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Washington, D.C. 20549 Form 10-K Ultragenyx Pharmaceutical Inc. (Exact name of registrant as specified in its charter) (Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Exchange Act: Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.YES☑NO☐ Indicate by check mark whether the registrant (1) hasfiled all reports required to befiled by Section 13 or 15(d) of the Exchange Act during the preceding 12months (or for such shorter period that the registrant was required tofile such reports), and (2) has been subject to suchfiling requirements for the past 90 days.YES☑NO☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 ofRegulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit suchfiles).Yes☑NO☐ Indicate by check mark whether the registrant is a large acceleratedfiler, an acceleratedfiler, a non-acceleratedfiler, a smaller reporting company, or anemerging growth company. See the definitions of “large acceleratedfiler,” “acceleratedfiler,” “smaller reporting company,” and “emerging growth company” inRule 12b-2 of the Exchange Act. Acceleratedfiler☐Non- acceleratedfiler☐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 newor revisedfinancial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant hasfiled a report on and attestation to its management’s assessment of the effectiveness of its internalcontrol overfinancial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accountingfirm that prepared or issuedits audit report.☑ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether thefinancial statements of the registrant included in thefilingreflect the correction of an error to previously issuedfinancial statements.☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation receivedby any of the registrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b).☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).YES☐NO☑ The aggregate market value of the voting and non-voting common equity held by non-affiliates of the Company as of June 30, 2025 was approximately $3.4billion, based upon the closing price on The Nasdaq Global Select Market reported for such date. Shares of common stock held by each executive officer anddirector and by each person who is known to own 10% or more of the outstanding common stock have been excluded as such persons may be deemed affiliates ofthe Company. This determination of affiliate status is not necessarily a conclusive determination for other purposes. As of February 13, 2026, the Company had 96,629,788 shares of common stock issued and outstanding. DOCUMENTS INCORPORATED BY REFERENCE Portions of the registrant’s definitive proxy statement relating to its 2026 Annual Meeting of Stockholders, to be held on or about May 14, 2026, areincorporated by reference into Part III of this Annual Report on Form 10-K where indicated. Such proxy statement will befiled with the U.S. Securities and ExchangeCommission within 120 days after the end of thefiscal year to which this report relates. Table of Contents PART I Item 1.BusinessItem 1A.Risk FactorsItem 1B.Unresolved StaffCommentsItem 1C.CybersecurityItem 2.PropertiesItem 3.Legal ProceedingsItem 4.Mine Safety Disclosures PART II Item 5.Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities66Item 6.Reserved67Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations68Item 7A.Quantitative and Qualitative Disclosures About Market Risk75Item 8.Financial Statements and Supplementary Data75Item 9.Changes in and Disagreements With Accountants on Accounting and Financial Disclosure75Item 9A.Controls and Procedures76Item 9B.Other Information77Item 9C.Disclosure Regarding Foreign Jurisdictions that Prevent Inspections78PART IIIItem 10.Directors, Executive Officers and Corporate Governance79Item 11.Executive Compensation79Item 12.Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters79Item 13.Certain Relationships and Related Transactions, and Director Independence79Item 14.Principal Accountant Fees and Services79PART IVItem 15.Exhibits and Financial Statement Schedules80Item 16.Form 10-K Summary86SIGNATURES87 CAUTIONARY