ | Unrealized | ​ | Realized | ​ | Unrealized | ​ | Investments | ​ | Redemptions/ | ​ | September 30,
​ |  | 2024 |  | Gain | ​ | Loss |  | Gain |  | Purchased |  | Sale | ​ | 2024
Marketable securities - equity investments | ​ | $ | 16,889 | ​ | ​ | 812 | ​ | ​ | — | ​ | ​ | 400 | ​ | ​ | 32,208 | ​ | ​ | (21,051) | ​ | $ | 29,258
ClearPoint Equity Investments | ​ | ​ | 4,822 | ​ | ​ | 5,206 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 10,028
ClearPoint convertible debt security | ​ | ​ | 10,622 | ​ | ​ | — | ​ | ​ | (622) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (10,000) | ​ | ​ | —
Total Fair Value | ​ | $ | 32,333 | ​ | $ | 6,018 | ​ | $ | (622) | ​ | $ | 400 | ​ | $ | 32,208 | ​ | $ | (31,051) | ​ | $ | 39,286

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Ending | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Ending | ​
​ | ​ | Balance at | ​ | ​ | ​ | ​ | Currency | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Balance at | ​
​ | ​ | December 31, | ​ | Unrealized | ​ | Unrealized | ​ | Investments | ​ | Redemptions/ | ​ | September 30, | ​
​ |  | 2024 |  | Gain |  | Gain |  | Purchased |  | Sale |  | 2025 | ​
Marketable securities - equity investments | ​ | $ | 29,034 | ​ | ​ | 3,160 | ​ | ​ | 5,337 | ​ | ​ | 46,537 | ​ | ​ | (40,112) | ​ | ​ | 43,956 | ​
ClearPoint Equity Investments | ​ | ​ | 13,759 | ​ | ​ | 5,734 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 19,493 | ​
Total Fair Value | ​ | $ | 42,793 | ​ | $ | 8,894 | ​ | $ | 5,337 | ​ | $ | 46,537 | ​ | $ | (40,112) | ​ | $ | 63,449 | ​

​

​

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​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Ending | ​ | ​ | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | ​ | ​ | ​ | ​ | Ending
​ | ​ | Balance at | ​ | ​ | ​ | ​ | ​ | ​ | Currency | ​ | ​ | ​ | ​ | ​ | ​ | Balance at
​ | ​ | December 31, | ​ | Unrealized | ​ | Realized | ​ | Unrealized | ​ | Investments | ​ | Redemptions/ | ​ | September 30,
​ |  | 2023 |  | Gain/(Loss) |  | Loss |  | Loss |  | Purchased |  | Sale |  | 2024
Marketable securities - equity investments | ​ | $ | 22,634 | ​ | ​ | 1,923 | ​ | ​ | — | ​ | ​ | (3,289) | ​ | ​ | 49,614 | ​ | ​ | (41,624) | ​ | $ | 29,258
ClearPoint Equity Investments | ​ | ​ | 6,074 | ​ | ​ | 3,954 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 10,028
ClearPoint convertible debt security | ​ | ​ | 12,553 | ​ | ​ | (1,931) | ​ | ​ | (622) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (10,000) | ​ | ​ | —
Total Fair Value | ​ | $ | 41,261 | ​ | $ | 3,946 | ​ | $ | (622) | ​ | $ | (3,289) | ​ | $ | 49,614 | ​ | $ | (51,624) | ​ | $ | 39,286

​

Fair value of marketable securities that are classified as available for sale debt securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining available for sale debt securities, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices.

​

The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2025 and December 31, 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
​ |  | ​ | ​ |  | Quoted prices |  | Significant |  | ​ | ​
​ | ​ | ​ | ​ |  | in active |  | other |  | Significant
​ | ​ | ​ | ​ |  | markets for |  | observable |  | unobservable
​ | ​ | ​ | ​ |  | identical assets |  | inputs |  | inputs
​ |  | Total |  | (level 1) |  | (level 2) |  | (level 3)
Marketable securities - available for sale | ​ | $ | 971,244 | ​ | $ | — | ​ | $ | 971,244 | ​ | $ | —
Marketable securities - equity investments | ​ | $ | 43,956 | ​ | $ | 43,956 | ​ | $ | — | ​ | $ | —
ClearPoint Equity Investments | ​ | $ | 19,493 | ​ | $ | 19,493 | ​ | $ | — | ​ | $ | —

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
​ |  | ​ | ​ |  | Quoted prices |  | Significant |  | ​ | ​
​ | ​ | ​ | ​ |  | in active |  | other |  | Significant
​ | ​ | ​ | ​ |  | markets for |  | observable |  | unobservable
​ | ​ | ​ | ​ |  | identical assets |  | inputs |  | inputs
​ |  | Total |  | (level 1) |  | (level 2) |  | (level 3)
Marketable securities - available for sale | ​ | $ | 330,953 | ​ | $ | — | ​ | $ | 330,953 | ​ | $ | —
Marketable securities - equity investments | ​ | $ | 29,034 | ​ | $ | 29,034 | ​ | $ | — | ​ | $ | —
ClearPoint Equity Investments | ​ | $ | 13,759 | ​ | $ | 13,759 | ​ | $ | — | ​ | $ | —
Contingent consideration payable- net sales milestones | ​ | $ | 800 | ​ | $ | — | ​ | $ | — | ​ | $ | 800

​

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2025 and December 31, 2024.

The following is a summary of marketable securities accounted for as available for sale debt securities at September 30, 2025 and December 31, 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
​ |  | Amortized |  | Gross Unrealized | ​ | ​ | ​
​ |  | Cost |  | Gains |  | Losses |  | Fair Value
Commercial paper | ​ | $ | 106,556 | ​ | $ | 8 | ​ | $ | (3) | ​ | $ | 106,561
Corporate debt securities | ​ | ​ | 243,257 | ​ | ​ | 160 | ​ | ​ | (2) | ​ | ​ | 243,415
Government obligations | ​ | ​ | 620,760 | ​ | ​ | 518 | ​ | ​ | (10) | ​ | ​ | 621,268
Total | ​ | $ | 970,573 | ​ | $ | 686 | ​ | $ | (15) | ​ | $ | 971,244

​

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​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
​ |  | Amortized |  | Gross Unrealized | ​ | ​ | ​
​ |  | Cost |  | Gains |  | Losses |  | Fair Value
Commercial paper | ​ | $ | 44,780 | ​ | $ | — | ​ | $ | (1) | ​ | $ | 44,779
Corporate debt securities | ​ |  | 89,320 | ​ | ​ | 76 | ​ | ​ | (75) | ​ | ​ | 89,321
Government obligations | ​ | ​ | 196,584 | ​ | ​ | 269 | ​ | ​ | — | ​ | ​ | 196,853
Total | ​ | $ | 330,684 | ​ | $ | 345 | ​ | $ | (76) | ​ | $ | 330,953

​

For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. For the three and nine months ended September 30, 2025 and 2024, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost basis, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three and nine months ended September 30, 2025 and 2024, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive income (loss) in stockholders’ deficit.

For the three and nine months ended September 30, 2025, realized gains from the sale of available for sale debt securities were immaterial. For the three and nine months ended September 30, 2024, the Company had $0.8 million and $0.8 million realized gains from the sale of available for sale debt securities, respectively. Realized gains and losses are reported as a component of interest expense, net in the consolidated statement of operations. Reclassified amounts from other comprehensive items were determined using the actual realized gains and losses from the sales of marketable securities.

The unrealized losses and fair values of available for sale debt securities that have been in an unrealized loss position for a period of less than and greater than or equal to 12 months as of September 30, 2025 are as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
​ |  | Securities in an unrealized loss |  | Securities in an unrealized loss |  | ​ | ​ | ​ | ​ | ​
​ |  | position less than 12 months |  | position greater than or equal to 12 months | ​ | Total
​ |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value
Commercial paper | ​ | $ | (3) | ​ | ​ | 59,850 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (3) | ​ | $ | 59,850
Corporate debt securities | ​ | $ | (2) | ​ | ​ | 44,500 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (2) | ​ | $ | 44,500
Government obligations | ​ | $ | (10) | ​ | ​ | 30,001 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (10) | ​ | $ | 30,001
Total | ​ | $ | (15) | ​ | $ | 134,351 | ​ | $ | — | ​ | $ | — | ​ | $ | (15) | ​ | $ | 134,351

​

The unrealized losses and fair values of available for sale debt securities that have been in an unrealized loss position for a period of less than and greater than or equal to 12 months as of December 31, 2024 are as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
​ |  | Securities in an unrealized loss |  | Securities in an unrealized loss |  | ​ | ​ | ​ | ​ | ​
​ |  | position less than 12 months |  | position greater than or equal to 12 months | ​ | Total
​ |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value
Commercial paper | ​ | $ | (1) | ​ | ​ | 29,810 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (1) | ​ | $ | 29,810
Corporate debt securities | ​ | $ | (75) | ​ | ​ | 59,550 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (75) | ​ | $ | 59,550
Total | ​ | $ | (76) | ​ | $ | 89,360 | ​ | $ | — | ​ | $ | — | ​ | $ | (76) | ​ | $ | 89,360

​

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Available for sale debt securities at September 30, 2025 and December 31, 2024 mature as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
​ |  | Less Than |  | More Than
​ |  | 12 Months |  | 12 Months
Commercial paper | ​ | $ | 106,561 | ​ | $ | —
Corporate debt securities | ​ | ​ | 243,415 | ​ | ​ | —
Government obligations | ​ | ​ | 621,268 | ​ | ​ | —
Total | ​ | $ | 971,244 | ​ | $ | —

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
​ |  | Less Than |  | More Than
​ |  | 12 Months |  | 12 Months
Commercial paper | ​ | $ | 44,779 | ​ | $ | —
Corporate debt securities | ​ |  | 89,321 | ​ |  | —
Government obligations | ​ | ​ | 196,853 | ​ | ​ | —
Total | ​ | $ | 330,953 | ​ | $ | —

​

The Company classifies all of its marketable securities as current as they are all either available for sale debt securities or equity investments and are available for current operations.

Convertible senior notes

In September 2019, the Company issued $287.5 million of 1.50% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes”). The fair value of the 2026 Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the 2026 Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the 2026 Convertible Notes at September 30, 2025 and December 31, 2024 was $369.0 million and $321.3 million, respectively.

Level 3 valuation

The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of contingent consideration on the consolidated statements of operations. During the first quarter of 2025, the probability of triggering the remaining contingent consideration was determined to be remote, and therefore the balance was written down to zero. The change in fair value of the contingent consideration for the nine months ended September 30, 2025 is $0.8 million and is recorded in the consolidated statement of operations. Refer to Note 10 for additional details.

5. Accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2025 and December 31, 2024 consist of the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, | ​ | December 31, | ​
​ |  | 2025 |  | 2024 | ​
Employee compensation, benefits, and related accruals | ​ | $ | 49,466 | ​ | $ | 61,575 | ​
Income tax payable | ​ | ​ | 2,927 | ​ | ​ | 4,701 | ​
Consulting and contracted research | ​ |  | 19,961 | ​ |  | 19,909 | ​
Sales allowance | ​ |  | 55,302 | ​ |  | 58,644 | ​
Sales rebates | ​ |  | 83,850 | ​ |  | 101,613 | ​
Royalties | ​ | ​ | 5,146 | ​ | ​ | 8,953 | ​
Accounts payable | ​ |  | 36,617 | ​ |  | 17,274 | ​
Milestone payable | ​ | ​ | 32,500 | ​ | ​ | 11,025 | ​
Other | ​ |  | 17,372 | ​ |  | 20,598 | ​
Total | ​ | $ | 303,141 | ​ | $ | 304,292 | ​

​

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As of September 30, 2025, the Company does no t have any accrued restructuring costs included above within employee compensation, benefits, and related accruals. As of December 31, 2024, there were $0.1 million of accrued restructuring costs included above within employee compensation, benefits, and related accruals from a reduction in workforce in the year ended December 31, 2023 in connection with the Company’s strategic pipeline prioritization and discontinuation of its preclinical and early research programs in its gene therapy platform.

6. Capitalization

In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. No shares were sold during the three and nine months ended September 30, 2025 and 2024. The remaining shares of the Company’s common stock available to be issued and sold, under the At the Market Offering, have an aggregate offering price of up to $93.0 million as of September 30, 2025.

7. Net income (loss) per share

Basic and diluted net income (loss) per share is computed by dividing net income (loss) by the weighted-average number of common shares outstanding.

The following tables set forth the computation of basic and diluted net income (loss) per share:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 |  | 2024 |  | ​ | 2025 |  | 2024 |
Numerator: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net income (loss), basic | ​ | $ | 15,896 |  | $ | (106,654) | ​ |  | ​ | $ | 817,609 |  | $ | (297,409) |
Add: Interest expense, net of tax, on the Company's 2026 Convertible Notes | ​ | ​ | 1,096 | ​ | ​ | — | ​ | ​ | ​ | ​ | 3,257 | ​ | ​ | — | ​
Net income (loss), diluted | ​ | $ | 16,992 | ​ | $ | (106,654) | ​ | ​ | ​ | $ | 820,866 | ​ | $ | (297,409) | ​
Denominator: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Weighted-average number of shares outstanding, basic | ​ | ​ | 78,471,119 |  | ​ | 76,925,523 | ​ |  | ​ |  | 78,642,478 |  |  | 76,716,340 |
Effect of dilutive securities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Common stock issuable under the Company's equity incentive plans | ​ |  | 3,170,135 | ​ |  | — | ​ | ​ | ​ | ​ | 2,783,134 | ​ | ​ | — | ​
Common stock issuable under the Company's 2026 Convertible Notes | ​ | ​ | 5,474,115 | ​ | ​ | — | ​ | ​ | ​ | ​ | 5,474,115 | ​ | ​ | — | ​
Weighted-average common shares outstanding, diluted | ​ | ​ | 87,115,369 | ​ | ​ | 76,925,523 | ​ | ​ | ​ | ​ | 86,899,727 | ​ | ​ | 76,716,340 | ​
Net income (loss) per common share, basic | ​ | $ | 0.20 | ​ | $ | (1.39) | * | ​ | ​ | $ | 10.40 | ​ | $ | (3.88) | *
Net income (loss) per common share, diluted | ​ | $ | 0.20 | ​ | $ | (1.39) | * | ​ | ​ | $ | 9.45 | ​ | $ | (3.88) | *

* In the three and nine months ended September 30, 2024, the Company experienced a net loss and therefore did not report any dilutive share impact.

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The following table shows historical common share equivalents outstanding, which are not included in the above calculation, as the effect of their inclusion is anti-dilutive during each period. The anti-dilutive shares are calculated as the unweighted outstanding shares as of the reporting period end date that are antidilutive using the treasury stock method.

​

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | As of September 30, | ​
​ |  | 2025 |  | 2024 |
Stock options | ​ | 2,282,923 | ​ | 9,173,460 | ​
Unvested restricted stock units |  | 3,788,803 |  | 3,596,329 |
Total |  | 6,071,726 |  | 12,769,789 |

​

8. Stock award plan

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long-Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. On June 8, 2022 (the “Restatement Effective Date”), the Company’s stockholders approved the Amended and Restated 2013 Long-Term Incentive Plan (the “Amended 2013 LTIP”). The Amended 2013 LTIP provides for the grant of incentive stock options, nonstatutory stock options, restricted stock units and other stock-based awards. The number of shares of common stock reserved for issuance under the Amended 2013 LTIP is the sum of (A) the number of shares of the Company’s common stock (up to 16,724,212 shares) that is equal to the sum of (1) the number of shares issued under the 2013 Long-Term Incentive Plan prior to the Restatement Effective Date, (2) the number of shares that remain available for issuance under the 2013 Long-Term Incentive Plan immediately prior to the Restatement Effective Date and (3) the number of shares subject to awards granted under the 2013 Long-Term Incentive Plan prior to the Restatement Effective Date that are outstanding as of the Restatement Effective Date, plus (B) from and after the Restatement Effective Date, an additional 8,475,000 shares of Common Stock. As of September 30, 2025, awards for 5,204,816 shares of common stock are available for issuance under the Amended 2013 LTIP.

In January 2020, the Company’s Board of Directors approved the 2020 Inducement Stock Incentive Plan. The 2020 Inducement Stock Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards for, initially, up to at the time, an aggregate of 1,000,000 shares of common stock. Any grants made under the 2020 Inducement Stock Incentive Plan must be made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company’s new hires’ employment compensation. In December 2020, the Company’s Board of Directors approved an additional 1,000,000 shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan. In April 2022, the Company’s Board of Directors approved a reduction in the total number of shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan to 1,300,000 shares. In December 2022, the Company’s Board of Directors approved an additional 1,700,000 shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan. As of September 30, 2025, awards for 1,802,161 shares of common stock were available for issuance under the 2020 Inducement Stock Incentive Plan.

The Board of Directors has the authority to select the individuals to whom options are granted and determine the terms of each option, including (i) the number of shares of common stock subject to the option; (ii) the date on which the option becomes exercisable; (iii) the option exercise price, which, in the case of incentive stock options, must be at least 100% (110% in the case of incentive stock options granted to a stockholder owning in excess of 10% of the Company’s stock) of the fair market value of the common stock as of the date of grant; and (iv) the duration of the option (which, in the case of incentive stock options, may not exceed ten years). Options typically vest over a four-year period.

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Inducement stock option awards

From January 1, 2025 through September 30, 2025, the Company issued a total of 841,945 stock options to various employees. Of those, 51,200 were inducement grants for non-statutory stock options, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

​

Stock option activity—A summary of stock option activity is as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | ​ |  | ​ | ​ |  | Weighted- |  |  | ​ | ​
​ | ​ | ​ | ​ | Weighted- | ​ | average | ​ | ​ | Aggregate
​ | ​ | ​ | ​ | average | ​ | remaining | ​ | ​ | intrinsic
​ | ​ | Number of | ​ | exercise | ​ | contractual | ​ | ​ | value(in
​ | ​ | options | ​ | price | ​ | term | ​ | ​ | thousands)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ |  | ​ | ​ | ​
Outstanding at December 31, 2024 |  | 8,482,489 | ​ | $ | 42.29 |  |  |  | ​ | ​ |
Granted |  | 841,945 | ​ | $ | 47.12 |  |  |  | ​ | ​ |
Exercised |  | (953,414) | ​ | $ | 35.75 |  |  |  | ​ | ​ |
Forfeited/Cancelled |  | (564,709) | ​ | $ | 53.91 |  |  |  | ​ | ​ |
Outstanding at September 30, 2025 |  | 7,806,311 | ​ | $ | 42.77 |  | 5.66 | years | ​ | $ | 151,190
Expected to vest at September 30, 2025 |  | 1,524,459 | ​ | $ | 39.30 |  | 8.53 | years | ​ | $ | 33,651
Exercisable at September 30, 2025 |  | 6,126,727 | ​ | $ | 43.71 |  | 4.86 | years | ​ | $ | 114,211

​

The fair value of grants made in the nine months ended September 30, 2025, was contemporaneously estimated on the date of grant using the following assumptions:

​

​ | ​ | ​ | ​
​ |  | Nine months ended |
​ |  | September 30, 2025 |
Risk-free interest rate |  | 3.81% - 4.44% |
Expected volatility |  | 55% - 56% |
Expected term |  | 5.5 years |

​

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine months ended September 30, 2025 was $25.44 per share.

The expected term of options was estimated based on the Company’s historical exercise data and the expected volatility of options was estimated based on the Company’s historical stock volatility. The risk-free rate of the options was based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.

Restricted Stock Units—Restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock units, which have been determined based upon the market value of the Company’s shares on the grant date, are expensed over the vesting period. From January 1, 2025, through September 30, 2025, the Company issued a total of 1,615,305 restricted stock units to various employees. Of those, 107,050 were inducement grants for restricted stock units, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

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The following table summarizes information on the Company’s restricted stock units, including performance-based restricted stock units (“PSUs”) for which the performance conditions were satisfied:

​

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Restricted Stock Units
​ | ​ | ​ | ​ | Weighted
​ | ​ | ​ | ​ | Average
​ | ​ | ​ | ​ | Grant
​ | ​ | Number of | ​ | Date
​ |  | Shares |  | Fair Value
Unvested at December 31, 2024 | ​ | 3,527,575 | ​ | $ | 33.39
Granted |  | 1,615,305 | ​ | ​ | 47.16
PSUs with conditions satisfied |  | 75,000 | ​ | ​ | 28.58
Vested | ​ | (1,201,681) | ​ | ​ | 36.79
Forfeited |  | (227,396) | ​ | ​ | 35.27
Unvested at September 30, 2025 |  | 3,788,803 | ​ | $ | 37.98

​

Performance-based Restricted Stock Units—In December 2023, the Company granted 150,000 PSUs to its Chief Executive Officer, Dr. Matthew Klein, which will vest only if certain regulatory milestones are achieved over an approximately two-year performance period. In December 2024, the Company granted 25,000 PSUs to Dr. Matthew Klein, which will vest only if challenging performance goals relating to development, regulatory, or commercial goals are achieved over an approximately five-year performance period. An additional 31,250 PSUs with market conditions were granted to Dr. Matthew Klein in December 2024.

During the quarter ended September 30, 2025, the performance conditions for 75,000 of these PSUs granted to Dr. Klein in December 2023 were satisfied due to the Company’s achievement of a regulatory milestone and are included in the restricted stock units table above. The expense related to these PSUs was $1.0 million for the three and nine months ended September 30, 2025. The achievement of the remaining performance goals for the PSU’s granted to Dr. Klein has not yet been deemed probable and therefore no expense has been recognized to date. The expense related to the PSUs with market conditions was $0.1 million and $0.5 million for the three and nine months ended September 30, 2025, respectively.

The following table summarizes information regarding the Company’s PSUs:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Performance-based Restricted Stock Units
​ |  | Performance based |  | Market Conditions | ​ | Total
Total PSUs granted for which the performance or market conditions were not yet satisfied at December 31, 2024 | ​ | 175,000 | ​ | 31,250 | ​ | 206,250
PSUs with performance or market conditions satisfied during the period |  | (75,000) | ​ | — | ​ | (75,000)
Total PSUs granted for which the performance or market conditions were not yet satisfied at September 30, 2025 |  | 100,000 | ​ | 31,250 | ​ | 131,250

​

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (as amended, the “ESPP” or the “Plan”), for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Company’s Board of Directors. In June 2021, the Plan was amended to increase the total number of shares available for purchase under the Plan from one million shares to two million shares of the Company’s common stock. Employees may participate over a six month period through payroll withholdings and may purchase, at the end of the six month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the three and nine months ended September 30, 2025, the Company recorded $0.6 million and $1.6 million, respectively, in compensation expense related to the ESPP.

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The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock units, performance-based restricted stock units and the ESPP as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30,
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024
Research and development | ​ | $ | 9,133 | ​ | $ | 9,416 | ​ | $ | 26,827 | ​ | $ | 27,810
Selling, general and administrative | ​ |  | 10,293 | ​ |  | 10,339 | ​ |  | 29,202 | ​ |  | 29,566
Total | ​ | $ | 19,426 | ​ | $ | 19,755 | ​ | $ | 56,029 | ​ | $ | 57,376

​

As of September 30, 2025, there was approximately $137.2 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s equity award plans. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 2.7 years.

9. Debt

Liability for sale of future royalties

On July 17, 2020, the Company, RPI Intermediate Finance Trust (“RPI”), and, for the limited purposes set forth in the agreement, Royalty Pharma plc, entered into a royalty purchase agreement (the “Original Royalty Purchase Agreement”). Pursuant to the Original Royalty Purchase Agreement, the Company sold to RPI 42.933% (the “Original Assigned Royalty Rights”) of the Company’s right to receive sales-based royalty payments (the “Royalty”) on worldwide net sales of Evrysdi and any other product developed pursuant to the SMA License Agreement. In consideration for the sale of the Original Assigned Royalty Rights, RPI paid the Company $650.0 million in cash consideration. The Company retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the License Agreement, which remaining milestone payments equal $150.0 million in the aggregate as of December 31, 2024. The Original Royalty Purchase Agreement was set to terminate 60 days following the earlier of the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the SMA License Agreement and the date on which RPI has received $1.3 billion in respect of the Original Assigned Royalty Rights.

Pursuant to the guidance in ASC 470-10-25-2, the Company determined that the $650.0 million cash consideration obtained pursuant to the Original Royalty Purchase Agreement should be classified as debt and recorded it as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI at the time of the transaction. The liability was subsequently amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance, utilizing the prospective method to account for subsequent changes in the estimated future payments to be made to RPI.

On October 18, 2023, the Company, Royalty Pharma, and, for the limited purposes set forth in the agreement, Royalty Pharma plc, entered into an Amended and Restated Royalty Purchase Agreement (the “A&R Royalty Purchase Agreement”), which amends and restates in its entirety the Original Royalty Purchase Agreement. Pursuant to the A&R Royalty Purchase Agreement, the Company has sold or agreed to sell to Royalty Pharma certain portions of the Company’s remaining Royalty on worldwide net sales of Evrysdi and any other product (the “Products”) developed pursuant to the SMA License Agreement (all such retained Royalty rights of the Company, the “Retained Royalty Rights,” and all such Royalty rights that are sold to Royalty Pharma pursuant to the A&R Royalty Purchase Agreement, the “A&R Assigned Royalty Rights”). At closing, Royalty Pharma paid the Company $1.0 billion in cash consideration for 38.0447% of the Company’s Retained Royalty Rights (which is in addition to the 42.9330% assigned to Royalty Pharma in connection with the Original Royalty Purchase Agreement, for a total of 80.9777% of the total Royalty) until such time as Royalty Pharma has received payments in respect of the Original Assigned Royalty Rights equal to $1.3 billion in the aggregate, and thereafter 66.6667% of the total Royalty. In addition, the Company may sell to Royalty Pharma the remainder of the Company’s Retained Royalty Rights in exchange for an aggregate of $500.0 million in additional cash consideration after the closing of the A&R Royalty Purchase Agreement, less royalties received in respect of the Retained Royalty Rights put to Royalty Pharma, which will be payable by Royalty Pharma pursuant to five put options held by the Company that are

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exercisable at the Company’s option between January 1, 2024 and December 31, 2025. If the Company exercises two or fewer of the put options, Royalty Pharma may exercise a call option during the period from and after January 1, 2026 until and including March 31, 2026 for up to 50% of the remainder of the Company’s Retained Royalty Rights less amounts exercised by the Company via its put options at a purchase price that is proportional to the purchase price of the Company’s unexercised put options. Royalty Pharma’s exercise of the call option would result in Royalty Pharma owning 90.4888% of the total Royalty until such time as Royalty Pharma has received payments in respect of the Original Assigned Royalty Rights equal to $1.3 billion in the aggregate, and thereafter 83.3333% of the total Royalty. The A&R Royalty Purchase Agreement will terminate 60 days following the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the SMA License Agreement.

The change in rights and obligations from the A&R Royalty Purchase Agreement resulted in a change in the terms of the liability for sale of future royalties, which was evaluated by the Company in accordance with ASC 470-50, Debt — Modifications and Extinguishments. The Company determined that the present value of the cash flows under the A&R Royalty Purchase Agreement were substantially different from the present value of the cash flows under the Original Royalty Purchase Agreement. This resulted in the derecognition of the old liability for sale of future royalties and the new liability for sale of future royalties being recorded at fair value, which was determined to be $1,809.9 million as of the date of the A&R Royalty Purchase Agreement. This resulted in an extinguishment loss of $44.9 million, which was recorded within loss on extinguishment of debt, within the Company’s statement of operations in the year ended December 31, 2023.

The fair value for the new liability for sale of future royalties on the date of the A&R Royalty Purchase Agreement was based on the Company’s estimates of future royalties expected to be paid to Royalty Pharma over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability is being amortized using the effective interest method over the life of the arrangement, in accordance with ASC 470 and ASC 835. The initial annual effective interest rate was determined to be 10.8%. The Company utilized the prospective method to account for subsequent changes in the estimated future payments to be made to Royalty Pharma and updates the effective interest rate on a quarterly basis. Issuance costs related to the transaction were determined to be immaterial.

In June 2024, the Company, Royalty Pharma and Royalty Pharma plc, entered into an amendment to the A&R Royalty Purchase Agreement. Under the A&R Royalty Purchase Agreement, the Company exercised a put option in June 2024, resulting in the Company receiving $241.8 million in cash consideration. In connection with the put option exercise, the change in rights and obligations resulted in a change in the terms of the liability for sale of future royalties, which was evaluated by the Company in accordance with ASC 470-50, Debt —Modifications and Extinguishments. The Company determined that the present value of the cash flows after the put option exercise was not substantially different and was therefore determined to be a modification. The $241.8 million in cash consideration obtained was added to the liability for sale of future royalties and the annual effective interest rate under the A&R Royalty Purchase Agreement was determined to be 9.9%. The liability is being amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance, utilizing the prospective method to account for subsequent changes in the estimated future payments to be made to Royalty Pharma and the Company updates the effective interest rate on a quarterly basis.

To date, the Company has sold to Royalty Pharma a total of 90.49% of the Royalty, which will be reduced to 83.33% (the “Assigned Royalty Rights”) after Royalty Pharma receives $1.3 billion in aggregate payments (the “Assigned Royalty Cap”) from the Royalty assigned at the closing of the Original Purchase Agreement. In exchange for the Assigned Royalty Rights, Royalty Pharma has paid to the Company upfront cash consideration totaling $1.9 billion, less Royalty payments received by the Company with respect to the Assigned Royalty Rights. The Company currently retains 9.51% of the Royalty, which increases to 16.67% after the Assigned Royalty Cap has been met. The Company has the option under the A&R Royalty Purchase Agreement to sell its retained portions of the Royalty to Royalty Pharma in up to three tranches for the following payments: (1) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, (2) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, and (3) $50.0 million in exchange for 1.90% of the Royalty, which increases to 3.33% after the Assigned Royalty Cap has been met, in each case less Royalty payments received by the Company with respect to the Assigned Royalty Rights. The A&R Royalty Purchase Agreement will terminate 60

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days following the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the License Agreement.

The following table shows the activity within the “liability for sale of future royalties- current” and “liability for sale of future royalties- noncurrent” accounts for the nine months ended September 30, 2025:

​

​ | ​ | ​ | ​ | ​
​ |  | Nine Months Ended September 30, | ​
Liability for sale of future royalties- (current and noncurrent) | ​ | 2025 | ​
Beginning balance as of December 31, 2024 | ​ | $ | 2,081,776 | ​
Less: Non-cash royalty revenue payable to Royalty Pharma | ​ | ​ | (149,160) | ​
Plus: Non-cash interest expense recognized | ​ | ​ | 149,305 | ​
Ending balance | ​ | $ | 2,081,921 | ​
Effective interest rate as of September 30, 2025 | ​ |  | 9.3% | ​

​

Non-cash interest expense is recorded in the statement of operations within “Interest expense, net”.

​

2026 Convertible Notes

In September 2019, the Company issued the 2026 Convertible Notes, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes, which was exercised in full by the initial purchasers. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.

The 2026 Convertible Notes are governed by an indenture (the “2026 Convertible Notes Indenture”) with U.S. Bank National Association as trustee (the “2026 Convertible Notes Trustee”).

Holders of the 2026 Convertible Notes may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances:

| ● | during any calendar quarter commencing on or after December 31, 2019 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;

| ● | during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;

| ● | during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or

| ● | upon the occurrence of specified corporate events.

On or after March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company’s common stock or any combination thereof at the Company’s election.

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The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.

The Company was not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically.

If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.

The 2026 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2026 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.

The 2026 Convertible Notes consist of the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025 |  | December 31, 2024 | ​
Principal | ​ | $ | 287,500 | ​ | $ | 287,500 | ​
Less: Debt issuance costs | ​ |  | (1,181) | ​ |  | (2,088) | ​
Net carrying amount | ​ | $ | 286,319 | ​ | $ | 285,412 | ​

As of September 30, 2025, the remaining contractual life of the 2026 Convertible Notes is approximately 1.0 year. The 2026 Convertible Notes were reclassified from long-term debt to current portion of long-term debt on the Company’s consolidated balance sheet as of September 30, 2025.

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The following table sets forth total interest expense recognized related to the 2026 Convertible Notes:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | Three Months Ended September 30, | ​ | ​ | Nine Months Ended September 30, | ​
​ |  | 2025 | ​ | 2024 |  | 2025 | ​ | 2024 | ​
Contractual interest expense | ​ | $ | 1,081 | ​ | $ | 1,081 | ​ | $ | 3,217 | ​ | $ | 3,224 | ​
Amortization of debt issuance costs | ​ |  | 306 | ​ | ​ | 300 | ​ | ​ | 906 | ​ | ​ | 891 | ​
Total | ​ | $ | 1,387 | ​ | $ | 1,381 | ​ | $ | 4,123 | ​ | $ | 4,115 | ​
Effective interest rate | ​ |  | 1.9 | % | ​ | 1.9 | % | ​ | 1.9 | % | ​ | 1.9 | %

​

10. Commitments and contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products.

Pursuant to the Agreement and Plan of Merger (the “Agilis Merger Agreement”), dated as of July 19, 2018 by and among the Company, Agilis Biotherapeutics, Inc. (“Agilis”) and Agility Merger Sub, Inc. (such merger pursuant thereto, the “Agilis Merger”), Agilis equityholders were previously entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for FA and Angelman syndrome during specified terms, ranging from 2%-6%. The Company was required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Agilis Merger, regardless of whether the applicable milestones have been achieved.

As of September 30, 2025, all of the milestones have either been paid or settled, with the exception of the regulatory milestones and net sales milestones related to FA and Angelman syndrome and the net sales milestones related to Upstaza/Kebilidi. In May 2023, as part of the Company’s strategic portfolio prioritization, the Company decided to discontinue its preclinical and early research programs in its gene therapy platform, which included FA and Angelman syndrome. As a result, the Company does not expect the milestones related to FA and Angelman syndrome to be achieved. In addition, the Company does not expect to pay the 2%–6% royalties on annual net sales related to FA and Angelman syndrome. As of September 30, 2025, the remaining potential sales milestones related to Upstaza/Kebilidi is $50.0 million, however the Company has determined that the probability of triggering these milestones is remote.

On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, including certain compounds that the Company has begun to develop as part of its inflammation and ferroptosis platform, pursuant to an asset purchase agreement by and between the Company and BioElectron, dated October 1, 2019 (the “BioElectron Asset Purchase Agreement”). BioElectron was a private company with a pipeline focused on inflammatory CNS disorders. The lead program, vatiquinone, is in late stage development for FA with substantial unmet need and significant commercial opportunity that are complementary to PTC’s existing pipeline.

Subject to the terms and conditions of the BioElectron Asset Purchase Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the BioElectron Asset Purchase Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products.

Subject to the terms and conditions of the Agreement and Plan of Merger, dated as of May 5, 2020 (the “Censa Merger Agreement”) by and among the Company, Censa Pharmaceuticals, Inc. (“Censa”), Hydro Merger Sub, Inc., the Company’s wholly owned, indirect subsidiary, and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representative Services LLC (such merger pursuant thereto, the “Censa Merger”), former Censa securityholders may become entitled to receive contingent payments from the Company based on (i) the

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achievement of certain development and regulatory milestones up to an aggregate maximum amount of $217.5 million for sepiapterin’s two most advanced programs and receipt of a priority review voucher from the FDA as set forth in the Censa Merger Agreement, (ii) $109.0 million in development and regulatory milestones for each additional indication of sepiapterin, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $160.0 million, (iv) a percentage of annual net sales during specified terms, ranging from single to low double digits of the applicable net sales threshold amount, and (v) any sublicense fees paid to the Company in consideration of any sublicense of Censa’s intellectual property to commercialize sepiapterin, on a country-by-country basis, which contingent payment shall equal to a mid-double digit percentage of any such sublicense fees. On August 5, 2025, the Company, certain former securityholders of Censa, and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC, entered into a Rights Satisfaction Agreement (the “Rights Satisfaction Agreement”) pursuant to which such former securityholders of Censa (the “Participating Rightsholders”) agreed to the cancellation and forfeiture of their rights to receive certain contingent payments from the Company based on worldwide annual net sales by the Company of products containing sepiapterin (“Net Sales of Product”) under the Censa Merger Agreement in exchange for the consideration set forth in the Rights Satisfaction Agreement and further detailed below.

Pursuant to the terms of the Rights Satisfaction Agreement, the Participating Rightsholders canceled and forfeited their rights under the Censa Merger Agreement to receive a percentage of annual net sales during the applicable payment term equal to (i) 8% of annual Net Sales of Product for that portion of annual Net Sales of Product less than or equal to $250.0 million, (ii) 10% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $250.0 million but less than $500.0 million and (iii) 12% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $500.0 million (collectively, the “Net Sales Payments”).

In consideration of the foregoing, the Company agreed to pay to the Participating Rightsholders an aggregate amount in cash up to $250.0 million (the “Upfront Consideration”) upon the consummation of the transactions contemplated by the Rights Satisfaction Agreement and potential milestone payments (each an “Additional Milestone Payment”) of up to $100.0 million each (or up to $500.0 million in the aggregate) based on the achievement of specified Net Sales Thresholds (as defined in the Censa Merger Agreement). The amount of the Upfront Consideration and the Additional Milestone Payments was subject to adjustment in the Rights Satisfaction Agreement based on the number of Participating Rightsholders.

At the consummation of the transactions contemplated by the Rights Satisfaction Agreement, based on the participation of former Censa securityholders holding approximately 90% of Censa’s equity securities prior to the consummation of the transactions contemplated by the Censa Merger Agreement, the Company paid an aggregate amount of Upfront Consideration in cash of $225.1 million. Additionally, the Company is obligated to make Additional Milestone Payments in an amount equal to approximately $90.0 million upon achievement of each of the (i) first occurrence of a three or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $3.0 billion, (ii) first occurrence of a five or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $5.0 billion, (iii) first occurrence of a seven or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $7.0 billion, (iv) first occurrence of a nine or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $9.0 billion and (v) first occurrence of an 11 or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $11.0 billion. If, after the consummation of the transactions contemplated by the Rights Satisfaction Agreement, any additional former securityholder of Censa executes and delivers a joinder to the Rights Satisfaction Agreement and becomes a party thereto, the Company will pay such former securityholder an amount in cash equal to such former securityholder’s applicable pro rata share of the Upfront Consideration (less any Net Sale Payments previously received) and any Additional Milestone Payments that become payable to Participating Rightsholders under the Rights Satisfaction Agreement.

The Rights Satisfaction Agreement has no effect on the Censa Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightsholders’ rights to receive the Net Sales Payments described above. As a result, all other rights and obligations under the Censa Merger Agreement remain in effect pursuant to their terms, including, without limitation, the Company’s obligation to pay certain contingent payments upon the achievement of certain development and Net Sales of Product milestones.

In July 2025, Sephience™ (sepiapterin) was granted FDA approval for the treatment of children and adults living with PKU. Pursuant to the Censa Merger Agreement, the approval triggered a $32.5 million milestone to the former Censa

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securityholders, which was recorded in accounts payable and accrued expenses on the Company’s consolidated balance sheet as of September 30, 2025. As of September 30, 2025, $120.0 million of the $217.5 million in development and regulatory milestones have been paid to the former Censa securityholders.

The Company also has the Tegsedi-Waylivra Agreement for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Akcea is entitled to receive royalty payments subject to certain terms set forth in the Tegsedi-Waylivra Agreement.

The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur. Additionally, the Company has royalty payments associated with Translarna, Emflaza, Sephience, and Upstaza/Kebilidi net product revenue, payable quarterly or annually in accordance with the terms of the related agreements.

From time to time in the ordinary course of its business, the Company is subject to claims, legal proceedings and disputes. The Company is not currently aware of any material legal proceedings against it.

11. Revenue recognition

Net product sales

The Company views its operations and manages its business in one operating segment: life science.

During the three and nine months ended September 30, 2025 and 2024, net product revenues consisted of the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30,
​ | ​ | ​ | 2025 | ​ | 2024
​ | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total
Translarna | ​ | $ | — | ​ | $ | 50,665 | ​ | $ | 50,665 | ​ | $ | — | ​ | $ | 72,283 | ​ | $ | 72,283
Emflaza | ​ | ​ | 35,160 | ​ | ​ | — | ​ | ​ | 35,160 | ​ | ​ | 51,941 | ​ | ​ | — | ​ | ​ | 51,941
Sephience | ​ | ​ | 14,365 | ​ | ​ | 5,198 | ​ | ​ | 19,563 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Upstaza/Kebilidi | ​ | ​ | 6,898 | ​ | ​ | 8,837 | ​ | ​ | 15,735 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
All other products | ​ | ​ | — | ​ | ​ | 9,833 | ​ | ​ | 9,833 | ​ | ​ | — | ​ | ​ | 11,197 | ​ | ​ | 11,197
Total net product revenue | ​ | $ | 56,423 | ​ | $ | 74,533 | ​ | $ | 130,956 | ​ | $ | 51,941 | ​ | $ | 83,480 | ​ | $ | 135,421
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | 2024
​ | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total
Translarna | ​ | $ | — | ​ | $ | 196,289 | ​ | $ | 196,289 | ​ | $ | — | ​ | $ | 246,217 | ​ | $ | 246,217
Emflaza | ​ | ​ | 119,303 | ​ | ​ | — | ​ | ​ | 119,303 | ​ | ​ | 156,718 | ​ | ​ | — | ​ | ​ | 156,718
Sephience | ​ | ​ | 14,365 | ​ | ​ | 5,198 | ​ | ​ | 19,563 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Upstaza/Kebilidi | ​ | ​ | 6,898 | ​ | ​ | 29,385 | ​ | ​ | 36,283 | ​ | ​ | — | ​ | ​ | 9,648 | ​ | ​ | 9,648
All other products | ​ | ​ | — | ​ | ​ | 31,273 | ​ | ​ | 31,273 | ​ | ​ | — | ​ | ​ | 33,662 | ​ | ​ | 33,662
Total net product revenue | ​ | $ | 140,566 | ​ | $ | 262,145 | ​ | $ | 402,711 | ​ | $ | 156,718 | ​ | $ | 289,527 | ​ | $ | 446,245

​

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Disaggregated net product revenues by country for the three and nine months ended September 30, 2025 and 2024 are as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | 2024 | ​ | 2025 | ​ | 2024
United States | ​ | $ | 56,423 | ​ | $ | 51,941 | ​ | $ | 140,566 | ​ | $ | 156,718
Russia | ​ | ​ | 25,107 | ​ | ​ | 965 | ​ | ​ | 81,745 | ​ | ​ | 55,716
Brazil | ​ | ​ | 9,222 | ​ | ​ | 29,219 | ​ | ​ | 59,678 | ​ | ​ | 68,304
All other countries | ​ | ​ | 40,204 | ​ | ​ | 53,296 | ​ | ​ | 120,722 | ​ | ​ | 165,507
Total net product revenue | ​ | $ | 130,956 | ​ | $ | 135,421 | ​ | $ | 402,711 | ​ | $ | 446,245

​

For the three months ended September 30, 2025, four of the Company’s distributors each accounted for over 10% of the Company’s net product sales. For the three months ended September 30, 2024, two of the Company’s distributors each accounted for over 10% of the Company’s net product sales. For the nine months ended September 30, 2025, three of the Company’s distributors each accounted for over 10% of the Company’s net product sales. For the nine months ended September 30, 2024, two of the Company’s distributors each accounted for over 10% of the Company’s net product sales.

As of September 30, 2025 and December 31, 2024, the Company does not have a contract liabilities balance related to net product sales, and has not made significant changes to the judgments made in applying ASC Topic 606.

Collaboration and License revenue

In November 2011, the Company and the SMA Foundation entered into a licensing and collaboration agreement with Roche. Under the terms of the SMA License Agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program.

Under the agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product.

The SMA program currently has one approved product, Evrysdi, which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. As of September 30, 2025, the Company does not have any remaining research and development event milestones that can be received. The remaining potential sales milestones that can be received is $150.0 million.

For the three and nine months ended September 30, 2025, collaboration revenue related to the SMA License Agreement with Roche was immaterial. For the three and nine months ended September 30, 2024, the Company did not recognize collaboration revenue related to the SMA License Agreement with Roche.

​

In addition to research and development and sales milestones, the Company is eligible to receive up to double-digit royalties on worldwide annual net sales of a commercial product under the SMA License Agreement. For the three and nine months ended September 30, 2025, the Company has recognized $70.8 million and $164.8 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2024, the Company has recognized $61.4 million and $145.7 million of royalty revenue, respectively, related to Evrysdi.

In November 2024, the Company entered into the Novartis Agreement with Novartis related to the Company’s votoplam HD program. The transaction contemplated by the Novartis Agreement closed in January 2025. Under the Novartis Agreement, and upon the closing of the transaction, the Company received an upfront nonrefundable payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

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The Company evaluated the Novartis Agreement in order to determine the proper accounting treatment and concluded that the arrangement was not subject to ASC 730 or ASC 808, as the upfront payment was nonrefundable with no obligation for the Company to repay it and as the Company is not exposed to significant risks. The Company evaluated the arrangement under ASC 606, as a contract with a customer was determined to exist.

Pursuant to the Novartis Agreement, the Company was required to transfer the applicable licenses and related manufacturing and other know how to Novartis and to complete the ongoing Phase 2A clinical trial and continue the ongoing open label extension (“OLE”) clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date of the Novartis Agreement. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. Therefore, the Company determined that there were three material and distinct performance obligations: the transfer of the licenses and know-how, completion of the Phase 2A clinical trial, and continuing the OLE clinical trial until transitioned to Novartis. As of September 30, 2025, all performance obligations were considered to be substantially complete.

The Company determined that the transaction included the fixed consideration of the $1.0 billion and variable consideration in the form of milestones, profit share, and royalties. Management evaluated the variable consideration under ASC 606 and determined that it would be fully constrained until the contingencies were resolved or any applicable sales occurred. Management allocated the transaction price of $1.0 billion to the performance obligations based on the guidance in ASC 606.

During the three and nine months ended September 30, 2025, the Company recognized $9.3 million and $1.0 billion in license revenues, respectively, related to Novartis. As all performance obligations are considered to be substantially complete, there is no remaining deferred revenue related to the Novartis Agreement on the consolidated balance sheet as of September 30, 2025. Collaboration and license revenue during the nine months ended September 30, 2025 was partially offset by $3.5 million related to a refund for a prior collaboration arrangement in relation to votoplam.

Manufacturing Revenue

​

For the three and nine months ended September 30, 2025, the Company did not recognize any revenue related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. For the three months ended September 30, 2024, the Company did not recognize any revenue related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. For the nine months ended September 30, 2024, the Company recognized $1.7 million of manufacturing revenue related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine months ended September 30, 2025 and 2024.

As of September 30, 2025 and December 31, 2024, the Company does not have a contract liabilities balance or contract assets related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers.

In June 2024, the Company sold its gene therapy manufacturing business in Hopewell Township, New Jersey. Accordingly, the Company does not expect to have manufacturing revenue going forward.

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12. Intangible assets and goodwill

Definite-lived intangibles

Definite-lived intangible assets consisted of the following at September 30, 2025 and December 31, 2024:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | Ending Balance at | ​ | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | Ending Balance at
Definite-lived | ​ | ​ | December 31, | ​ | ​ | ​ | ​ | ​ | currency | ​ | ​ | September 30,
intangible assets, gross |  | ​ | 2024 |  | ​ | Additions |  | ​ | translation | ​ | ​ | 2025
Waylivra | ​ | ​ | 12,397 | ​ | ​ | 4,290 | ​ | ​ | 1,709 | ​ | ​ | 18,396
Tegsedi | ​ | ​ | 18,249 | ​ | ​ | 3,448 | ​ | ​ | 2,367 | ​ | ​ | 24,064
Kebilidi | ​ | ​ | 10,731 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 10,731
Upstaza | ​ | ​ | 106,937 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 106,937
Sephience | ​ | ​ | — | ​ | ​ | 282,763 | ​ | ​ | — | ​ | ​ | 282,763
Total definite-lived intangibles, gross | ​ | $ | 148,314 | ​ | $ | 290,501 | ​ | $ | 4,076 | ​ | $ | 442,891

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | Ending Balance at | ​ | ​ | ​ | ​ | ​ | Foreign | ​ | ​ | Ending Balance at
Definite-lived | ​ | ​ | December 31, | ​ | ​ | ​ | ​ | ​ | currency | ​ | ​ | September 30,
intangible assets, accumulated amortization |  | ​ | 2024 |  | ​ | Amortization |  | ​ | translation |  | ​ | 2025
Waylivra | ​ | ​ | (5,273) | ​ | ​ | (1,921) | ​ | ​ | (721) | ​ | ​ | (7,915)
Tegsedi | ​ | ​ | (5,609) | ​ | ​ | (2,774) | ​ | ​ | (791) | ​ | ​ | (9,174)
Kebilidi | ​ | ​ | (112) | ​ | ​ | (671) | ​ | ​ | — | ​ | ​ | (783)
Upstaza | ​ | ​ | (18,526) | ​ | ​ | (6,684) | ​ | ​ | — | ​ | ​ | (25,210)
Sephience | ​ | ​ | — | ​ | ​ | (3,343) | ​ | ​ | — | ​ | ​ | (3,343)
Total definite-lived intangibles, accumulated amortization | ​ | $ | (29,520) | ​ | $ | (15,393) | ​ | $ | (1,512) | ​ | $ | (46,425)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Total definite-lived intangibles, net | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | $ | 396,466

​

Akcea is entitled to receive royalty payments subject to certain terms set forth in the Tegsedi-Waylivra Agreement related to sales of Waylivra and Tegsedi. In accordance with the guidance for an asset acquisition, the Company records royalty payments when they become payable to Akcea and increase the cost basis for the Waylivra and Tegsedi intangible assets. For the nine months ended September 30, 2025, royalty payments of $3.4 million and $4.3 million were recorded for Tegsedi and Waylivra, respectively. As of September 30, 2025, a royalty payable of $1.2 million and $0.9 million for Tegsedi and Waylivra, respectively, was recorded on the consolidated balance sheet within accounts payable and accrued expenses.

Pursuant to the Censa Rights Satisfaction Agreement, in August 2025, upfront cash consideration of $225.1 million was paid to the former Censa securityholders. The upfront cash consideration was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. Pursuant to the Censa Merger Agreement, in June 2025, a $25.0 million milestone from the Company to the former Censa securityholders was triggered when the EC granted marketing authorization to Sephience for the treatment of children and adults living with PKU. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis.

​

Pursuant to the Censa Merger Agreement, in July 2025, a $32.5 million milestone from the Company to the former Censa securityholders was triggered when the FDA approved Sephience for the treatment of children and adults living with PKU. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. As of September 30, 2025, the $32.5 million milestone was recorded on the consolidated balance sheet within accounts payable and accrued expenses.

​

The former Censa securityholders may also be entitled to receive other contingent payments subject to certain terms set forth in the Censa Merger Agreement related to sales of Sephience. In accordance with the guidance for an asset acquisition, the Company will record such payments when they become payable to the former Censa securityholders and increase the cost basis for the Sephience intangible asset. For the nine months ended September 30, 2025, royalty payments

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of $0.2 million were recorded for Sephience. As of September 30, 2025, a royalty payable of $0.2 million for Sephience was recorded on the consolidated balance sheet within accounts payable and accrued expenses.

For the three months ended September 30, 2025 and 2024, the Company recognized amortization expense of $7.5 million and $3.0 million, respectively, related to its intangible assets. For the nine months ended September 30, 2025 and 2024, the Company recognized amortization expense of $15.4 million and $57.4 million, respectively, related to its intangible assets. The estimated future amortization of the Company’s intangible assets is expected to be as follows:

​

​ | ​ | ​ | ​
​ |  | As of September 30, 2025
2025 | ​ | $ | 9,280
2026 | ​ |  | 37,098
2027 | ​ |  | 37,098
2028 | ​ |  | 37,098
2029 and thereafter | ​ |  | 275,892
Total | ​ | $ | 396,466

​

The weighted average remaining amortization period of the definite-lived intangibles as of September 30, 2025 is 12.2 years.

Goodwill

As a result of the Agilis Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. As of September 30, 2025, there have been no changes to the balance of goodwill since the date of the Agilis Merger. Accordingly, the goodwill balance as of September 30, 2025 is $82.3 million.

13. Segment information

The Company views its operations and manages its business in one operating segment: life science. The table below summarizes the significant expense categories for the life science segment regularly reviewed by the CODM for the three and nine months ended September 30, 2025 and 2024:

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | Three months ended September 30, | ​ | Nine months ended September 30,
​ | ​ | 2025 | ​ | 2024 | ​ | 2025 | ​ | 2024 | ​
Total revenues | ​ | $ | 211,007 | ​ | $ | 196,786 | ​ | $ | 1,565,978 | ​ | $ | 593,608 | ​
Less: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of product, collaboration and license sales | ​ | ​ | 12,441 | ​ | ​ | 3,468 | ​ | ​ | 28,241 | ​ | ​ | 13,140 | ​
Program spend | ​ | ​ | 45,940 | ​ | ​ | 51,174 | ​ | ​ | 143,803 | ​ | ​ | 152,497 | ​
Employee costs | ​ | ​ | 64,470 | ​ | ​ | 57,801 | ​ | ​ | 197,762 | ​ | ​ | 181,355 | ​
Manufacturing costs | ​ | ​ | 11,048 | ​ | ​ | 14,229 | ​ | ​ | 45,517 | ​ | ​ | 44,635 | ​
Administrative costs | ​ | ​ | 18,614 | ​ | ​ | 18,719 | ​ | ​ | 54,924 | ​ | ​ | 54,213 | ​
Occupancy costs | ​ | ​ | 7,852 | ​ | ​ | 7,855 | ​ | ​ | 21,678 | ​ | ​ | 27,337 | ​
Milestones | ​ | ​ | — | ​ | ​ | 50,000 | ​ | ​ | — | ​ | ​ | 65,000 | ​
Other segment items (a) | ​ | ​ | 34,746 | ​ | ​ | 100,194 | ​ | ​ | 256,444 | ​ | ​ | 352,840 | ​
Segment net income (loss) | ​ | $ | 15,896 | ​ | $ | (106,654) | ​ | $ | 817,609 | ​ | $ | (297,409) | ​
Reconciliation of profit or loss | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Adjustments and reconciling items | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Consolidated net income (loss) | ​ | $ | 15,896 | ​ | $ | (106,654) | ​ | $ | 817,609 | ​ | $ | (297,409) | ​

​

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(a) | Other segment items includes the following:

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | Three months ended September 30, | ​ | ​ | Nine months ended September 30,
​ | ​ | ​ | 2025 | ​ | 2024 | ​ | ​ | 2025 | ​ | 2024
Interest income | ​ | $ | (19,089) | ​ | $ | (12,821) | ​ | $ | (57,325) | ​ | $ | (34,255)
Interest expense | ​ | ​ | 51,681 | ​ | ​ | 54,430 | ​ | ​ | 154,367 | ​ | ​ | 160,188
Income tax (benefit) expense | ​ | ​ | (38,970) | ​ | ​ | 8,663 | ​ | ​ | 18,093 | ​ | ​ | 28,989
Depreciation | ​ | ​ | 3,569 | ​ | ​ | 3,468 | ​ | ​ | 10,600 | ​ | ​ | 11,489
Amortization | ​ | ​ | 7,534 | ​ | ​ | 3,036 | ​ | ​ | 15,393 | ​ | ​ | 57,431
All other (b) | ​ | ​ | 30,021 | ​ | ​ | 43,418 | ​ | ​ | 115,316 | ​ | ​ | 128,998
Total other segment items | ​ | $ | 34,746 | ​ | $ | 100,194 | ​ | $ | 256,444 | ​ | $ | 352,840

​

(b) | All other includes cost of goods sold, royalty, travel and entertainment, distribution costs, bad debt expense, finance costs, contract labor costs, stock compensation expense, change in the fair value of contingent consideration, and other expense.

14. Subsequent events

The Company has evaluated subsequent events and transactions through the filing date. There were no material events that impacted the consolidated financial statements or disclosures.

​

​

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.

The following discussion and analysis is meant to provide material information relevant to an assessment of the financial condition and results of operations of our company, including an evaluation of the amounts and certainty of cash flows from operations and from outside resources, so as to allow investors to better view our company from management’s perspective. The following discussion of our financial condition and results of operations should be read in conjunction with our financial statements and the notes to those financial statements appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto and management’s discussion and analysis of financial condition and results of operations for the year ended December 31, 2024 included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission on February 27, 2025, or our 2024 Annual Report. This discussion contains forward-looking statements that involve significant risks and uncertainties. As a result of many factors, such as those set forth in Part II, Item 1A. (Risk Factors) of this Quarterly Report on Form 10-Q and Part I, Item 1A. (Risk Factors) of our 2024 Annual Report, our actual results may differ materially from those anticipated in these forward-looking statements.

Our Company

We are a global biopharmaceutical company dedicated to the discovery, development and commercialization of clinically differentiated medicines for children and adults living with rare disorders. We are advancing a robust and diversified pipeline of transformative medicines as part of our mission to provide access to best-in-class treatments for patients with unmet medical needs. Our strategy is to leverage our scientific expertise and global commercial infrastructure to optimize value for our patients and other stakeholders. We have a diversified therapeutic portfolio pipeline that includes several commercial products and product candidates in various stages of development, including clinical, pre-clinical and research and discovery stages, focused on the development of new treatments for multiple therapeutic areas for rare diseases relating to neurology and metabolism.

Corporate Updates

Sephience™ (sepiapterin)

Sephience (sepiapterin) is a product for the treatment of phenylketonuria, or PKU, a rare inherited metabolic disease characterized by the body’s inability to break down an essential amino acid called phenylalanine, and which can result in neurological and other symptoms. On July 28, 2025, Sephience was approved by the U.S. Food and Drug Administration, or the FDA, for the treatment of pediatric and adult patients living with PKU in the United States age one month and above. On June 19, 2025, Sephience was granted marketing authorization by the European Commission, or the EC, for the treatment of children and adults living with PKU within the European Economic Area, or the EEA. We also made regulatory submissions for Sephience for the treatment of PKU in Brazil in the third quarter of 2024, and in Japan in the fourth quarter of 2024, with regulatory decisions expected in the fourth quarter of 2025. During the quarter ended September 30, 2025, we recognized $19.6 million in net sales of Sephience.

Censa Rights Satisfaction Agreement

On August 5, 2025, we, certain of the former securityholders of Censa, and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC, a Colorado limited liability company, entered into a Rights Satisfaction Agreement, or the Rights Satisfaction Agreement, pursuant to which such former securityholders of Censa, or the Participating Rightsholders, agreed to the cancellation and forfeiture of their rights to receive certain contingent payments from us based on worldwide annual net sales by us of products containing sepiapterin, or Net Sales of Product, under the Agreement and Plan of Merger, dated as of May 5, 2020, or the Censa Merger Agreement, by and among us, Hydro Merger Sub, Inc., our wholly owned, indirect subsidiary, Censa and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representative Services LLC, in exchange for the consideration set forth in the Rights Satisfaction Agreement and further detailed below.

Pursuant to the terms of the Rights Satisfaction Agreement, the Participating Rightsholders have canceled and forfeited their rights under the Censa Merger Agreement to receive a percentage of annual net sales during the applicable payment

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term equal to (i) 8% of annual Net Sales of Product for that portion of annual Net Sales of Product less than or equal to $250.0 million, (ii) 10% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $250.0 million but less than $500.0 million and (iii) 12% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $500.0 million, which we refer to collectively as the Net Sales Payments.

In consideration of the foregoing, we agreed to pay to the Participating Rightsholders an aggregate amount in cash up to $250.0 million, or the Upfront Consideration, upon the consummation of the transactions contemplated by the Rights Satisfaction Agreement, or the Closing, and potential milestone payments, each, an Additional Milestone Payment, of up to $100.0 million each (or up to $500.0 million in the aggregate) based on the achievement of specified Net Sales Thresholds (as defined in the Censa Merger Agreement). The amount of the Upfront Consideration and the Additional Milestone Payments was subject to adjustment in the Rights Satisfaction Agreement based on the number of Participating Rightsholders.

At the Closing, based on the participation of former Censa securityholders holding approximately 90% of Censa’s equity securities prior to the consummation of the transactions contemplated by the Censa Merger Agreement, we paid an aggregate amount of Upfront Consideration in cash of $225.1 million. Additionally, we are obligated to make Additional Milestone Payments in an amount equal to approximately $90.0 million upon achievement of each of the (i) first occurrence of a three or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $3.0 billion, (ii) first occurrence of a five or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $5.0 billion, (iii) first occurrence of a seven or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $7.0 billion, (iv) first occurrence of a nine or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $9.0 billion and (v) first occurrence of an 11 or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $11.0 billion. If, after the Closing, any additional former securityholder of Censa executes and delivers a joinder to the Rights Satisfaction Agreement and becomes a party thereto, we will pay such former securityholder an amount in cash equal to such former securityholder’s applicable pro rata share of the Upfront Consideration (less any Net Sale Payments previously received) and any Additional Milestone Payments that become payable to Participating Rightsholders under the Rights Satisfaction Agreement.

In addition to the Additional Milestone Payments, and pursuant to the terms of the Censa Merger Agreement, we will make payments of $30.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product (as defined in the Censa Merger Agreement) exceed $250.0 million, $50.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product exceed $500.0 million, and $80.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product exceed $1.0 billion.

The Rights Satisfaction Agreement has no effect on the Censa Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightsholders’ rights to receive the Net Sales Payments described above. As a result, all other rights and obligations under the Censa Merger Agreement remain in effect pursuant to their terms, including, without limitation, our obligation to pay certain contingent payments upon the achievement of certain development and Net Sales of Product milestones.

The Rights Satisfaction Agreement contains customary representations, warranties and covenants of us and the Participating Rightsholders and provided for a simultaneous signing and closing.

Global Commercial Footprint

Global DMD Franchise

We have two products, Translarna™ (ataluren) and Emflaza® (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life-threatening disorder. Translarna has marketing authorization in Russia for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in patients aged two years and older, and in Brazil for the treatment of nmDMD in ambulatory patients two years and older and for continued treatment of patients that become non-ambulatory, as well as in various other countries. During the quarter ended September 30, 2025, we recognized $50.7

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million in net sales of Translarna. We hold worldwide commercialization rights to Translarna for all indications in all territories. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. During the quarter ended September 30, 2025, we recognized $35.2 million in net sales of Emflaza.

We previously had a marketing authorization for Translarna in the EEA, which had been subject to annual review and renewal by the EC, following reassessment by the European Medicines Agency, or EMA, of the benefit-risk balance of the authorization. In September 2022, we submitted a Type II variation to the EMA to support conversion of the conditional marketing authorization for Translarna to a standard marketing authorization, which included a report on the placebo-controlled trial of Study 041 and data from the open-label extension as further described below. Study 041 was an 18-month, placebo-controlled trial, followed by an 18-month open-label extension of Translarna in the treatment of ambulatory patients with nmDMD aged five years or older. In February 2023, we also submitted an annual marketing authorization renewal request to the EMA. In September 2023, the Committee for Medicinal Products for Human Use, or CHMP, gave a negative opinion on the conversion of the conditional marketing authorization to full marketing authorization of Translarna for the treatment of nmDMD and a negative opinion on the renewal of the existing conditional marketing authorization of Translarna for the treatment of nmDMD. In January 2024, the CHMP issued a negative opinion for the renewal of the conditional marketing authorization following a re-examination procedure. In May 2024, the EC decided not to adopt the CHMP’s negative opinion for the renewal of the conditional marketing authorization of Translarna and returned such opinion to the CHMP for re-evaluation. In June 2024, following the EC’s request for re-review, the CHMP issued a negative opinion on the renewal of the conditional marketing authorization of Translarna for the treatment of nmDMD. In October 2024, the CHMP maintained its negative opinion for the renewal of the conditional marketing authorization following the requested reexamination procedure. In March 2025, the EC adopted the opinion of the CHMP to not renew the authorization of Translarna for the treatment of nmDMD. However, the EC indicated that individual countries within the European Union, or EU, can leverage Articles 117(3) and 5(1) of the EU Directive 2001/83 to allow continued commercial use of Translarna. There is a substantial risk that as a result of the EC’s adoption of the CHMP’s negative opinion we will lose a significant portion of our ability to generate revenue from sales of Translarna in the EEA.

Translarna is an investigational new drug in the United States. During the first quarter of 2017, we filed a New Drug Application, or NDA, for Translarna for the treatment of nmDMD over protest with the FDA. In October 2017, the Office of Drug Evaluation I of the FDA issued a Complete Response Letter, or CRL, for the NDA, stating that it was unable to approve the application in its current form. In response, we filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied our appeal of the CRL. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a resubmission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. We followed the FDA’s recommendation and collected, using newer technologies via procedures and methods that we designed, such dystrophin data in a new study, Study 045, and announced the results of Study 045 in February 2021. Study 045 did not meet its pre-specified primary endpoint. In June 2022, we announced top-line results from the placebo-controlled trial of Study 041. Following this announcement, we submitted a meeting request to the FDA to gain clarity on the regulatory pathway for a potential resubmission of an NDA for Translarna. The FDA provided initial written feedback that Study 041 does not provide substantial evidence of effectiveness to support an NDA resubmission. We held a Type C meeting with the FDA in the fourth quarter of 2023 to discuss the totality of Translarna data. Based on feedback from the FDA, we resubmitted the NDA in July 2024, based on the results from Study 041 and from our international drug registry study for nmDMD patients receiving Translarna. In October 2024, the FDA accepted for review the resubmission of the NDA for Translarna for the treatment of nmDMD. As this was an NDA resubmission following a complete response letter to the NDA which was filed over protest in 2016, the FDA is not obligated to follow the review timelines under Prescription Drug User Fee Act guidelines, and an action date has not been provided.

We have previously relied on Emflaza’s seven-year marketing exclusivity period in the United States for its approved indications under the provisions of the Orphan Drug Act of 1983, or the Orphan Drug Act, when commercializing Emflaza. Emflaza’s seven-year period of orphan drug exclusivity related to the treatment of DMD in patients five years and older expired in February 2024. We expect the expiration of this orphan drug exclusivity to potentially have a significant negative impact on Emflaza net product revenue. Emflaza’s orphan drug exclusivity related to the treatment of DMD in patients two years of age to less than five expires in June 2026.

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Upstaza™ (eladocagene exuparvovec) / Kebilidi™ (eladocagene exuparvovec-tneq)

Upstaza/Kebilidi is a gene therapy for the treatment of Aromatic L Amino Acid Decarboxylase, or AADC, deficiency, a rare central nervous system, or CNS, disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. In July 2022, the EC approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the EEA. In November 2022, the Medicines and Healthcare Products Regulatory Agency approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the United Kingdom. In November 2024, the FDA granted accelerated approval of our gene therapy for the treatment of children and adults with AADC deficiency, which is marketed with the brand name Kebilidi in the United States.

Tegsedi® (inotersen) and Waylivra™ (volanesorsen)

We hold the rights for the commercialization of Tegsedi and Waylivra for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to a Collaboration and License Agreement, or the Tegsedi-Waylivra Agreement, dated August 1, 2018, by and between us and Akcea Therapeutics, Inc., or Akcea, a subsidiary of Ionis Pharmaceuticals, Inc. Tegsedi has received marketing authorization in the United States, EU, and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis, or hATTR amyloidosis. In August 2021, ANVISA, the Brazilian health regulatory authority, approved Waylivra as the first treatment for familial chylomicronemia syndrome, or FCS, in Brazil. In December 2022, ANVISA approved Waylivra for the treatment of familial partial lipodystrophy, or FPL. Waylivra has also received marketing authorization in the EU for the treatment of FCS.

Evrysdi® (risdiplam)

We also have a spinal muscular atrophy, or SMA, collaboration with F. Hoffman-La Roche Ltd. and Hoffman La Roche Inc., which we refer to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. The SMA program has one approved product, Evrysdi (risdiplam), which was approved by the FDA in August 2020 for the treatment of SMA in adults and children two months and older and by the EC in March 2021 for the treatment of 5q SMA in patients two months and older with a clinical diagnosis of SMA Type 1, Type 2 or Type 3 or with one to four SMN2 copies. Evrysdi also received marketing authorization for the treatment of SMA in over 100 countries. In May 2022, the FDA approved a label expansion for Evrysdi to include infants under two months old with SMA. In August 2023, the EC approved an extension of the Evrysdi marketing authorization to include infants under two months old in the EU.

Diversified Development Pipeline

Splicing Platform

In addition to our SMA program, our splicing platform also includes votoplam (PTC518), which is being developed for the treatment of Huntington’s disease, or HD. We announced the results from our Phase 1 study of votoplam in healthy volunteers in September 2021 demonstrating dose-dependent lowering of huntingtin messenger ribonucleic acid and protein levels, that votoplam efficiently crosses blood brain barrier at significant levels and that votoplam was well tolerated. We initiated a Phase 2 study of votoplam for the treatment of HD in the first quarter of 2022, which consisted of an initial 12-week placebo-controlled phase focused on safety, pharmacology and pharmacodynamic effects followed by a nine-month placebo-controlled phase focused on votoplam biomarker effect. In June 2024, we announced interim results from the full Phase 2 study of votoplam. At month 12, votoplam treatment demonstrated durable dose-dependent lowering of mHTT protein in the blood and dose-dependent lowering of mHTT protein in the cerebrospinal fluid in the interim cohort of stage 2 patients. In addition, favorable trends were demonstrated on several relevant HD clinical assessments. Furthermore, following 12 months of treatment, votoplam continued to be well tolerated. In September 2024, the FDA granted Fast Track designation to the votoplam program for the treatment of HD. In December 2024, we held a Type C meeting with the FDA to discuss whether huntingtin protein lowering could be considered a surrogate endpoint for accelerated approval of votoplam. The FDA was aligned on the scientific rationale and asked to see additional data supportive of an association between huntingtin protein lowering and changes in clinical outcome scores. In May 2025, we announced that the Phase 2 study of votoplam met its primary endpoints of blood HTT lowering and safety. The results on the full study population are consistent with the previously reported evidence of dose-dependent HTT lowering, favorable safety profile and early signals of dose-dependent clinical effect at 12 months in Stage 2 patients. In addition, at

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24 months of treatment, there were continued trends of dose-dependent favorable clinical effect relative to a propensity-matched natural history cohort as well as dose-dependent NfL lowering. In November 2024, we entered into the License and Collaboration Agreement, or the Novartis Agreement, with Novartis Pharmaceuticals Corporation, or Novartis, relating to our votoplam program. This transaction closed in January 2025. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing open label extension, or OLE, clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date of the Novartis Agreement. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. We continue to collaborate with Novartis on next steps and aim to meet with FDA in the fourth quarter of 2025 to discuss Phase 3 clinical trial design and potential accelerated approval pathway.

Inflammation and Ferroptosis Platform

Our inflammation and ferroptosis platform consists of small molecule compounds that target key enzymes that regulate oxidative stress and inflammatory pathways central to the pathology of a number of CNS and non-CNS diseases. The most advanced molecule in our inflammation and ferroptosis platform is vatiquinone. We announced topline results from a registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich’s Ataxia, called MOVE-FA, in May 2023. While the study did not meet its primary endpoint of statistically significant change in modified Friedreich Ataxia Rating Scale, or mFARS, score at 72 weeks in the primary analysis population, vatiquinone treatment did demonstrate significant benefit on key disease subscales and secondary endpoints. In addition, in the population of subjects that completed the study protocol, significance was reached in the mFARS endpoint and several secondary endpoints, including the upright stability subscale. Furthermore, vatiquinone was well tolerated. In October 2024, we announced that the pre-specified endpoint for two different FA long-term extension studies was met, with statistically significant evidence of durable treatment benefit on disease progression. In December 2024, we submitted an NDA to the FDA for vatiquinone for the treatment of children and adults living with FA. In August 2025, the FDA issued a complete response letter related to the NDA stating that substantial evidence of efficacy was not demonstrated for vatiquinone and that an additional adequate and well-controlled study would be needed to support NDA resubmission. We plan to meet with the FDA in the fourth quarter to discuss the vatiquinone development program.

Multi-Platform Discovery

In addition, we have a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas for rare diseases.

Funding

The success of our products and any other product candidates we may develop depends largely on obtaining and maintaining reimbursement from governments and third-party insurers. Our revenues are primarily generated from sales of Translarna in countries where we were able to obtain acceptable commercial pricing and reimbursement terms and in select countries where we are permitted to distribute Translarna under our early access programs, or EAP, programs or through similar styled programs, and from sales of Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, our revenues are also generated from sales of Sephience for the treatment of PKU in the United States and in territories outside of the United States. We also generate revenue from sales of Upstaza/Kebilidi for the treatment of AADC deficiency based on regulatory approvals in the EEA and the United States, we have recognized revenue associated with milestone and royalty payments from Roche pursuant to a License and Collaboration Agreement, or the SMA License Agreement, by and among us, Roche and, for the limited purposes set forth therein, the SMA Foundation, under our SMA program and we have recognized license revenues related to performance obligations already completed pursuant to the Novartis Agreement.

We have financed our operations to date primarily through the private offerings of convertible senior notes, public and “at the market offerings” of common stock, proceeds from royalty purchase agreements, private placements of our convertible preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding

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and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by our product candidates. We have relied on revenue generated from net sales of our products. We have also relied on revenue associated with milestone and royalty payments from Roche pursuant to the SMA License Agreement under our SMA program, revenue generated from net sales of Tegsedi and Waylivra in Latin America and the Caribbean, and license revenues related to performance obligations already completed pursuant to the Novartis Agreement.

In June 2024, we entered into an amendment with Royalty Pharma Investments 2019 ICAV, or Royalty Pharma, and Royalty Pharma plc, to the Amended and Restated Royalty Purchase Agreement, dated October 18, 2023, or the A&R Royalty Purchase Agreement, which amends and restated in its entirety the Royalty Purchase Agreement by and among us, RPI Intermediate Finance Trust, and for the limited purposes set forth in the agreement, Royalty Pharma plc, dated as of July 17, 2020, or the Original Royalty Purchase Agreement, and we exercised our first put option in exchange for $241.8 million in cash consideration. To date, Royalty Pharma has paid to us cash consideration of $1.9 billion (less payments on our right to receive sales-based royalty payments, or the Royalty, on worldwide net sales of Evrysdi and any other product in development pursuant to the SMA License Agreement received by us with respect to assigned Royalties, or the Assigned Royalty Rights) in exchange for 90.49% of the Royalty, which will be reduced to 83.33% after Royalty Pharma receives $1.3 billion in aggregate payments, or the Assigned Royalty Cap, from the Royalty assigned under the Original Royalty Purchase Agreement. We currently retain 9.51% of the Royalty, which increases to 16.67% after the Assigned Royalty Cap has been met. We have the option to sell our retained portions of the Royalty to Royalty Pharma in up to three tranches for the following payments: (1) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, (2) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, and (3) $50.0 million in exchange for 1.90% of the Royalty, which increases to 3.33% after the Assigned Royalty Cap has been met, in each case less Royalty payments received by us with respect to the Assigned Royalty Rights.

In November 2024, we entered into the Novartis Agreement relating to our votoplam HD program which includes related molecules. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing OLE clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. Under the Novartis Agreement, and upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

In August 2019, we entered into an At the Market Offering Sales Agreement, or the Sales Agreement, with Cantor Fitzgerald and RBC Capital Markets, LLC, or together, the Sales Agents, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended, or the Securities Act. During the three and nine months ended September 30, 2025, we did not issue or sell any shares of common stock pursuant to the Sales Agreement. The remaining shares of our common stock available to be issued and sold, under the Sales Agreement, have an aggregate offering price of up to $93.0 million as of September 30, 2025.

As of September 30, 2025, we had an accumulated deficit of $2,829.3 million. We had a net income of $817.6 million and a net loss of $297.4 million for the nine months ended September 30, 2025 and 2024, respectively.

We anticipate that we will continue to incur significant expenses in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including expenses related to our commercial infrastructure and corresponding sales and marketing, legal and regulatory, and distribution and manufacturing undertakings as well as administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with ongoing, planned and potential future clinical trials and studies for our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications. We continue to seek marketing authorization for Translarna for the treatment of nmDMD and Sephience for

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the treatment of pediatric and adult patients living with PKU in territories in which we do not currently have marketing authorization. These efforts may significantly impact the timing and extent of our commercialization and manufacturing expenses.

We may seek to expand and diversify our product pipeline through opportunistically in-licensing or acquiring the rights to products, product candidates or technologies and we may incur expenses, including with respect to transaction costs, subsequent development costs or any upfront, milestone or other payments or other financial obligations associated with any such transaction, which would increase our future capital requirements.

With respect to our outstanding 1.50% convertible senior notes due September 15, 2026, or the 2026 Convertible Notes,

cash interest payments are payable on a semi-annual basis in arrears, which will require total funding of $4.3 million

annually.

In July 2025, Sephience™ (sepiapterin) was granted FDA approval for the treatment of children and adults living with PKU. Pursuant to the Censa Merger Agreement, the approval triggered a $32.5 million milestone to the former Censa securityholders, which was recorded in accounts payable and accrued expenses on our consolidated balance sheet as of September 30, 2025.

We also have certain significant contractual obligations and commercial commitments that require funding and we have disclosed these items under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Funding Obligations” in our 2024 Annual Report. There were no material changes to these obligations and commitments during the period ended September 30, 2025. Furthermore, since we are a public company, we have incurred and expect to continue to incur additional costs associated with operating as such including significant legal, accounting, investor relations and other expenses.

We will need to generate significant revenues to sustain profitability, and we may never do so. Accordingly, we may need to obtain substantial additional funding in connection with our continuing operations. Adequate additional financing may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed or on attractive terms, we could be forced to delay, reduce or eliminate our research and development programs or our commercialization efforts.

Financial operations overview

Revenues

Net product revenues. To date, our net product revenues have consisted primarily of sales of Translarna for the treatment of nmDMD in territories outside of the United States, sales of Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, net product revenues also includes Sephience for the treatment of PKU. We recognize revenue when performance obligations with customers have been satisfied and if it is probable that a significant revenue reversal will not occur. Our performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when our customer obtains control of the product, which is typically upon delivery. We invoice customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of invoice date. We determine the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods not yet provided. As we have identified only one distinct performance obligation, the transaction price is allocated entirely to the product sale. In determining the transaction price, a significant financing component does not exist since the timing from when we deliver product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.

We record product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. We use the expected value or most likely amount method when estimating variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact

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such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.

During the three and nine months ended September 30, 2025 and 2024, net product revenues consisted of the following:

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30,
​ | ​ | ​ | 2025 | ​ | 2024
​ | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total
Translarna | ​ | $ | — | ​ | $ | 50,665 | ​ | $ | 50,665 | ​ | $ | — | ​ | $ | 72,283 | ​ | $ | 72,283
Emflaza | ​ | ​ | 35,160 | ​ | ​ | — | ​ | ​ | 35,160 | ​ | ​ | 51,941 | ​ | ​ | — | ​ | ​ | 51,941
Sephience | ​ | ​ | 14,365 | ​ | ​ | 5,198 | ​ | ​ | 19,563 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Upstaza/Kebilidi | ​ | ​ | 6,898 | ​ | ​ | 8,837 | ​ | ​ | 15,735 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
All other products | ​ | ​ | — | ​ | ​ | 9,833 | ​ | ​ | 9,833 | ​ | ​ | — | ​ | ​ | 11,197 | ​ | ​ | 11,197
Total net product revenue | ​ | $ | 56,423 | ​ | $ | 74,533 | ​ | $ | 130,956 | ​ | $ | 51,941 | ​ | $ | 83,480 | ​ | $ | 135,421
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | 2024
​ | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total | ​ | ​ | United States | ​ | ​ | International | ​ | ​ | Total
Translarna | ​ | $ | — | ​ | $ | 196,289 | ​ | $ | 196,289 | ​ | $ | — | ​ | $ | 246,217 | ​ | $ | 246,217
Emflaza | ​ | ​ | 119,303 | ​ | ​ | — | ​ | ​ | 119,303 | ​ | ​ | 156,718 | ​ | ​ | — | ​ | ​ | 156,718
Sephience | ​ | ​ | 14,365 | ​ | ​ | 5,198 | ​ | ​ | 19,563 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | —
Upstaza/Kebilidi | ​ | ​ | 6,898 | ​ | ​ | 29,385 | ​ | ​ | 36,283 | ​ | ​ | — | ​ | ​ | 9,648 | ​ | ​ | 9,648
All other products | ​ | ​ | — | ​ | ​ | 31,273 | ​ | ​ | 31,273 | ​ | ​ | — | ​ | ​ | 33,662 | ​ | ​ | 33,662
Total net product revenue | ​ | $ | 140,566 | ​ | $ | 262,145 | ​ | $ | 402,711 | ​ | $ | 156,718 | ​ | $ | 289,527 | ​ | $ | 446,245

​

Disaggregated net product revenues by country for the three and nine months ended September 30, 2025 and 2024, are as follows:

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30,
​ | ​ | 2025 | ​ | 2024 | ​ | 2025 | ​ | 2024
United States | ​ | $ | 56,423 | ​ | $ | 51,941 | ​ | $ | 140,566 | ​ | $ | 156,718
Russia | ​ | ​ | 25,107 | ​ | ​ | 965 | ​ | ​ | 81,745 | ​ | ​ | 55,716
Brazil | ​ | ​ | 9,222 | ​ | ​ | 29,219 | ​ | ​ | 59,678 | ​ | ​ | 68,304
All other countries | ​ | ​ | 40,204 | ​ | ​ | 53,296 | ​ | ​ | 120,722 | ​ | ​ | 165,507
Total net product revenue | ​ | $ | 130,956 | ​ | $ | 135,421 | ​ | $ | 402,711 | ​ | $ | 446,245

​

For the three months ended September 30, 2025, four of our distributors each accounted for over 10% of our net product sales. For the three months ended September 30, 2024, two of our distributors each accounted for over 10% of our net product sales. For the nine months ended September 30, 2025, three of our distributors each accounted for over 10% of our net product sales. For the nine months ended September 30, 2024, two of our distributors each accounted for over 10% of our net product sales.

In relation to customer contracts, we incur costs to fulfill a contract but do not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. We consider any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Roche and the SMA Foundation Collaboration. In November 2011, we entered into the SMA License Agreement pursuant to which we are collaborating with Roche and the SMA Foundation to further develop and commercialize compounds identified under our SMA program with the SMA Foundation. The research component of this agreement terminated

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effective December 31, 2014. We are eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. As of September 30, 2025, we had recognized a total of $310.0 million in milestone payments and $710.4 million royalties on net sales pursuant to the SMA License Agreement. As of September 30, 2025, there are no remaining research and development event milestones that we can receive. The remaining potential sales milestones as of September 30, 2025 are $150.0 million upon achievement of certain sales events.

For the three and nine months ended September 30, 2025, collaboration revenue related to the SMA License Agreement with Roche was immaterial. For the three and nine months ended September 30, 2024, we did not recognize collaboration revenue related to the SMA License Agreement with Roche.

​

For the three and nine months ended September 30, 2025, we recognized $70.8 million and $164.8 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2024, we recognized $61.4 million and $145.7 million of royalty revenue, respectively, related to Evrysdi.

Novartis Collaboration for votoplam HD. In November 2024, we entered into the Novartis Agreement with Novartis related to our votoplam HD program. Upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

During the three and nine months ended September 30, 2025, we recognized $9.3 million and $1.0 billion in license revenues, respectively, related to Novartis. As all performance obligations are considered to be substantially complete, there is no remaining deferred revenue on the consolidated balance sheet as of September 30, 2025. Collaboration and license revenue during the nine months ended September 30, 2025 was partially offset by $3.5 million related to a refund for a prior collaboration arrangement in relation to votoplam.

Research and development expense

Research and development expenses consist of the costs associated with our research activities, as well as the costs associated with our drug discovery efforts, conducting preclinical studies and clinical trials, manufacturing development efforts and activities related to regulatory filings. Our research and development expenses consist of:

●external research and development expenses incurred under agreements with third-party contract research organizations and investigative sites, third-party manufacturing organizations and consultants;
●employee-related expenses, which include salaries and benefits, including share-based compensation, for the personnel involved in our drug discovery and development activities; and
●facilities, depreciation and other allocated expenses, which include direct and allocated expenses for rent and maintenance of facilities, IT, human resources and other support functions, depreciation of leasehold improvements and equipment, and laboratory and other supplies.

We use our employee and infrastructure resources across multiple research projects, including our drug development programs. We track expenses related to our clinical programs and certain preclinical programs on a per project basis.

We expect our research and development expenses to fluctuate in connection with our ongoing activities, particularly in connection with our activities under our splicing and inflammation and ferroptosis programs and performance of our post-marketing requirements imposed by regulatory agencies with respect to our products. The timing and amount of these expenses will depend upon the outcome of our ongoing clinical trials and the costs associated with our planned clinical trials. The timing and amount of these expenses will also depend on the costs associated with potential future clinical trials of our products or product candidates and the related expansion of our research and development organization, regulatory requirements, advancement of our preclinical programs, and product candidate manufacturing costs.

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The following tables provides research and development expense for our most advanced principal product development programs, for the three and nine months ended September 30, 2025 and 2024.

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​
​ |  | 2025 |  | 2024 | ​
​ | ​ | (in thousands) | ​
Sephience | ​ | $ | 27,618 | ​ | $ | 23,386 | ​
Inflammation & Ferroptosis platform | ​ | ​ | 10,991 | ​ | ​ | 11,547 | ​
Global DMD | ​ | ​ | 1,755 | ​ | ​ | 7,129 | ​
Gene Therapy | ​ | ​ | 2,749 | ​ | ​ | 3,663 | ​
Splicing platform | ​ | ​ | 660 | ​ | ​ | 5,641 | ​
Other development programs | ​ | ​ | 285 | ​ | ​ | 473 | ​
Total Development | ​ | ​ | 44,058 | ​ | ​ | 51,839 | ​
Research | ​ | ​ | 9,680 | ​ | ​ | 16,301 | ​
Milestones | ​ | ​ | — | ​ | ​ | 50,000 | ​
Payroll, benefits, and share-based stock compensation | ​ | ​ | 36,613 | ​ | ​ | 33,950 | ​
Facilities and other indirect costs | ​ |  | 9,807 | ​ |  | 9,322 | ​
Total research and development | ​ | $ | 100,158 | ​ | $ | 161,412 | ​

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended September 30,
​ |  | 2025 |  | 2024
​ | ​ | (in thousands)
Sephience | ​ | $ | 78,500 | ​ | $ | 65,739
Inflammation & Ferroptosis platform | ​ |  | 26,282 | ​ |  | 37,667
Global DMD | ​ |  | 17,450 | ​ |  | 18,287
Gene Therapy | ​ | ​ | 10,984 | ​ | ​ | 12,155
Splicing platform | ​ | ​ | 8,338 | ​ | ​ | 17,408
Other development programs | ​ | ​ | 1,490 | ​ | ​ | 3,938
Total Development | ​ | ​ | 143,044 | ​ | ​ | 155,194
Research | ​ | ​ | 39,230 | ​ | ​ | 48,004
Milestones | ​ | ​ | — | ​ | ​ | 65,000
Payroll, benefits, and share-based stock compensation | ​ |  | 111,843 | ​ |  | 110,605
Facilities and other indirect costs | ​ |  | 28,004 | ​ |  | 30,907
Total research and development | ​ | $ | 322,121 | ​ | $ | 409,710

​

Development. Consists of costs incurred for product candidates following initiation of a clinical trial.

​

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the changes reflect progressing through different phases of studies as we continue to focus our resources on our differentiated, high potential research and development programs. The decrease is primarily due to a decrease relating to Global DMD, Gene Therapy, and Splicing platform, offset by an increase in Sephience related development.

​

Research. Consists of costs incurred for product candidates before initiation of a clinical trial.

​

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the decrease in research expenses primarily reflected our continued focus of our resources on product candidates approaching approval during the current year periods.

​

Milestones. Consists of development and regulatory milestone expenses incurred in connection with our collaborative arrangements.

​

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For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the decrease in milestone expenses related to the achievement of a total of $65.0 million regulatory success-based milestones paid to the former Censa securityholders for the nine months ended September 30, 2024.

​

Payroll, benefits, and share-based stock compensation. Consists of costs incurred for salaries and wages, bonus, payroll taxes, benefits and share-based stock compensation associated with employees involved in research and development activities. Share-based stock compensation may fluctuate from period to period based on factors that are not within our control, such as our stock price on the dates share-based grants are issued.

​

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the change in payroll, benefits, and share-based stock compensation expenses was relatively flat.

​

Facilities and other. Consists of indirect costs incurred for the benefit of multiple programs, including information technology, and other facility-based expenses, such as rent expense.

​

For the three months ended September 30, 2025, compared to the three months ended September 30, 2024, the change in facilities and other expenses was relatively flat. For the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, the decrease in facilities and other expenses primarily related to decreases in facility-based expenses at our facility in Hopewell Township, New Jersey as a result of an amendment and restatement of our lease for such facility in June 2024 and at our facility in Warren, New Jersey as a result of an amendment to our lease for such facility in December 2024.

​

The successful development of our products and product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with developing drugs, including the uncertainty of:

| ● | the scope, rate of progress and expense of our clinical trials and other research and development activities;

| ● | the potential benefits of our products and product candidates over other therapies;

| ● | our ability to market, commercialize and achieve market acceptance for any of our products or product candidates that we are developing or may develop in the future, including our ability to negotiate pricing and reimbursement terms acceptable to us;

| ● | clinical trial results;

| ● | the terms and timing of regulatory approvals; and

| ● | the expense of filing, prosecuting, defending and enforcing patent claims and other intellectual property rights.

A change in the outcome of any of these variables with respect to the development of our products or product candidates could mean a significant change in the costs and timing associated with the development of those products or product candidates. For example, if the EMA or FDA or other regulatory authority were to require us to conduct clinical trials beyond those which we currently anticipate will be required for the completion of clinical development of any of our products or product candidates or if we experience significant delays in enrollment in any of our clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

Selling, general and administrative expense

Selling, general and administrative expenses consist primarily of salaries and other related costs for personnel, including share-based compensation expenses, in our executive, legal, business development, commercial, finance, accounting, information technology and human resource functions. Other selling, general and administrative expenses include facility-related costs not otherwise included in research and development expense; advertising and promotional expenses; costs associated with industry and trade shows; and professional fees for legal services, including patent-related expenses, accounting services and miscellaneous selling costs.

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We expect that selling, general and administrative expenses will increase in future periods in connection with our continued efforts to commercialize our products, including increased payroll, expanded infrastructure, commercial operations, increased consulting, legal, accounting and investor relations expenses.

Interest expense, net

Interest expense, net consists of interest expense from the liability for the sale of future royalties related to the A&R Royalty Purchase Agreement and the 2026 Convertible Notes outstanding, offset by interest income earned on investments.

​
Critical accounting policies and significant judgments and estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our financial statements, which we have prepared in accordance with generally accepted accounting principles in the United States. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenues and expenses during the reporting periods. Actual results may differ from these estimates under different assumptions or conditions.

During the three and nine months ended September 30, 2025, there were no material changes to our critical accounting policies as reported in our 2024 Annual Report.

Results of operations

Three months ended September 30, 2025 compared to the three months ended September 30, 2024

The following table summarizes revenues and selected expense and other income data for the three months ended September 30, 2025 and 2024.

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | ​ | ​
​ | ​ | September 30, | ​ | Change
(in thousands) |  | 2025 |  | 2024 |  | 2025 vs. 2024
Net product revenue | ​ | $ | 130,956 | ​ | $ | 135,421 | ​ | $ | (4,465)
Collaboration and license revenue | ​ | ​ | 9,258 | ​ | ​ | — | ​ | ​ | 9,258
Royalty revenue | ​ | ​ | 70,793 | ​ | ​ | 61,365 | ​ | ​ | 9,428
Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets | ​ |  | 15,781 | ​ |  | 10,848 | ​ | ​ | 4,933
Amortization of acquired intangible assets | ​ |  | 7,534 | ​ |  | 3,036 | ​ | ​ | 4,498
Research and development expense | ​ |  | 100,158 | ​ |  | 161,412 | ​ | ​ | (61,254)
Selling, general and administrative expense | ​ |  | 84,046 | ​ |  | 73,456 | ​ | ​ | 10,590
Change in the fair value of contingent consideration | ​ |  | — | ​ |  | 700 | ​ | ​ | (700)
Tangible asset impairment and losses (gains) on transactions, net | ​ | ​ | 472 | ​ | ​ | 1,844 | ​ | ​ | (1,372)
Interest expense, net | ​ |  | (32,592) | ​ |  | (41,609) | ​ | ​ | 9,017
Other income (expense), net | ​ |  | 6,502 | ​ |  | (1,872) | ​ | ​ | 8,374
Income tax benefit (expense) | ​ | ​ | 38,970 | ​ | ​ | (8,663) | ​ | ​ | 47,633

​

Net product revenue. Net product revenue was $131.0 million for the three months ended September 30, 2025, a decrease of $4.5 million, or 3%, from $135.4 million for the three months ended September 30, 2024. The decrease in net product revenue was primarily due to a decrease in net product sales of Emflaza and Translarna, partially offset by an increase in net product sales of Kebilidi/Upstaza and Sephience due to the timing of approvals for those products. The decrease in Emflaza sales is primarily driven by additional generic competition. The decrease in Translarna sales is primarily due to the EC’s adoption of the CHMP’s negative opinion.

Collaboration and license revenue. Collaboration and license revenue was $9.3 million for the three months ended September 30, 2025, an increase of $9.3 million, or 100%, from $0.0 million for the three months ended

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September 30, 2024. For the three months ended September 30, 2025, we recognized $9.3 million related to license revenue from the Novartis Agreement for performance obligations completed during the period. For the three months ended September 30, 2024, we did not recognize any collaboration or license revenue.

Royalty revenue. Royalty revenue was $70.8 million for the three months ended September 30, 2025, an increase of $9.4 million, or 15%, from $61.4 million for the three months ended September 30, 2024. The increase in royalty revenue was due to higher Evrysdi sales in the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. In accordance with the SMA License Agreement, we are entitled to royalties on worldwide annual net sales of the product.

Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets was $15.8 million for the three months ended September 30, 2025, an increase of $4.9 million, or 45%, from $10.8 million for the three months ended September 30, 2024. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets during the period consisted primarily of costs associated with the Novartis agreement, as well as production costs, royalty payments, and costs associated with sales of Emflaza, Translarna, Sephience, and Upstaza/Kebilidi. The increase was primarily due to costs associated with the Novartis agreement, inventory costs associated with the Sephience launch, Upstaza/Kebilidi royalty payments, and costs associated with new product sales, which was partially offset by a decrease in Emflaza royalties as a result of the completion of the royalty agreement with Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC).

Amortization of acquired intangible assets. Amortization of acquired intangible assets was $7.5 million for the three months ended September 30, 2025, an increase of $4.5 million, or over 100%, from $3.0 million for the three months ended September 30, 2024. These amounts are related to the Waylivra, Tegsedi, Upstaza/Kebilidi, and Sephience intangible assets, which are all being amortized on a straight-line basis over their estimated useful lives. The amortization increase was driven by a string of approvals received, beginning with PTC-AADC in October 2024. In October 2024, we received regulatory approval for Upstaza in Brazil, and in November 2024, the BLA for our gene therapy treatments of AADC deficiency was approved by the FDA, marketed under the brand name Kebilidi. With these approvals, $10.7 million and $17.4 million for Kebilidi and Upstaza, respectively, was reclassed from the PTC-AADC indefinite lived intangible asset to definite lived intangible assets. We will amortize these allocated balances of $10.7 million and $17.4 million over their expected useful lives of 12 years on a straight-line basis. In June 2025, the EC granted marketing authorization to Sephience for the treatment of children and adults living with PKU in the EEA, which triggered a $25.0 million milestone to the former Censa securityholders. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. Pursuant to the Censa Merger Agreement, in July 2025, a $32.5 million milestone from the Company to the former Censa securityholders was triggered when the FDA approved Sephience for the treatment of children and adults living with PKU. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. Pursuant to the Censa Rights Satisfaction Agreement, in August 2025, an upfront cash consideration of $225.1 million was paid to the former Censa securityholders. The upfront consideration was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis.

​

Research and development expense. Research and development expense was $100.2 million for the three months ended September 30, 2025, a decrease of $61.3 million, or 38%, from $161.4 million for the three months ended September 30, 2024. The decrease in research and development expenses primarily related to a $50.0 million regulatory success-based milestone payable to the former Censa securityholders for the three months ended September 30, 2024.

Selling, general and administrative expense. Selling, general and administrative expense was $84.0 million for the three months ended September 30, 2025, an increase of $10.6 million, or 14%, from $73.5 million for the three months ended September 30, 2024. The increase reflected our continued investment to support our commercial activities including our expanding commercial portfolio.

​

Change in the fair value of contingent consideration. The change in the fair value of contingent consideration was $0.0 million for the three months ended September 30, 2025, a change of $0.7 million, or 100%, from a loss of $0.7 million for the three months ended September 30, 2024. During the first quarter of 2025, the probability of triggering the remaining contingent consideration was determined to be remote, and therefore the balance was written down to zero.

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Tangible asset impairment and losses (gains) on transactions, net. Tangible asset impairment and losses (gains) on transactions, net was $0.5 million for the three months ended September 30, 2025, a decrease of $1.4 million, or 74%, from $1.8 million for the three months ended September 30, 2024. This decrease was primarily related to a $1.3 million loss for fixed asset impairments related to the South Plainfield, New Jersey office closure in August 2024, as well as a $0.5 million loss on sales of fixed assets during the three months ended September 30, 2024. During the three months ended September 30, 2025, we recorded fixed asset impairments of $0.4 million, as well as a $0.1 million loss related to sales of fixed assets.

Interest expense, net. Interest expense, net was $32.6 million for the three months ended September 30, 2025, a decrease of $9.0 million, or 22%, from $41.6 million for the three months ended September 30, 2024. Interest income was $19.1 million for the three months ended September 30, 2025, an increase of $6.3 million, from $12.8 million for the three months ended September 30, 2024, which primarily related to an increase in interest from marketable securities-available for sale. Interest expense was $51.7 million for the three months ended September 30, 2025, a decrease of $2.7 million, from $54.4 million for the three months ended September 30, 2024, which primarily related to a decrease in interest related to RPI.

Other income (expense), net. Other income, net was $6.5 million for the three months ended September 30, 2025, a change of $8.4 million, or over 100%, from other expense, net of $1.9 million for the three months ended September 30, 2024. Other income, net primarily related to net unrealized gains of $8.8 million on our ClearPoint Neuro. Inc. equity investments, partially offset by net realized and unrealized foreign exchange losses of $2.4 million for the three months ended September 30, 2025. Other expense, net for the three months ended September 30, 2024 was primarily related to net unrealized and realized gains of $4.6 million on our ClearPoint Neuro. Inc. equity investments and convertible debt security, offset by net realized and unrealized foreign exchange losses of $6.0 million for the three months ended September 30, 2024.

Income tax benefit (expense). Income tax benefit was $39.0 million for the three months ended September 30, 2025, a change of $47.6 million, or over 100%, compared to income tax expense of $8.7 million for the three months ended September 30, 2024. The change in income tax benefit (expense) was driven by the projected utilization of additional tax attributes in 2025 as a result of the provisions within the One Big Beautiful Bill Act.

Nine months ended September 30, 2025 compared to the nine months ended September 30, 2024

The following table summarizes revenues and selected expense and other income data for the nine months ended September 30, 2025 and 2024.

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended | ​ | ​ | ​
​ | ​ | September 30, | ​ | Change
(in thousands) |  | 2025 |  | 2024 |  | 2025 vs. 2024
Net product revenue | ​ | $ | 402,711 | ​ | $ | 446,245 | ​ | $ | (43,534)
Collaboration and license revenue | ​ |  | 998,430 | ​ |  | — | ​ | ​ | 998,430
Royalty revenue | ​ | ​ | 164,837 | ​ | ​ | 145,702 | ​ | ​ | 19,135
Manufacturing revenue | ​ | ​ | — | ​ | ​ | 1,661 | ​ | ​ | (1,661)
Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets | ​ |  | 40,063 | ​ |  | 41,115 | ​ | ​ | (1,052)
Amortization of acquired intangible assets | ​ |  | 15,393 | ​ |  | 57,431 | ​ | ​ | (42,038)
Research and development expense | ​ |  | 322,121 | ​ |  | 409,710 | ​ | ​ | (87,589)
Selling, general and administrative expense | ​ |  | 250,269 | ​ |  | 216,228 | ​ | ​ | 34,041
Change in the fair value of contingent consideration | ​ |  | (800) | ​ |  | 5,700 | ​ | ​ | (6,500)
Tangible asset impairment and losses (gains) on transactions, net | ​ | ​ | 648 | ​ | ​ | 3,605 | ​ | ​ | (2,957)
Interest expense, net | ​ |  | (97,042) | ​ |  | (125,933) | ​ | ​ | 28,891
Other expense, net | ​ |  | (5,540) | ​ |  | (2,306) | ​ | ​ | (3,234)
Income tax expense | ​ | ​ | (18,093) | ​ | ​ | (28,989) | ​ | ​ | 10,896

​

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Net product revenue. Net product revenue was $402.7 million for the nine months ended September 30, 2025, a decrease of $43.5 million, or 10%, from $446.2 million for the nine months ended September 30, 2024. The decrease in net product revenue was primarily due to a decrease in net product sales of Emflaza and Translarna, partially offset by an increase in net product sales of Kebilidi/Upstaza and Sephience due to the timing of approvals for those products. The decrease in Emflaza sales is primarily driven by additional generic competition. The decrease in Translarna sales is primarily due to the EC’s adoption of the CHMP’s negative opinion.

Collaboration and license revenue. Collaboration and license revenue was $998.4 million for the nine months ended September 30, 2025, an increase of $998.4 million, or 100%, from $0.0 million for the nine months ended September 30, 2024. The increase in collaboration and license revenue was due to the receipt of the $1.0 billion upfront payment upon the effective date of the license and collaboration agreement with Novartis related to our votoplam HD program. For the nine months ended September 30, 2025, we recognized $1.0 billion related to license revenue from the Novartis Agreement which was partially offset by $3.5 million related to a refund for a prior collaboration arrangement in relation to votoplam. For the nine months ended September 30, 2024, we did not recognize any collaboration or license revenue.

Royalty revenue. Royalty revenue was $164.8 million for the nine months ended September 30, 2025, an increase of $19.1 million, or 13%, from $145.7 million for the nine months ended September 30, 2024. The increase in royalty revenue was due to higher Evrysdi sales in the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. In accordance with the SMA License Agreement, we are entitled to royalties on worldwide annual net sales of the product.

Manufacturing revenue. Manufacturing revenue was $0.0 million for the nine months ended September 30, 2025, a decrease of $1.7 million, or 100%, from $1.7 million for the nine months ended September 30, 2024. The decrease was due to the prior completion of all manufacturing services related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. In June 2024, we sold our gene therapy manufacturing business in Hopewell Township, New Jersey. Accordingly, we do not expect to have manufacturing revenue going forward.

Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets was $40.1 million for the nine months ended September 30, 2025, a decrease of $1.1 million, or 3%, from $41.1 million for the nine months ended September 30, 2024. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets during the period consisted primarily of costs associated with the Novartis agreement, as well as production costs, royalty payments, inventory reserves, and costs associated with sales of Emflaza, Translarna, Sephience, and Upstaza/Kebilidi. The decrease was primarily due to decreases in royalty costs driven by Emflaza as a result of the completion of the royalty agreement with Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), which was partially offset by costs associated with the Novartis Agreement, inventory costs associated with the Sephience launch, Upstaza/Kebilidi royalty payments, an increase in inventory reserves, and costs associated with new product sales.

Amortization of acquired intangible assets. Amortization of acquired intangible assets was $15.4 million for the nine months ended September 30, 2025, a decrease of $42.0 million, or 73%, from $57.4 million for the nine months ended September 30, 2024. These amounts are related to the Waylivra, Tegsedi, Upstaza/Kebilidi, Sephience, and Emflaza intangible assets, which are all being amortized on a straight-line basis over their estimated useful lives. The amortization decrease was primarily driven by the Emflaza intangible asset being fully amortized as of February 2024. As a result, there is no further amortization for Emflaza as of February 2024.

Research and development expense. Research and development expense was $322.1 million for the nine months ended September 30, 2025, a decrease of $87.6 million, or 21%, from $409.7 million for the nine months ended September 30, 2024. The decrease in research and development expenses related to decreases in program spend as we continued to focus our resources on our differentiated, high potential research and development programs. For the nine months ended September 30, 2024, research and development expense also includes $65.0 million regulatory success-based milestones paid to the former Censa securityholders.

Selling, general and administrative expense. Selling, general and administrative expense was $250.3 million for the nine months ended September 30, 2025, an increase of $34.0 million, or 16%, from $216.2 million for the nine months ended

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September 30, 2024. The increase reflected our continued investment to support our commercial activities including our expanding commercial portfolio.

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Change in the fair value of contingent consideration. The change in the fair value of contingent consideration was a gain of $0.8 million for the nine months ended September 30, 2025, a change of $6.5 million, or over 100%, from a loss of $5.7 million for the nine months ended September 30, 2024. During the first quarter of 2025, the probability of triggering the remaining contingent consideration was determined to be remote, and therefore the balance was written down to zero.

Tangible asset impairment and losses (gains) on transactions, net. Tangible asset impairment and losses (gains) on transactions, net was $0.6 million for the nine months ended September 30, 2025, a decrease of $3.0 million, or 82%, from $3.6 million for the nine months ended September 30, 2024. This decrease was primarily related to a $4.4 million loss primarily related to the sale of certain assets for gene therapy manufacturing, and a $1.5 million loss primarily related to fixed asset impairments in connection with the South Plainfield, New Jersey office closure in August 2024. These amounts were partially offset by a gain of $2.2 million on lease terminations and a $0.1 million gain on sales of fixed assets. During the nine months ended September 30, 2025, we recorded fixed asset impairments of $0.5 million, as well as a $0.1 million loss related to sales of fixed assets.

Interest expense, net. Interest expense, net was $97.0 million for the nine months ended September 30, 2025, a decrease of $28.9 million, or 23%, from $125.9 million for the nine months ended September 30, 2024. Interest income was $57.3 million for the nine months ended September 30, 2025, an increase of $23.0 million, from $34.3 million for the nine months ended September 30, 2024, which primarily related to an increase in interest from marketable securities-available for sale. Interest expense was $154.4 million for the nine months ended September 30, 2025, a decrease of $5.8 million, from $160.2 million for the nine months ended September 30, 2024, which primarily related to a decrease in interest related to RPI.

Other expense, net. Other expense, net was $5.5 million for the nine months ended September 30, 2025, an increase of $3.2 million, or over 100%, from other expense, net of $2.3 million for the nine months ended September 30, 2024. Other expense, net, for the nine months ended September 30, 2025, was primarily related to net realized and unrealized losses from foreign currency of $17.4 million, partially offset by unrealized gains on our ClearPoint Neuro, Inc. equity investments of $5.7 million and $6.0 million related to other income items. Other expense, net for the nine months ended September 30, 2024, was primarily related to net realized and unrealized losses from foreign currency of $3.8 million for the nine months ended September 30, 2024, partially offset by net unrealized and realized gains on our ClearPoint Neuro, Inc. convertible debt security and equity investments of $1.4 million.

Income tax expense. Income tax expense was $18.1 million for the nine months ended September 30, 2025, a decrease of $10.9 million, or 38%, compared to income tax expense of $29.0 million for the nine months ended September 30, 2024. The decrease in income tax expense was driven by the projected utilization of additional tax attributes in 2025 as a result of the provisions within the One Big Beautiful Bill Act. Additionally, we incur income tax expenses in various foreign jurisdictions, and our foreign tax liabilities are largely dependent upon the distribution of pre-tax earnings among these different jurisdictions.

Liquidity and capital resources

Sources of liquidity

While we have generated net income in the three and nine months ended September 30, 2025, we have historically incurred significant operating losses.

As a growing commercial-stage biopharmaceutical company, we are engaging in significant commercialization efforts for our products while also devoting a substantial portion of our efforts on research and development related to our products, product candidates and other programs. To date, our product revenue has primarily consisted of sales of Translarna for the treatment of nmDMD in territories outside of the United States and from Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, net product revenues also includes sales of Sephience for the treatment of PKU in the United States and in territories outside of the United States. Our ongoing ability to generate

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revenue from sales of Translarna for the treatment of nmDMD is dependent upon our ability to maintain our marketing authorizations in Brazil and Russia and secure market access through commercial programs following the conclusion of pricing and reimbursement terms at sustainable levels in the member states of the EEA or through EAP programs or similar styled programs in the EEA and other territories. In March 2025, the EC adopted the opinion of the CHMP to not renew the authorization of Translarna for the treatment of nmDMD. However, the EC indicated that individual countries within the EU can leverage Articles 117(3) and 5(1) of the EU Directive 2001/83 to allow continued use of Translarna. Our ability to generate product revenue from Sephience and Emflaza will largely depend on the coverage and reimbursement levels set by governmental authorities, private health insurers and other third-party payors. Additionally, Emflaza’s seven-year period of orphan drug exclusivity related to the treatment of DMD in patients five years and older expired in February 2024. We have previously relied on this exclusivity period to commercialize Emflaza in the United States. We expect the expiration of this orphan drug exclusivity to potentially have a significant negative impact on Emflaza net product revenue. Emflaza’s orphan drug exclusivity related to the treatment of DMD in patients two years of age to less than five expires in June 2026.

We have financed our operations to date primarily through the private offerings of convertible senior notes, public offerings and “at the market offerings” of common stock, proceeds from royalty purchase agreements, private placements of our preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product candidates. We expect to continue to incur significant expenses and operating losses for at least the next fiscal year. The net income and losses we incur may fluctuate significantly from quarter to quarter.

In August 2019, we entered into the Sales Agreement, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act. See “Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations—Corporate Updates—Funding” for additional information.

In September 2019, we closed a private offering of $287.5 million aggregate principal amount of 2026 Convertible Notes, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes, which was fully exercised by the initial purchasers. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. We received net proceeds of $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by us.

We have received fundings from Royalty Pharma under the A&R Royalty Purchase Agreement in July 2020, October 2023 and June 2024 totaling $1.9 billion (less Royalty payments received by us with respect to the Assigned Royalty Rights). In exchange for these fundings, we sold Royalty Pharma 90.49% of the Royalty, which will be reduced to 83.33% after Royalty Pharma receives the Assigned Royalty Cap from the Royalty assigned under the Original Royalty Purchase Agreement. We currently retain 9.51% of the Royalty, which increases to 16.67% after the Assigned Royalty Cap has been met. We have the option to sell our retained portions of the Royalty to Royalty Pharma in up to three tranches for the following payments: (1) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, (2) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, and (3) $50.0 million in exchange for 1.90% of the Royalty, which increases to 3.33% after the Assigned Royalty Cap has been met, in each case less Royalty payments received by us with respect to the Assigned Royalty Rights.

In November 2024, we and Novartis entered into the Novartis Agreement relating to our votoplam HD program which includes related molecules. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing OLE clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed

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products worldwide. Under the Novartis Agreement, and upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

Cash flows

As of September 30, 2025, we had cash, cash equivalents and marketable securities of $1.69 billion.

The following table provides information regarding our cash flows and our capital expenditures for the periods indicated.

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​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended | ​
​ | ​ | September 30, | ​
(in thousands) |  | 2025 |  | 2024 | ​
Cash provided (used in) by: |  |  |  |  | ​
Operating activities | ​ | 745,469 | ​ | (77,684) | ​
Investing activities | ​ | (895,992) | ​ | (223,530) | ​
Financing activities | ​ | 28,590 | ​ | 229,395 | ​

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Net cash provided by operating activities was $745.5 million for the nine months ended September 30, 2025, compared to net cash used in operating activities of $77.7 million for the nine months ended September 30, 2024. The net cash provided by operating activities for the nine months ended September 30, 2025, was primarily related to the upfront payment of $1.0 billion in cash received upon the closing of the Novartis Agreement in January 2025, partially offset by spend supporting clinical development and commercial activities. The net cash used in operating activities for the nine months ended September 30, 2024, was primarily related to spend supporting clinical development and commercial activities, partially offset by the cash received from the sales milestone of $100.0 million for the achievement of $1.5 billion in worldwide net sales from Evrysdi.

Net cash used in investing activities was $896.0 million for the nine months ended September 30, 2025, compared to $223.5 million for the nine months ended September 30, 2024. Cash used in investing activities for the nine months ended September 30, 2025 and 2024, were primarily related to the acquisition of product rights, purchases of marketable securities, and purchases of fixed assets, partially offset by net sales and redemption of marketable securities and proceeds from sale of fixed assets.

Net cash provided by financing activities was $28.6 million for the nine months ended September 30, 2025, compared to $229.4 million for the nine months ended September 30, 2024. Cash provided by financing activities for the nine months ended September 30, 2025 was primarily attributable to proceeds from our employee stock purchase plan and proceeds from the exercise of options, partially offset by payments on contingent consideration obligation and payments on our finance lease principal. Cash provided by financing activities for the nine months ended September 30, 2024 was primarily attributable to proceeds from sales of future royalties, proceeds from our employee stock purchase plan, and proceeds from the exercise of options, partially offset by payments on contingent consideration obligation and payments on our finance lease principal.

Funding requirements

We anticipate that we will continue to incur significant expenses in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including expenses related to our commercial infrastructure and corresponding sales and marketing, legal and regulatory, and distribution and manufacturing undertakings as well as administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with ongoing, planned and potential future clinical trials and studies for our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications. We continue to seek marketing authorization for Translarna for the treatment of nmDMD in territories that we do not currently have marketing authorization in. We submitted an NDA to the FDA for vatiquinone for the treatment of FA in December 2024. In August 2025, the FDA issued a complete response letter related to the NDA stating that

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substantial evidence of efficacy was not demonstrated for vatiquinone and that an additional adequate and well-controlled study would be needed to support NDA resubmission. We plan to meet with the FDA in the fourth quarter to discuss the vatiquinone development program. These efforts may significantly impact the timing and extent of our commercialization and manufacturing expenses.

In addition, our expenses will increase if and as we:

| ● | seek to satisfy contractual and regulatory obligations that we assumed through our acquisitions and collaborations;

| ● | execute our commercialization strategy for our products, including initial commercialization launches of our products, label extensions or entering new markets;

| ● | are required to complete any additional clinical trials, non-clinical studies or Chemistry, Manufacturing and Controls, or CMC, assessments or analyses in order to advance our products or product candidates in the United States or elsewhere;

| ● | are required to take other steps to maintain our current marketing authorization in Brazil and Russia for Translarna for the treatment of nmDMD or to obtain further marketing authorizations for Translarna for the treatment of nmDMD or other indications;

| ● | initiate or continue the research and development of Sephience and our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications;

| ● | seek to discover and develop additional product candidates;

| ● | seek to expand and diversify our product pipeline through strategic transactions;

| ● | maintain, expand and protect our intellectual property portfolio; and

| ● | add operational, financial and management information systems and personnel, including personnel to support our product development and commercialization efforts.

We believe that our cash flows from product sales, together with existing cash and cash equivalents, and marketable securities, will be sufficient to fund our operating expenses and capital expenditure requirements for at least the next twelve months. We have based this estimate on assumptions that may prove to be wrong, and we could use our capital resources sooner than we currently expect.

Our future capital requirements will depend on many factors, including:

| ● | our ability to commercialize and market our products and product candidates that may receive marketing authorization;

| ● | our ability to negotiate, secure and maintain adequate pricing, coverage and reimbursement terms, on a timely basis, with third-party payors for our products and products candidates;

| ● | our ability to successfully launch and commercialize Sephience in markets where we receive regulatory approval;

| ● | our ability to maintain the marketing authorization for Translarna and our other products in territories outside of the EEA;

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| ● | the amount of generic drug competition that we face for Emflaza for the treatment of DMD in patients five years and older;

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| ● | our ability to obtain marketing authorization for Translarna for the treatment of nmDMD in the United States;

| ● | our plans for vatiquinone including with respect to the expected timing of clinical trials and studies, availability of data, regulatory submissions and responses, meetings with regulatory agencies, and other matters;

| ● | our ability to successfully complete all post-marketing requirements imposed by regulatory agencies with respect to our products;

| ● | the progress and results of activities for Sephience and our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications;

| ● | the scope, costs and timing of our commercialization activities, including product sales, marketing, legal, regulatory, distribution and manufacturing, for any of our products and for any of our other product candidates that may receive marketing authorization or any additional territories in which we receive authorization to market Sephience or Translarna;

| ● | the costs, timing and outcome of regulatory review of our splicing and inflammation and ferroptosis programs and Sephience, Translarna and Upstaza/Kebilidi in other territories;

| ● | our ability to satisfy our obligations under the indenture governing the 2026 Convertible Notes;

| ● | the timing and scope of any potential future growth in our employee base;

| ● | the scope, progress, results and costs of preclinical development, laboratory testing and clinical trials for our other product candidates, including those in our splicing and inflammation and ferroptosis programs;

| ● | revenue received from commercial sales of our products or any of our product candidates;

| ● | our ability to obtain additional and maintain existing reimbursed named patient and cohort EAP programs for Translarna for the treatment of nmDMD on adequate terms, or at all;

| ● | the ability and willingness of patients and healthcare professionals to access Translarna through alternative means if pricing and reimbursement negotiations in the applicable territory do not have a positive outcome;

| ● | the costs of preparing, filing and prosecuting patent applications, maintaining, and protecting our intellectual property rights and defending against intellectual property-related claims;

| ● | the extent to which we acquire or invest in other businesses, products, product candidates, and technologies, including the success of any acquisition, in-licensing or other strategic transaction we may pursue, and the costs of subsequent development requirements and commercialization efforts, including with respect to our acquisitions of Emflaza, Agilis, our inflammation and ferroptosis platform and Censa and our licensing of Tegsedi and Waylivra;

| ● | our ability to establish and maintain collaborations, including our collaborations with Roche and the SMA Foundation, and our ability to obtain research funding and achieve milestones under these agreements.

| ● | the progress and results of activities for our votoplam program, including our right to receive any development, regulatory and sales milestones, profit sharing and royalty payments from Novartis; and

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| ● | unexpected decreases in revenue or increase in expenses resulting from potential widespread outbreaks of contagious disease.

With respect to our outstanding 2026 Convertible Notes, cash interest payments are payable on a semi-annual basis in arrears, which will require total funding of $4.3 million annually.

In July 2025, Sephience™ (sepiapterin) was granted FDA approval for the treatment of children and adults living with PKU. Pursuant to the Censa Merger Agreement, the approval triggered a $32.5 million milestone to the former Censa securityholders, which was recorded in accounts payable and accrued expenses on our consolidated balance sheet as of September 30, 2025.

We also have certain significant contractual obligations and commercial commitments that require funding and we have disclosed these items under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Funding Obligations” in our 2024 Annual Report. There were no material changes to these obligations and commitments during the period ended September 30, 2025.

We will need to generate significant revenues to achieve and sustain profitability, and we may never do so. We may need to obtain substantial additional funding in connection with our continuing operations. Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs primarily through a combination of equity offerings, debt financings, collaborations, strategic alliances, grants and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product and product candidates and marketing, distribution or licensing arrangements. Adequate additional financing may not be available to us on acceptable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, our shareholders ownership interests will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. If we raise additional funds through collaborations, strategic alliances or marketing, distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or to grant licenses on terms that may not be favorable to us.

If we are unable to raise additional funds through equity, debt or other financings when needed or on attractive terms, we may be required to delay, limit, reduce or terminate our product development or commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

Item 3. Quantitative and Qualitative Disclosures About Market Risk.

During the period ended September 30, 2025, there were no material changes in our market risk or how our market risk is managed, compared to those disclosed under the heading “Quantitative and Qualitative Disclosures about Market Risk” in our 2024 Annual Report.

Item 4. Controls and Procedures.

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our Chief Executive Officer and our Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures as of September 30, 2025. The term “disclosure controls and procedures”, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the Securities and Exchange Commission’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as

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appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of September 30, 2025, our Chief Executive Officer and Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting

No change in our internal control over financial reporting occurred during the quarter ended September 30, 2025 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

PART II—OTHER INFORMATION

Item 1. Legal Proceedings.

From time to time in the ordinary course of our business, we are subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in our clinical trials or otherwise gain access to our product candidates. We are not currently aware of any material legal proceedings to which we are a party or of which any of our property is subject.

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Item 1A. Risk Factors.

We have set forth in Item 1A to our Annual Report on Form 10-K for the year ended December 31, 2024, risk factors relating to our business, our industry, our structure and our common stock. Readers of this Quarterly Report on Form 10-Q are referred to such Item 1A for a more complete understanding of risks concerning us. There have been no material changes in our risk factors since those published in such Form 10-K for the year ended December 31, 2024, other than as reported in Item 1A to our Quarterly Form 10-Q for the period ended June 30, 2025.

Item 5. Other Information.

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Director and Officer Trading Arrangements

A portion of the compensation of our directors and officers (as defined in Rule 16a-1(f) under the Securities Exchange Act of 1934, as amended, or the Exchange Act) is in the form of equity awards and, from time to time, directors and officers engage in open-market transactions with respect to the securities acquired pursuant to such equity awards or other Company securities, including to satisfy tax withholding obligations when equity awards vest or are exercised, and for diversification or other personal reasons.

Transactions in Company securities by directors and officers are required to be made in accordance with our insider trading policy, which requires that the transactions be in accordance with applicable U.S. federal securities laws that prohibit trading while in possession of material nonpublic information. Rule 10b5-1 under the Exchange Act provides an affirmative defense that enables directors and officers to prearrange transactions in Company securities in a manner that avoids concerns about initiating transactions while in possession of material nonpublic information.

The following table describes, for the quarterly period covered by this report, each trading arrangement for the sale or purchase of Company securities adopted or terminated by our directors and officers that is either (1) a contract, instruction or written plan intended to satisfy the affirmative defense conditions of Rule 10b5-1(c), or a “Rule 10b5-1 trading arrangement”, or (2) a “non-Rule 10b5-1 trading arrangement” (as defined in Item 408(c) of Regulation S-K):

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Name (Title) | Action Taken (Date of Action) | Type of Trading Arrangement | Nature of Trading Arrangement | Duration of Trading Arrangement | Aggregate Number of Securities
Christine Utter (Chief Accounting Officer and Head of People Services) | Adoption (September 16, 2025) | Rule 10b5-1 trading arrangement | Sale | Until September 15, 2026, or until such earlier date upon which all transactions are completed | Up to 57,654 shares
Eric Pauwels (Chief Business Officer) | Amendment (September 16, 2025) | Rule 10b5-1 trading arrangement | Sale | Until June 3, 2026, or until such earlier date upon which all transactions are completed | Up to 72,700 shares
Mark Boulding (Chief Legal Officer) | Adoption (September 10, 2025) | Rule 10b5-1 trading arrangement | Sale | Until March 5, 2027, or until such earlier date upon which all transactions are completed | Up to 259,346 shares*
Glenn D. Steele Jr. (Director) | Adoption (September 8, 2025) | Rule 10b5-1 trading arrangement | Sale | Until January 5, 2026, or until such earlier date upon which all transactions are completed | Up to 12,000 shares

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* | This Rule 10b5-1 trading arrangement includes up to 86,812 shares of Company common stock available to be sold under Mr. Boulding’s previously executed Rule 10b5-1 trading arrangement, or the Prior Plan, which expires on March 3, 2026. Such shares are only available to be sold under this trading arrangement to the extent they remain unsold under the Prior Plan upon its expiration or termination.

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Item 6. Exhibits.

​ | ​ | ​
Exhibit Number |  | Description of Exhibit
​ | ​ | ​
10.1*† | ​ | Rights Satisfaction Agreement, dated August 5, 2025, by and among PTC Therapeutics, Inc., certain of the former securityholders of Censa Pharmaceuticals, Inc., and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC
31.1* |  | Certification of Principal Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2* |  | Certification of Principal Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1* |  | Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2* |  | Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS* |  | Inline XBRL Instance Document
101.SCH* |  | Inline XBRL Taxonomy Extension Schema Document
101.CAL* |  | Inline XBRL Taxonomy Extension Calculation Linkbase Document
101.LAB* |  | Inline XBRL Taxonomy Extension Label Linkbase Database
101.PRE* |  | Inline XBRL Taxonomy Extension Presentation Linkbase Document
101.DEF* |  | Inline XBRL Taxonomy Extension Definition Linkbase Document
104 | ​ | The cover page from this Quarterly Report on Form 10-Q, formatted in Inline XBRL

* Submitted electronically herewith.

† Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.

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In accordance with SEC Release 33-8238, Exhibits 32.1 and 32.2 are being furnished and not filed.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

​ | ​ | ​
| PTC THERAPEUTICS, INC.
Date: November 4, 2025 | By: | /s/ Pierre Gravier
​ | ​ | Pierre Gravier
​ | ​ | Chief Financial Officer
​ | ​ | (Principal Financial Officer and Duly Authorized Signatory)

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