Ultragenyx Pharmaceutical Inc. 10-K

Item 9A. Controls and Procedures Evaluation of Disclosure Controls and Procedures Management carried out an evaluation, under the supervision and with the participation of our Principal Executive Officer and our Principal Financial Officer, of the effectiveness of our “disclosure controls and procedures” as of the end of the period covered by this Annual Report, pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, or the Exchange Act. In connection with that evaluation, our Principal Executive Officer and our Principal Financial Officer concluded that our disclosure controls and procedures were effective and designed to provide reasonable assurance that the information required to be disclosed is recorded, processed, summarized, and reported within the time periods specified in the SEC rules and forms as of December 31, 2023. For the purpose of this review, disclosure controls and procedures means controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. These disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is accumulated and communicated to management, including our Principal Executive Officer and our Principal Financial Officer, as appropriate to allow timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Management’s Annual Report on Internal Control Over Financial Reporting Management is responsible for establishing and maintaining adequate internal control over financial reporting as defined in Rules 13a-15(f) and 15d-15(f) of the Exchange Act. Our management used the Committee of Sponsoring Organizations of the Treadway Commission Internal Control - Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework), or the COSO framework, to evaluate the effectiveness of internal control over financial reporting. Management believes that the COSO framework is a suitable framework for its evaluation of financial reporting because it is free from bias, permits reasonably consistent qualitative and quantitative measurements of our internal control over financial reporting, is sufficiently complete so that those relevant factors that would alter a conclusion about the effectiveness of our internal control over financial reporting are not omitted and is relevant to an evaluation of internal control over financial reporting. Management has assessed the effectiveness of our internal control over financial reporting as of December 31, 2023, and has concluded that as of such date, our internal control over financial reporting was effective. Our independent registered public accounting firm, Ernst & Young LLP, has audited the financial statements included in this Annual Report and has issued a report on the effectiveness of our internal control over financial reporting. The report of Ernst & Young LLP is included below. Changes in Internal Control over Financial Reporting There have been no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during our fourth quarter ended December 31, 2023, that have materially affected, or are reasonably likely to materially affect our internal control over financial reporting. Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of Ultragenyx Pharmaceutical Inc. Opinion on Internal Control Over Financial Reporting We have audited Ultragenyx Pharmaceutical Inc.’s internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the 80 Treadway Commission ( 2013 framework) (the COSO criteria). In our opinion, Ultragenyx Pharmaceutical Inc. (the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2023, based on the COSO criteria. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2023 and 2022, the related consolidated statements of operations, comprehensive loss, stockholders’ equity and cash flows for each of the three years in the period ended December 31, 2023, and the related notes and our report dated February 21, 2024 expressed an unqualified opinion thereon. Basis for Opinion The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. /s/ Ernst & Young LLP San Mateo, California February 21, 2024 I tem 9B. Other Information On November 10, 2023 , Corsee Sanders , Ph.D., a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 2,322 shares of the Company’s common stock through July 12, 2024, subject to certain conditions. On December 7, 2023 , Matthew Fust , a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 12,195 shares of the Company’s common stock through December 6, 2024, subject to certain conditions. Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections Not applicable. 81 P ART III Item 10. Di rectors, Executive Officers and Corporate Governance Except as set forth below, the information required by this Item is incorporated herein by reference to information in the proxy statement for our 2024 Annual Meeting of Stockholders, which we will file with the SEC within 120 days of the end of the fiscal year to which this Annual Report relates, or the “2024 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,” “Executive Officers,” ““Board of Directors and Committees,” and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.” We have adopted a code of ethics that applies to all of our directors, officers and employees, including our principal executive, principal financial and principal accounting officers, or persons performing similar functions, or Code of Ethics. Our Code of Ethics is posted on our website located at https://ir.ultragenyx.com/ under “Corporate Governance”. We intend to disclose future amendments to certain provisions of the Code of Ethics, and waivers of the Code of Ethics granted to executive officers and directors, on the website within four business days following the date of the amendment or waiver. I tem 11. Executive Compensation The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Executive Compensation,” “Director Compensation,” and “Board of Directors and Committees.” Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Security Ownership of Certain Beneficial Owners and Management” and “Equity Compensation Plan Information.” Item 13. Certain Relationships and Related Transactions, and Director Independence The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Certain Relationships and Related-Person Transactions,” “Corporate Governance,” and “Board of Directors and Committees.” Item 14. Principal Accountant Fees and Services The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the heading “Proposal No. 3—Ratification of the Selection of Independent Registered Public Accounting Firm.” 82 PA RT IV Item 15. Ex hibits and Financial Statement Schedules (a) The following documents are filed as part of this Annual Report. (1) Consolidated Financial Statements Consolidated Financial Statements—See Index to Consolidated Financial Statements at page F-1 of this Annual Report. (2) Consolidated Financial Statement Schedules Consolidated Financial Statement schedules have been omitted in this Annual Report because they are not applicable, not required under the instructions, or the information requested is set forth in the Consolidated Financial Statements or related notes thereto. (b) Exhibits Exhibit Incorporated by Reference Filed Number Exhibit Description Form Date Number Herewith 3.1 Amended and Restated Certificate of Incorporation 8-K 2/5/2014 3.1 3.2 Second Amended and Restated Bylaws 8-K 12/21/2023 3.1 4.1 Form of Common Stock Certificate S-1 11/8/2013 4.2 4.2 Form of Indenture S-3 ASR 2/12/2021 4.2 4.3 Form of Pre-Funded Warrant 8-K 10/23/2023 4.1 4.4 Description of Common Stock 10-K 2/14/2020 4.3 10.1* Collaboration and License Agreement, effective as of August 29, 2013, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. S-1/A 12/23/2013 10.1 10.2 Amendment No. 1 to Collaboration and License Agreement, effective as of August 24, 2015, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-Q 11/10/2015 10.2 10.3 Amendment No. 2 to Collaboration and License Agreement, effective as of November 28, 2016, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-K 2/21/2018 10.3 10.4* Amendment No. 3 to Collaboration and License Agreement, effective September 29, 2017, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-K 2/21/2018 10.4 10.5* Amendment No. 4 to Collaboration and License Agreement, effective as of January 29, 2018, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-K 2/21/2018 10.5 10.6* Amendment No. 5 to Collaboration and License Agreement, effective as of April 30, 2018, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-Q 8/3/2018 10.1 10.7* Amendment No. 6 to Collaboration and License Agreement, effective as of February 1, 2019, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-Q 5/7/2019 10.2 83 10.8* Amendment No. 7 to Collaboration and License Agreement, effective as of December 5, 2018, between Ultragenyx Pharmaceutical Inc. and Kyowa Hakko Kirin Co., Ltd. 10-Q 5/7/2019 10.3 10.9* Amendment No. 8 to Collaboration and License Agreement, effective as of July 4, 2019, between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. (formerly, Kyowa Hakko Kirin Co., Ltd.) 10-Q 8/2/2019 10.1 10.10* Amendment No. 9 to Collaboration and License Agreement, effective December 23, 2019, between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. 10-K 2/14/2020 10.10 10.11* Amendment No. 10 to Collaboration and License Agreement, effective as of April 1, 2020, between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. 10-Q 5/7/2020 10.2 10.12* Amendment No. 11 to Collaboration and License Agreement, effective as of December 17, 2021 between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. 10-K 2/16/2022 10.13 10.13* Amendment No. 12 to Collaboration and License Agreement, effective as of September 29, 2022, between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. 10-Q 11/3/2022 10.1 10.14* Amendment No. 13 to Collaboration and License Agreement, effective as of May 16, 2023, between Ultragenyx Pharmaceutical Inc. and Kyowa Kirin Co., Ltd. 10-Q 8/3/2023 10.1 10.15* Unit Purchase Agreement, dated as of July 15, 2022, by and among Ultragenyx Pharmaceutical Inc., GeneTx Biotherapeutics LLC, the Unitholders and Deborah A. Guagliardo 10-Q 7/29/2022 10.2 10.16* Commercial Supply and Services Agreement – Drug Substance, effective December 7, 2017, between Ultragenyx Europe GmbH and Rentschler Biopharma SE 10-K 2/21/2018 10.18 10.17* Commercial Master Service Agreement – Drug Product, effective February 22, 2021, between Ultragenyx Pharmaceutical Inc. and BSP Pharmaceuticals S.p.A 10-K 2/17/2023 10.25 10.18* Commercial Supply Agreement, dated June 19, 2023, between Ultragenyx Pharmaceutical Inc. and IOI Oleo GmbH X 10.19* Royalty Purchase Agreement, dated as of December 17, 2019, between Ultragenyx Pharmaceutical Inc. and RPI Finance Trust 10-K 2/14/2020 10.25 10.20* Royalty Purchase Agreement, dated as of July 14, 2022, by and among Rare Delaware Inc., Ultragenyx Pharmaceutical Inc. and OCM LS23 Holdings LP 10-Q 7/29/2022 10.1 10.21# 2014 Incentive Plan (as amended) 10-K 2/17/2017 10.20 10.22# Form of Incentive Stock Option Agreement (2014 Plan) S-1/A 1/17/2014 10.14 10.23# Form of Non Statutory Stock Option Agreement (Employees) (2014 Plan) S-1/A 1/17/2014 10.15 10.24# Form of Restricted Stock Unit Agreement (Employees) (2014 Plan ) 10-Q 5/10/2016 10.1 84 10.25# Form of Non-Statutory Stock Option Agreement (Annual Grant for Directors) (2014 Plan) 10-Q 8/3/2021 10.2 10.26# Form of Restricted Stock Unit Agreement (Annual Grant for Directors ) (2014 Plan) 10-Q 8/3/2021 10.3 10.27# Form of Non-Statutory Stock Option Agreement (Grant for New Directors) (2014 Plan) 10-Q 8/3/2021 10.4 10.28# Form of Restricted Stock Unit Agreement (Grant for New Directors) (2014 Plan) 10-Q 8/3/2021 10.5 10.29# 2023 Incentive Plan S-8 6/8/2023 4.4 10.30# Form of Incentive Stock Option Agreement (2023 Plan) X 10.31# Form of Non Statutory Stock Option Agreement (Employees)(2023 Plan) X 10.32# Form of Restricted Stock Unit Agreement (Employees)(2023 Plan) X 10.33# Form of Non-Statutory Stock Option Agreement (Annual Grant for Directors) (2023 Plan) X 10.34# Form of Restricted Stock Unit Agreement (Annual Grant for Directors) (2023 Plan) X 10.35# Form of Non-Statutory Stock Option Agreement (Grant for New Directors)(2023 Plan) X 10.36# Form of Restricted Stock Unit Agreement (Grant for New Directors) (2023 Plan) X 10.37# Form of Performance Stock Unit Agreement (2022) 10-Q 5/6/2022 10.1 10.38# Form of Performance Stock Unit Agreement (2023) 10-Q 5/4/2023 10.1 10.39# Amended and Restated 2014 Employee Stock Purchase Plan S-8 6/8/2023 4.5 10.40# Corporate Bonus Plan S-1/A 1/17/2014 10.27 10.41# Employment Inducement Plan 10-K 2/12/2021 10.43 10.42# First Amendment to Employment Inducement Plan S-8 6/8/2023 4.7 10.43# Form of Non Statutory Stock Option Agreement (Inducement Plan) 10-K 2/12/2021 10.44 10.44# Form of Non Statutory Stock Option Agreement (Inducement Plan) (ex-US) 10-K 2/12/2021 10.45 10.45# Form of Restricted Stock Unit Agreement (Inducement Plan) 10-K 2/12/2021 10.46 10.46# Form of Restricted Stock Unit Agreement (Inducement Plan)(ex-US) 10-K 2/12/2021 10.47 10.47# Ultragenyx Pharmaceutical Inc. Deferred Compensation Plan 10-Q 8/3/2021 10.1 10.48# Amendment No. 1 to the Ultragenyx Pharmaceutical Inc. Deferred Compensation Plan 10-Q 11/3/2021 10.1 10.49# Executive Employment Agreement, dated as of June 15, 2011, between Ultragenyx Pharmaceutical Inc. and Emil D. Kakkis, M.D., Ph.D. S-1 11/8/2013 10.18 10.50# Amendment No. 1 to Executive Employment Agreement, dated August 8, 2014, between Ultragenyx Pharmaceutical Inc. and Emil D. Kakkis, M.D., Ph.D. 10-Q 8/11/2014 10.2 85 10.51# Amendment No. 2, dated September 13, 2022, to Executive Employment Agreement between Ultragenyx Pharmaceutical Inc. and Emil D. Kakkis, M.D., Ph.D. 10-Q 11/3/2022 10.2 10.52# Offer Letter, dated as of October 31, 2011, between Ultragenyx Pharmaceutical Inc. and Thomas Kassberg S-1 11/8/2013 10.19 10.53# Amendment No. 1 to Offer Letter, dated as of August 8, 2014, between Ultragenyx Pharmaceutical Inc. and Thomas Kassberg 10-Q 8/11/2014 10.3 10.54# Amendment No. 2, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc. and Thomas Kassberg 10-Q 11/3/2022 10.5 10.55# Offer Letter, dated as of April 26, 2016, between Ultragenyx Pharmaceutical Inc. and Karah Parschauer 10-Q 8/9/2016 10.3 10.56# Amendment, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc. and Karah Parschauer 10-Q 11/3/2022 10.6 10.57# Offer Letter, dated as of February 20, 2015, between Ultragenyx Pharmaceutical Inc. and Dennis Huang 10-K 2/17/2017 10.36 10.58# Amendment, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc. and Dennis Huang 10-Q 11/3/2022 10.7 10.59# Offer Letter, dated as of June 11, 2015, between Ultragenyx Pharmaceutical Inc. and John R. Pinion II 10-K 2/17/2017 10.37 10.60# Amendment, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc. and John R. Pinion II 10-Q 11/3/2022 10.9 10.61# Amended and Restated Offer Letter, dated March 31, 2023, between Ultragenyx Pharmaceutical Inc. and Eric Crombez, M.D. 10-Q 5/4/2023 10.2 10.62# Offer Letter, dated June 2, 2023, between Ultragenyx Pharmaceutical Inc. and Howard Horn 8-K 7/12/2023 10.1 10.63# Amendment, dated September 6, 2023, to the Offer Letter between Ultragenyx Pharmaceutical Inc. and Howard Horn 8-K 9/8/2023 10.1 10.64# Offer Letter, dated May 16, 2017, between Ultragenyx Pharmaceutical Inc. and Erik Harris 10-Q 8/2/2019 10.4 10.65# Addendum #1, dated August 8, 2017, to Offer Letter dated May 16, 2017 between Ultragenyx Pharmaceutical Inc. and Erik Harris 10-Q 8/2/2019 10.5 10.66# Addendum #2, dated June 19, 2019, to Offer Letter dated May 16, 2017 between Ultragenyx Pharmaceutical Inc. and Erik Harris 10-Q 8/2/2019 10.6 10.67# Amendment No. 3, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc. and Erik Harris 10-Q 11/3/2022 10.8 10.68# Form of Indemnification Agreement 10-K 3/24/2014 10.23 10.69 Standard Lease, dated as of July 5, 2011, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. S-1 11/8/2013 10.22 86 10.70 Addendum One to Standard Lease, dated as of July 5, 2011, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 10-K 2/26/2016 10.34 10.71 Addendum Two to Standard Lease, dated as of March 7, 2012, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 10-K 2/26/2016 10.35 10.72 Addendum #3 to Standard Lease, effective as of February 12, 2014, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 8-K 2/25/2014 10.1 10.73 Addendum #4 to Standard Lease, effective as of March 9, 2015, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 8-K 3/13/2015 10.1 10.74 Addendum #5 to Standard Lease, effective as of April 7, 2015, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 10-K 2/26/2016 10.38 10.75 Addendum #6 to Standard Lease, effective as of April 29, 2019, between Ultragenyx Pharmaceutical Inc. and Condiotti Enterprises, Inc. 10-Q 8/2/2019 10.3 10.76 Lease Agreement, dated as of December 8, 2015, between Marina Boulevard Property, LLC and Ultragenyx Pharmaceutical Inc. 10-K 2/26/2016 10.43 10.77 Lease Agreement, dated November 2, 2015, between Dimension Therapeutics, Inc. and ARE-MA Region No. 20, LLC, and Consent to Assignment to Ultragenyx Pharmaceutical Inc. 10-K 2/21/2018 10.66 10.78 First Amendment to Lease Agreement, dated March 20, 2018, between Ultragenyx Pharmaceutical Inc. and ARE-MA Region No. 20, LLC 10-Q 5/8/2018 10.6 10.79 Second Amendment to Lease Agreement, dated July 1, 2018, between Ultragenyx Pharmaceutical Inc. and ARE-MA Region No. 20, LLC 10-Q 8/3/2018 10.3 10.80 Third Amendment to the Lease Agreement, dated July 29, 2019, between Ultragenyx Pharmaceutical Inc. and ARE-MA Region No., LLC. 10-Q 7/30/2020 10.2 10.81 Amended and Restated Fourth Amendment, dated August 4, 2020, to the Lease Agreement between Ultragenyx Pharmaceutical Inc. and ARE-MA Region No., LLC. 10-Q 10/27/2020 10.5 10.82 Lease Agreement, dated December 15, 2019, between Ultragenyx Pharmaceutical Inc. and ARE-San Francisco No. 17, LLC. 10-K 2/12/2021 10.81 10.83 First Amendment, dated September 20, 2020, to the Lease Agreement between Ultragenyx Pharmaceutical Inc. and ARE-San Francisco No. 17, LLC. 10-K 2/12/2021 10.82 10.84 Second Amendment, dated October 21, 2020, to the Lease Agreement between Ultragenyx Pharmaceutical Inc. and ARE-San Francisco No. 17, LLC. 10-K 2/12/2021 10.83 10.85 Third Amendment, dated July 27, 2022, to the Lease Agreement between Ultragenyx Pharmaceutical Inc. and ARE-San Francisco No. 17, LLC 10-K 2/16/2023 10.92 87 10.86 Office Lease, dated April 19, 2019, between Ultragenyx Pharmaceutical Inc. and Woburn MCB II, LLC 10-K 2/14/2020 10.70 10.87 Commercial Lease, dated July 2, 2018, between Ultragenyx Pharmaceutical Inc. and 32 Leveroni LLC 10-K 2/14/2020 10.71 10.88 Lease, dated August 18, 2022, between Ultragenyx Pharmaceutical Inc. and Brickbottom I QOZB L.P. 10-K 2/17/2023 10.95 21.1 Subsidiaries of Ultragenyx Pharmaceutical Inc. X 23.1 Consent of Independent Registered Public Accounting Firm X 24.1 Power of Attorney (included on the signature page of this report) 31.1 Certification of Principal Executive Officer of Ultragenyx Pharmaceutical Inc., as required by Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 X 31.2 Certification of Principal Financial Officer of Ultragenyx Pharmaceutical Inc., as required by Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 X 32.1§ Certification by the Principal Executive Officer and Principal Financial Officer, as required by Rule 13a-14(b) or Rule 15d-14(b) and Section 1350 of Chapter 36 of Title 18 of the United States Code (18 U.S.C. §1350) X 97.1 Ultragenyx Pharmaceutical Inc. Clawback Policy X 101.INS XBRL Instance Document, formatted in Inline XBRL X 101.SCH Inline XBRL Taxonomy Extension Schema Document X 104 The cover page from this Annual Report on Form 10-K, formatted in Inline XBRL and contained in Exhibit 101 X * Certain identified information has been omitted by means of marking such information with asterisks in reliance on Item 601(b)(10)(iv) of Regulation S-K because it is both (i) not material and (ii) the type that the registrant treats as private or confidential. # Indicates management contract or compensatory plan. § The certification attached as Exhibit 32.1 that accompanies this Annual Report is not deemed filed with the SEC and is not to be incorporated by reference into any filing of Ultragenyx Pharmaceutical Inc. under the Securities Act or the Exchange Act, whether made before or after the date of this Annual Report, irrespective of any general incorporation language contained in such filing. Item 16. Form 10-K Summary None. 88 SIGN ATURES Pursuant to the requirements of Section 13 or 15(d) 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. U LTRAGENYX P HARMACEUTICAL I nc . By: /s/ Emil D. Kakkis Emil D. Kakkis, M.D., Ph.D. President and Chief Executive Officer (Principal Executive Officer) Date: February 21, 2024 PO WER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Emil D. Kakkis, M.D., Ph.D. and Howard Horn, and each of them, as his or her true and lawful attorneys-in-fact and agents, with full power of substitution for him or her, and in his or her name in any and all capacities, to sign any and all amendments to this Annual Report, and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done therewith, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, and any of them, his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof. Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated. Signature Title Date /s/ Emil D. Kakkis Emil D. Kakkis, M.D., Ph.D. President and Chief Executive Officer and Director (Principal Executive Officer) February 21, 2024 /s/ Howard Horn Howard Horn Executive Vice President, Chief Financial Officer, Corporate Strategy (Principal Financial Officer) February 21, 2024 /s/ Theodore A. Huizenga Theodore A. Huizenga Senior Vice President and Chief Accounting Officer (Principal Accounting Officer) February 21, 2024 /s/ Daniel G. Welch Daniel G. Welch Chairman of the Board February 21, 2024 /s/ Deborah Dunsire Deborah Dunsire, M.D. Director February 21, 2024 /s/ Matthew K. Fust Matthew K. Fust Director February 21, 2024 /s/ Michael Narachi Michael Narachi Director February 21, 2024 /s/ Amrit Ray Director February 21, 2024 Amrit Ray, M.D. /s/ Corsee D. Sanders Director February 21, 2024 Corsee D. Sanders, Ph.D. /s/ Shehnaaz Suliman Director February 21, 2024 Shehnaaz Suliman, M.D. 89 Ultragenyx Pharmaceutical Inc. INDEX TO FINANCIAL STATEMENTS Page Report of Independent Registered Public Accounting Firm (PCAOB ID: 42 ) F- 2 Consolidated Financial Statements: Consolidated Balance Sheets F- 4 Consolidated Statements of Operations F- 5 Consolidated Statements of Comprehensive Loss F- 5 Consolidated Statements of Stockholders’ Equity F- 6 Consolidated Statements of Cash Flows F- 7 Notes to Consolidated Financial Statements F- 9 F- 1 Report of Independent R egistered Public Accounting Firm To the Stockholders and the Board of Directors of Ultragenyx Pharmaceutical Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Ultragenyx Pharmaceutical Inc. (the Company) as of December 31, 2023 and 2022, the related consolidated statements of operations, comprehensive loss, stockholders' equity and cash flows for each of the three years in the period ended December 31, 2023, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2023 and 2022, and the results of its operations and its cash flows for each of the three years in the period ended December 31, 2023, in conformity with U.S. generally accepted accounting principles. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the Company's internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework), and our report dated February 21, 2024 expressed an unqualified opinion thereon. Basis for Opinion These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. Critical Audit Matter The critical audit matter communicated below is a matter arising from the current period audit of the financial statements that was communicated or required to be communicated to the audit committee and that: (1) relates to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective or complex judgments. The communication of the critical audit matter does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing a separate opinion on the critical audit matter or on the accounts or disclosures to which it relates. Liabilities for sales of future royalties Description of the Matter As discussed in Note 10, the Company has entered into two royalty purchase agreements, under which the Company sold its rights to receive royalty payments arising from the net sales of Crysvita in the European and North American markets in exchange for $320 million and $500 million, respectively. The proceeds from each transaction were recorded as liabilities that are being amortized using the effective interest method over the estimated lives of the respective arrangements. In order to determine the amortization of the liabilities, the Company is required to estimate the total amount of future royalty payments to be paid to the respective counterparty, subject to the capped amount, over the life of the arrangement. The Company estimates an imputed interest on the unamortized portion of the liability and records non-cash interest expense relating to the transaction. Auditing the Company’s liabilities related to the sale of future royalties was complex due to the subjective judgments required to forecast the expected royalty payments subject to each agreement. Specifically, the forecasted revenues of Crysvita involve significant estimation uncertainty given the limited historical Crysvita sales data. F- 2 How We Addressed the Matter in Our Audit We obtained an understanding, evaluated the design and tested the operating effectiveness of controls over the Company’s process of accounting for the liabilities related to the sale of future royalties, including controls over the Company’s estimates of projected sales of Crysvita in the European and North American markets. To test management’s estimates of the future royalties and the imputed effective interest rates, we performed audit procedures that included, among others, evaluating the reasonableness of management’s assumptions related to the treatable patient populations, estimated pricing and reimbursement, and the rate of adoption. We compared the significant assumptions with historical trends of actual sales, analyst expectations and performed sensitivity analyses of estimated future royalties to evaluate the changes in the future royalties on the implied effective interest rates. /s/ Ernst & Young LLP We have served as the Company’s auditor since 2012. San Mateo, California February 21, 2024 F- 3 ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED BA LANCE SHEETS (In thousands, except share and per share amounts) December 31, 2023 2022 ASSETS Current assets: Cash and cash equivalents $ 213,584 $ 132,944 Marketable debt securities 363,625 614,818 Accounts receivable, net 73,390 40,445 Inventory 33,969 26,766 Other assets 47,616 68,926 Total current assets 732,184 883,899 Property, plant, and equipment, net 290,566 259,726 Marketable debt securities 199,901 148,970 Intangible assets, net 166,271 160,105 Goodwill 44,406 44,406 Other assets 57,685 48,338 Total assets $ 1,491,013 $ 1,545,444 LIABILITIES AND STOCKHOLDERS' EQUITY Current liabilities: Accounts payable $ 42,114 $ 43,274 Accrued liabilities 196,486 204,678 Contract liabilities — 1,479 Lease liabilities 12,595 11,779 Liabilities for sales of future royalties 29,242 — Total current liabilities 280,437 261,210 Lease liabilities 30,574 19,814 Deferred tax liabilities 30,058 31,667 Liabilities for sales of future royalties 862,325 875,439 Other liabilities 12,205 4,820 Total liabilities 1,215,599 1,192,950 Commitments and contingencies (Notes 9 and 15) Stockholders’ equity: Preferred stock, par value of $ 0.001 per share— 25,000,000 shares authorized; nil outstanding in 2023 and in 2022 — — Common stock, par value of $ 0.001 per share— 250,000,000 shares authorized; outstanding— 82,315,590 in 2023 and 70,197,297 in 2022 82 70 Treasury stock, at cost, 9,559 in 2023 and nil in 2022 ( 432 ) — Deferred compensation obligation 432 — Additional paid-in capital 3,662,346 3,140,019 Accumulated other comprehensive income (loss) 647 ( 6,573 ) Accumulated deficit ( 3,387,661 ) ( 2,781,022 ) Total stockholders’ equity 275,414 352,494 Total liabilities and stockholders’ equity $ 1,491,013 $ 1,545,444 See accompanying notes. F- 4 ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED ST ATEMENTS OF OPERATIONS (In thousands, except share and per share amounts) Year Ended December 31, 2023 2022 2021 Revenues: Product sales $ 180,413 $ 118,927 $ 77,017 Royalty revenue 182,652 21,692 17,951 Collaboration and license 71,184 222,710 256,438 Total revenues 434,249 363,329 351,406 Operating expenses: Cost of sales 45,209 28,320 16,008 Research and development 648,449 705,789 497,153 Selling, general and administrative 309,799 278,139 219,982 Total operating expenses 1,003,457 1,012,248 733,143 Loss from operations ( 569,208 ) ( 648,919 ) ( 381,737 ) Interest income 26,688 11,074 1,928 Change in fair value of equity investments 397 ( 19,299 ) ( 42,063 ) Non-cash interest expense on liabilities for sales of future royalties ( 66,004 ) ( 43,015 ) ( 29,422 ) Other expense ( 337 ) ( 1,566 ) ( 1,687 ) Loss before income taxes ( 608,464 ) ( 701,725 ) ( 452,981 ) Benefit from (provision for) income taxes 1,825 ( 5,696 ) ( 1,044 ) Net loss $ ( 606,639 ) $ ( 707,421 ) $ ( 454,025 ) Net loss per share, basic and diluted $ ( 8.25 ) $ ( 10.12 ) $ ( 6.70 ) Shares used in computing net loss per share, basic and diluted 73,543,862 69,914,225 67,795,540 See accompanying notes. ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED STATEM ENTS OF COMPREHENSIVE LOSS (In thousands) Year Ended December 31, 2023 2022 2021 Net loss $ ( 606,639 ) $ ( 707,421 ) $ ( 454,025 ) Other comprehensive income (loss): Foreign currency translation adjustments 239 ( 724 ) ( 550 ) Unrealized gain (loss) on available-for-sale securities 6,981 ( 4,445 ) ( 1,543 ) Other comprehensive income (loss): 7,220 ( 5,169 ) ( 2,093 ) Total comprehensive loss $ ( 599,419 ) $ ( 712,590 ) $ ( 456,118 ) See accompanying notes. F- 5 ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED STATE MENTS OF STOCKHOLDERS’ EQUITY (In thousands, except share amounts) Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Treasury Deferred Compensation Total Stockholders' Shares Amount Capital Income (Loss) Deficit Stock Obligation Equity Balance as of December 31, 2020 66,818,520 $ 67 $ 2,773,195 $ 689 $ ( 1,619,576 ) $ — $ — $ 1,154,375 Issuance of common stock in connection with at-the-market offering, net of issuance costs 1,050,372 1 78,942 — — — — 78,943 Stock-based compensation — — 105,260 — — — — 105,260 Issuance of common stock under equity plan awards, net of tax 1,476,106 1 40,100 — — — — 40,101 Other comprehensive loss — — — ( 2,093 ) — — — ( 2,093 ) Net loss — — — — ( 454,025 ) — — ( 454,025 ) Balance as of December 31, 2021 69,344,998 $ 69 $ 2,997,497 $ ( 1,404 ) $ ( 2,073,601 ) $ — $ — $ 922,561 Stock-based compensation — — 131,710 — — — — 131,710 Issuance of common stock under equity plan awards, net of tax 852,299 1 10,812 — — — — 10,813 Other comprehensive loss — — — ( 5,169 ) — — — ( 5,169 ) Net loss — — — — ( 707,421 ) — — ( 707,421 ) Balance as of December 31, 2022 70,197,297 $ 70 $ 3,140,019 $ ( 6,573 ) $ ( 2,781,022 ) $ — $ — $ 352,494 Issuance of common stock and pre-funded warrants in connection with underwritten public offering, net of issuance costs 9,833,334 10 326,446 — — — — 326,456 Issuance of common stock in connection with at-the-market offering, net of issuance costs 1,175,584 1 53,298 — — — — 53,299 Stock-based compensation — — 134,169 — — — — 134,169 Issuance of common stock under equity plan awards, net of tax 1,109,375 1 8,414 — — — — 8,415 Deferred compensation — — — — — ( 432 ) 432 — Other comprehensive income — — — 7,220 — — — 7,220 Net loss — — — — ( 606,639 ) — — ( 606,639 ) Balance as of December 31, 2023 82,315,590 $ 82 $ 3,662,346 $ 647 $ ( 3,387,661 ) $ ( 432 ) $ 432 $ 275,414 See accompanying notes. F- 6 ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED STA TEMENTS OF CASH FLOWS (In thousands) Year Ended December 31, 2023 2022 2021 Operating activities: Net loss $ ( 606,639 ) $ ( 707,421 ) $ ( 454,025 ) Adjustments to reconcile net loss to net cash used in operating activities: Stock-based compensation 135,227 130,377 104,952 Acquired in-process research and development — 75,033 — Amortization of premium (discount) on marketable debt securities, net ( 12,842 ) 2,699 6,606 Depreciation and amortization 26,006 18,220 13,239 Change in fair value of equity investments ( 397 ) 19,299 42,063 Non-cash collaboration royalty revenue ( 69,364 ) ( 21,692 ) ( 17,951 ) Non-cash interest expense on liabilities for sales of future royalties 66,004 43,015 29,422 Other 2,300 ( 230 ) 235 Changes in operating assets and liabilities: Accounts receivable ( 22,778 ) ( 12,068 ) ( 5,432 ) Inventory ( 6,930 ) ( 9,701 ) ( 3,117 ) Other assets 15,325 3,798 ( 29,508 ) Accounts payable, accrued, and other liabilities 2,380 87,442 32,313 Contract liabilities, net ( 1,479 ) ( 7,597 ) ( 57,492 ) Deferred tax liabilities ( 1,619 ) ( 1,639 ) — Net cash used in operating activities ( 474,806 ) ( 380,465 ) ( 338,695 ) Investing activities: Purchase of property, plant, and equipment ( 44,267 ) ( 116,123 ) ( 73,093 ) Acquisition, net of cash acquired — ( 75,025 ) — Purchase of marketable debt securities ( 526,382 ) ( 614,735 ) ( 1,012,187 ) Proceeds from sale of marketable debt securities 50,672 84,275 92,896 Proceeds from sale of equity investments — 10,094 79,843 Proceeds from maturities of marketable debt securities 695,525 450,706 718,111 Payment for intangible asset ( 2,500 ) ( 30,000 ) — Other ( 5,048 ) ( 844 ) ( 942 ) Net cash provided by (used in) investing activities 168,000 ( 291,652 ) ( 195,372 ) Financing activities: Proceeds from the sale of future royalties, net — 490,950 — Proceeds from the issuance of common stock and pre-funded warrants in connection with underwritten public offerings, net of issuance costs 326,456 — — Proceeds from the issuance of common stock in connection with at-the-market offering, net of issuances costs 53,299 — 78,943 Proceeds from the issuance of common stock from exercise of warrants and equity plan awards, net 8,415 10,813 40,101 Other ( 28 ) ( 555 ) ( 492 ) Net cash provided by financing activities 388,142 501,208 118,552 Effect of exchange rate changes on cash 462 ( 1,075 ) ( 1,194 ) Net increase (decrease) in cash, cash equivalents, and restricted cash 81,798 ( 171,984 ) ( 416,709 ) Cash, cash equivalents, and restricted cash at beginning of year 137,601 309,585 726,294 Cash, cash equivalents, and restricted cash at end of year $ 219,399 $ 137,601 $ 309,585 F- 7 See accompanying notes. ULTRAGENYX PHARMACEUTICAL INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands) Year Ended December 31, 2023 2022 2021 Supplemental disclosures of non-cash investing and financing information: Acquired lease liabilities arising from obtaining right-of-use assets and property, plant, and equipment $ 22,162 $ 1,168 $ 3,142 Costs of property, plant and equipment included in accounts payable, accrued, and other liabilities $ 1,577 $ 17,963 $ 18,993 Non-cash interest expense on liabilities for sales of future royalties capitalized during the year into ending property, plant and equipment $ 9,431 $ 11,380 $ 4,650 See accompanying notes. F- 8 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements 1. Organizat ion and Basis of Presentation Ultragenyx Pharmaceutical Inc., or the Company, is a biopharmaceutical company incorporated in Delaware. The Company is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultrarare genetic diseases. The Company operates as one reportable segment and has four commercially approved products. Crysvita® (burosumab) is approved in the United States, or U.S., the European Union, or EU, and certain other regions for the treatment of X-linked hypophosphatemia, or XLH, in adult and pediatric patients one year of age and older. Crysvita is also approved in the U.S. and certain other regions for the treatment of fibroblast growth factor 23, or FGF23-related hypophosphatemia in tumor-induced osteomalacia, or TIO, associated with phosphaturic mesenchymal tumors that cannot be curatively resected or localized in adults and pediatric patients 2 years of age and older. Mepsevii® (vestronidase alfa) is approved in the U.S., the EU and certain other regions, as the first medicine for the treatment of children and adults with mucopolysaccharidosis VII, or MPS VII, also known as Sly syndrome. Dojolvi® (triheptanoin) is approved in the U.S. and certain other regions for the treatment of pediatric and adult patients severely affected by long-chain fatty acid oxidation disorders, or LC-FAOD. Evkeeza® (evinacumab) is approved in the U.S. and the European Economic Area, or EEA, for the treatment of homozygous familial hypercholesterolemia, or HoFH. The Company has exclusive rights to commercialize Evkeeza® (evinacumab) outside of the U.S. In addition to the approved products, the Company has the following ongoing clinical development programs: • UX111 (formerly ABO-102) is an AAV9 gene therapy product candidate for the treatment of patients with Sanfilippo syndrome type A, or MPS IIIA, a rare lysosomal storage disease; • DTX401 is an adeno-associated virus 8, or AAV8, gene therapy product candidate for the treatment of patients with glycogen storage disease type Ia, or GSDIa; • DTX301 is an AAV8 gene therapy product candidate in development for the treatment of patients with ornithine transcarbamylase, or OTC deficiency, the most common urea cycle disorder; • UX143 (setrusumab), which is subject to the Company ’ s collaboration agreement with Mereo BioPharma 3, or Mereo, is a fully human monoclonal antibody that inhibits sclerostin, a protein that acts on a key bone-signaling pathway and inhibits the activity of bone-forming cells for the treatment of patients with osteogenesis imperfect, or OI; • GTX-102 is an antisense oligonucleotide, or ASO for the treatment of Angelman syndrome, a debilitating and rare neurogenetic disorder caused by loss-of-function of the maternally inherited allele of the UBE3A gene.; and • UX701 is an adeno-associated virus 9, or AAV9, gene therapy designed to deliver stable expression of a truncated version of the ATP7B copper transporter following a single intravenous infusion to improve copper distribution and excretion from the body and reverse pathological findings of Wilson liver disease; The Company has sustained operating losses and expects such annual losses to continue over the next several years. The Company’s ultimate success depends on the outcome of its research and development and commercialization activities. Through December 31, 2023 , the Company has relied primarily on its sale of equity securities, its revenues from commercial products, its sale of future royalties, and strategic collaboration arrangements to finance its operations. The Company may need to raise additional capital to fully implement its business plans through the issuance of equity, borrowings, or strategic alliances with partner companies. However, if such financing is not available at adequate levels, the Company would need to reevaluate its operating plans. 2. Summary of Significant Accounting Policies Basis of Consolidation The Consolidated Financial Statements include the accounts of Ultragenyx Pharmaceutical Inc. and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated. ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Use of Estimates The accompanying Consolidated Financial Statements have been prepared in accordance with U.S. generally accepted accounting principles, or GAAP. The preparation of the Consolidated Financial Statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent liabilities and the reported amounts of expenses in the Consolidated Financial Statements and the accompanying notes. On an ongoing basis, management evaluates its estimates, including those related to clinical trial accruals, fair value of assets and liabilities, income taxes, stock-based compensation, revenue recognition, and the liabilities for sales of future royalties. Management bases its estimates on historical experience and on various other market-specific and relevant assumptions that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Cash, Cash Equivalents, and Restricted Cash The Company considers all highly liquid investments with original maturities of three months or less from the date of purchase to be cash equivalents. Cash equivalents consist primarily of amounts invested in money market accounts. Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility leases and the gene therapy building construction project. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the Consolidated Balance Sheets that sum to the total of the same such amounts shown in the Consolidated Statements of Cash Flows (in thousands): December 31, 2023 2022 2021 Cash and cash equivalents $ 213,584 $ 132,944 $ 307,584 Restricted cash included in other current assets 2,008 862 — Restricted cash included in other non-current assets 3,807 3,795 2,001 Total cash, cash equivalents, and restricted cash shown in the statements of cash flows $ 219,399 $ 137,601 $ 309,585 Marketable Debt Securities All marketable debt securities have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its investments at the time of purchase and reevaluates such designation as of each balance sheet date. Investments with a maturity of one year or less from the balance sheet date are reported as current marketable debt securities and investments with a maturity of greater than one year from the balance sheet date are reported as non-current marketable debt securities. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive loss. Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in other income (expense). The cost of securities sold is based on the specific-identification method. Interest on investments is included in interest income. Equity Investments The Company records investments in equity securities, other than equity method investments, at fair market value, if the fair value is readily determinable. Equity securities with no readily determinable fair values are recorded using the measurement alternative of cost adjusted for observable price changes in orderly transactions for identical or similar investments of the same issuer less impairment, if any. Investments in equity securities are recorded in Equity investments on the Company's Consolidated Balance Sheets. Unrealized gains and losses are reported in Change in fair value of equity investments on the Company’s Consolidated Statements of Operations. The Company regularly reviews its non-marketable equity securities for indicators of impairment. F- 10 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Concentration of Credit Risk, Credit Losses, and Other Risks and Uncertainties Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents, and investments. The Company’s cash, cash equivalents, and investments are held by financial institutions that management believes are of high credit quality. The Company’s investment policy limits investments to fixed income securities denominated and payable in U.S. dollars such as U.S. government obligations, money market instruments and funds, corporate bonds, commercial paper, and asset-backed securities and places restrictions on maturities and concentrations by type and issuer. Such deposits may, at times, exceed federally insured limits. The Company has not experienced any losses on its deposits of cash and cash equivalents and its accounts are monitored by management to mitigate risk. The Company is exposed to credit risk in the event of default by the financial institutions holding its cash and cash equivalents, corporate issuers, and other financial instruments, to the extent recorded in the Consolidated Balance Sheets. The Company is exposed to credit losses primarily through receivables from customers and collaborators and through its available-for-sale debt securities. For trade receivables and other instruments, the Company uses a forward-looking expected loss model that generally results in the earlier recognition of allowances for losses. For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities. The Company’s expected loss allowance methodology for the receivables is developed using historical collection experience, current and future economic market conditions, a review of the current aging status and financial condition of the entities. Specific allowance amounts are established to record the appropriate allowance for customers that have a higher probability of default. Balances are written off when determined to be uncollectible. The Company’s expected loss allowance methodology for the debt securities is developed by reviewing the extent of the unrealized loss, the size, term, geographical location, and industry of the issuer, the issuers’ credit ratings and any changes in those ratings, as well as reviewing current and future economic market conditions and the issuers’ current status and financial condition. There was no allowance for losses on available-for-sale debt securities which were attributable to credit risk for the years ended December 31, 2023 and 2022. The Company is dependent on third-party manufacturers to supply products for research and development activities in its programs. In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to these programs. These programs could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs. Inventory The Company values inventory at the lower of cost and net realizable value and determines the cost of inventory using the average-cost method. The Company expenses costs associated with the manufacture of product candidates prior to regulatory approval. Inventories consist of currently approved products. 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. Management determines excess inventory based on expected future demand. Estimates related to future demand are sensitive to significant inputs and assumptions such as acceptance by patients and physicians and the availability of formulary coverage and adequate reimbursement from private third-party payers for the product. Property, Plant, and Equipment Property, plant, and equipment are stated at cost, less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the respective assets. Depreciation and amortization begins when the asset is placed in service. Interest costs incurred during the construction of major capital projects are capitalized until the underlying asset is ready to be placed in service. Maintenance and repairs are charged to operations as incurred. Upon sale or retirement of assets, the cost and related accumulated depreciation or amortization are removed from the balance sheet and the resulting gain or loss, if any, is reflected in operations. See “Note 4. Balance Sheet Components” for further disclosure on the useful lives of property, plant, and equipment. Intangible Assets Finite-lived intangibles consist of contractual payments made for certain milestones achieved with collaboration partners. The contractual payments are recorded as intangible assets and are amortized over their estimated useful lives. The Company reviews its definite-lived intangible assets when events or circumstances may indicate that the carrying value of these assets is not recoverable and exceeds their fair value. The Company measures fair value based on the estimated future undiscounted cash flows associated with these assets in addition to other assumptions and projections that the Company deems to be reasonable and supportable. F- 11 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Indefinite-lived intangibles consist of acquired in-process research and development, or IPR&D. IPR&D assets represent capitalized incomplete research projects that the Company acquired through business combinations. Such assets are initially measured at their acquisition date fair values and are tested for impairment annually and whenever events or changes in circumstances indicate that the carrying amount may not be recoverable. When development of the project is complete, which generally occurs when regulatory approval to market a product is obtained, the associated assets will be deemed finite-lived and will be amortized over a period that best reflects the economic benefits provided by these assets. If it is determined that an intangible asset becomes impaired, the carrying value is written down to its fair value with the related impairment charge recognized in Consolidated Statements of Operations in the period in which the impairment occurs. The Company has not recorded any impairments of intangible assets to date. Goodwill Goodwill represents the excess of purchase price over fair value of net assets acquired in a business combination and is not amortized. Goodwill is subject to impairment testing at least annually during the fourth quarter or when a triggering event occurs that could indicate a potential impairment. If it is determined that the goodwill becomes impaired, the carrying value is written down to its fair value with the related impairment charge recognized in Consolidated Statements of Operations in the period in which the impairment occurs. The Company has not recorded any impairments of goodwill. Impairment of Long-Lived Assets The Company evaluates its long-lived assets, including property and equipment, for impairment whenever events or changes in circumstances indicate that the carrying value of these assets may not be recoverable. Recoverability of these assets is measured by comparison of the carrying amount of each asset to the future undiscounted cash flows expected to result from the use of the asset and its eventual disposition. If the asset is considered to be impaired, the amount of any impairment is measured as the difference between the carrying value and the fair value of the impaired asset. The Company has not recorded material impairment of any long-lived assets. Accruals of Research and Development Costs The Company records accruals for estimated costs of research, preclinical and clinical studies and manufacturing development. These costs are a significant component of the Company’s research and development expenses. A substantial portion of the Company’s ongoing research and development activities are conducted by third-party service providers, including contract research organizations. The Company accrues the costs incurred under its agreements with these third parties based on actual work completed in accordance with agreements established with these third parties. The Company determines the actual costs through obtaining information from external service providers as to the progress or stage of completion of the services and the agreed-upon fee to be paid for such services. Revenue Recognition Product Sales The Company sells its approved products through a limited number of distributors. Under ASC 606, revenue from product sales is recognized at the point in time when control is transferred to these distributors. The Company also recognizes revenue from sales of certain products on a “named patient” basis, which are allowed in certain countries prior to the commercial approval of the product. Prior to recognizing revenue, the Company makes estimates of the transaction price, including any variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Product sales are recorded net of estimated government-mandated rebates and chargebacks, estimated product returns, and other deductions. Provisions for returns and other adjustments are provided for in the period the related revenue is recorded, as estimated by management. These reserves are based on estimates of the amounts earned or to be claimed on the related sales and are reviewed periodically and adjusted as necessary. The Company’s estimates of government mandated rebates, chargebacks, estimated product returns, and other deductions depends on the identification of key customer contract terms and conditions, as well as estimates of sales volumes to different classes of payors. If actual results vary, the Company may need to adjust these estimates, which could have a material effect on earnings in the period of the adjustment. F- 12 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Collaboration, License, and Royalty Revenue The Company has certain license and collaboration agreements that are within the scope of Accounting Standards Codification, or ASC, 808, Collaborative Agreements , which provides guidance on the presentation and disclosure of collaborative arrangements. Generally, the classification of the transactions under the collaborative arrangements is determined based on the nature of contractual terms of the arrangement, along with the nature of the operations of the participants. The Company records its share of collaboration revenue, net of transfer pricing related to net sales in the period in which such sales occur, if the Company is considered as an agent in the arrangement. The Company is considered an agent when the collaboration partner controls the product before transfer to the customers and has the ability to direct the use of and obtain substantially all of the remaining benefits from the product. Funding received related to research and development services and commercialization costs is generally classified as a reduction of research and development expenses and selling, general and administrative expenses, respectively, in the Consolidated Statements of Operations, because the provision of such services for collaborative partners are not considered to be part of the Company’s ongoing major or central operations. The Company utilizes certain information from its collaboration partners to record collaboration revenue, including revenue from the sale of the product, associated reserves on revenue, and costs incurred for development and sales activities. For the periods covered in the financial statements presented, there have been no material changes to prior period estimates of revenues and expenses. The Company also records royalty revenues under certain of the Company’s license or collaboration agreements in exchange for license of intellectual property. The Company sold the right to receive certain royalty payments from net sales of Crysvita in certain territories to RPI Finance Trust, or RPI, an affiliate of Royalty Pharma, and to OCM LS23 Holdings LP, an investment vehicle for Ontario Municipal Employees Retirement System, or OMERS, as further described in “Note 10. Liabilities for Sales of Future Royalties.” The Company records the royalty revenue from the net sales of Crysvita in the applicable territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the applicable arrangement. The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities. The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers, or ASC 606, to determine the distinct performance obligations. The Company analogizes to ASC 606 for the accounting for distinct performance obligations for which there is a customer relationship. Prior to recognizing revenue, the Company makes estimates of the transaction price, including variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Total consideration may include nonrefundable upfront license fees, payments for research and development activities, reimbursement of certain third-party costs, payments based upon the achievement of specified milestones, and royalty payments based on product sales derived from the collaboration. If there are multiple distinct performance obligations, the Company allocates the transaction price to each distinct performance obligation based on its relative standalone selling price. The standalone selling price is generally determined based on the prices charged to customers or using expected cost-plus margin. The Company estimates the efforts needed to complete the performance obligations and recognizes revenue by measuring the progress towards complete satisfaction of the performance obligations using input measures. Deferred Compensation Plan The Company maintains a nonqualified deferred compensation plan whereby certain employees and members of the board of directors are able to defer certain equity awards and other compensation. Amounts deferred are invested into shares of the Company's common stock, mutual funds, and other investment options. The plan complies with the provisions of Section 409A of the Internal Revenue Code. All of the various mutual funds held in the plan are classified as trading securities and recorded at fair value in other non-current assets in the Consolidated Balance Sheets with changes in fair value recognized as earnings in the period they occur. The short-term portion of the corresponding liability for the plan is included in accrued expenses. The long-term portion of the liability is included in other non-current liabilities in the Consolidated Balance Sheets. Certain equity awards deferred under the plan are required to be settled through the issuance of Company stock. These awards are recorded as treasury stock and deferred compensation obligation within stockholders’ equity. Leases Lease agreements are evaluated to determine whether an arrangement is or contains a lease in accordance with ASC 842, Leases . The Company determines if an arrangement includes a lease at inception. Right-of-use lease assets and lease liabilities are F- 13 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) recognized based on the present value of the future minimum lease payments over the lease term at the commencement date. The right-of-use lease asset includes any lease payments made and excludes lease incentives. Incremental borrowing rate is used in determining the present value of future payments. The Company applies a portfolio approach to the property leases to apply an incremental borrowing rate to leases with similar lease terms. The lease terms may include options to extend or terminate the lease. The Company recognizes the options to extend the lease as part of the right-of-use lease assets and lease liabilities only if it is reasonably certain that the option would be exercised. Lease expense for minimum lease payments is recognized on a straight-line basis over the non-cancelable lease term. The Company has elected to not separate lease and non-lease components. See “Note 9. Leases” for further disclosure. Comprehensive Loss Comprehensive loss is the change in stockholders’ equity from transactions and other events and circumstances other than those resulting from investments by stockholders and distributions to stockholders. The Company’s other comprehensive loss is comprised of unrealized gains and losses on investments in available-for-sale securities and foreign currency translation adjustments. Research and Development Research and development costs are expensed as incurred and consist of salaries and benefits, stock-based compensation expense, lab supplies and facility costs, as well as fees paid to other nonemployees and entities that conduct certain research and development activities on the Company’s behalf. Amounts incurred in connection with license agreements are also included in research and development expense. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are deferred. The deferred amounts are expensed as the related goods are delivered or the services are performed. Stock-Based Compensation Stock-based awards issued to employees, including stock options, performance stock options, or PSOs, restricted stock units, or RSUs, and performance stock units, or PSUs are recorded at fair value as of the grant date and recognized as expense on a straight-line basis over the employee’s requisite service period (generally the vesting period). PSOs and PSUs vest only if certain specified criteria are achieved and the employees’ continued service requirements are met; therefore, the expense recognition occurs when the likelihood of the PSOs and PSUs being earned is deemed probable. Stock compensation expense on awards expected to vest is recognized net of estimated forfeitures. Income Taxes The Company uses the liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the differences between the financial reporting and the tax bases of assets and liabilities and are measured using the enacted tax rates and laws that will be in effect when the differences are expected to reverse. The Company must then assess the likelihood that the resulting deferred tax assets will be realized. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized. Due to the Company’s lack of earnings history, the net deferred tax assets have been fully offset by a valuation allowance. In conjunction with the acquisition of Dimension Therapeutics, Inc., or Dimension, a deferred tax liability was recorded reflecting the tax impact of the difference between the book basis and tax basis of acquired IPR&D. Such deferred income tax liability is not used to offset deferred tax assets when analyzing the Company’s valuation allowance as the acquired IPR&D is considered to have an indefinite life until the Company completes or abandons development of the acquired IPR&D. The Company recognizes benefits of uncertain tax positions if it is more likely than not that such positions will be sustained upon examination based solely on their technical merits, as the largest amount of benefit that is more likely than not to be realized upon the ultimate settlement. The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit. To date, there have been no interest or penalties charged in relation to the unrecognized tax benefits. F- 14 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Foreign Currency Assets and liabilities of non-U.S. subsidiaries that operate in a local currency environment, where the local currency is the functional currency, are translated to U.S. dollars at exchange rates in effect at the balance sheet date, with the resulting translation adjustments directly recorded to a separate component of accumulated other comprehensive loss. Income and expense accounts are translated at average exchange rates for the period. Transactions which are not in the functional currency of the entity are remeasured into the functional currency and gains or losses resulting from the remeasurement recorded in other income (expense). Net Loss per Share Basic net loss per share is calculated by dividing the net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Shares of common stock into which pre-funded warrants may be exercised are considered outstanding for the purposes of computing basic net loss per share because the shares may be issued for little or no consideration, are fully vested and are exercisable after the original issuance date. Diluted net loss per share is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive. In periods when we have incurred a net loss, options and warrants to purchase common stock are considered common stock equivalents, but have been excluded from the calculation of diluted net loss per share, as their effect is antidilutive. 3. Fair Value Measurements Financial assets and liabilities are recorded at fair value. The carrying amount of certain financial instruments, including cash and cash equivalents, accounts receivable, accounts payable and accrued liabilities approximate fair value due to their relatively short maturities. Assets and liabilities recorded at fair value on a recurring basis in the balance sheets are categorized based upon the level of judgment associated with the inputs used to measure their fair values. Fair value is defined as the exchange price that would be received for an asset or an exit price that would be paid to transfer a liability in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. The authoritative guidance on fair value measurements establishes a three-tier fair value hierarchy for disclosure of fair value measurements as follows: Level 1 —Inputs are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date; Level 2 —Inputs are observable, unadjusted quoted prices in active markets for similar assets or liabilities, unadjusted quoted prices for identical or similar assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities; and Level 3 —Unobservable inputs that are significant to the measurement of the fair value of the assets or liabilities that are supported by little or no market data. The Company’s financial instruments consist of Level 1, Level 2, and Level 3 assets. Where quoted prices are available in an active market, securities are classified as Level 1. Money market funds and U.S. Government treasury bills are classified as Level 1. Level 2 assets consist primarily of corporate bonds, asset backed securities, commercial paper, U.S. Government Treasury and agency securities, and debt securities in government-sponsored entities based upon quoted market prices for similar movements in active markets, quoted prices for identical or similar instruments in markets that are not active and model-based valuation techniques for which all significant inputs are observable in the market or can be corroborated by observable market data for substantially the full term of the assets. Where applicable these models project future cash flows and discount the future amounts to a present value using market-based observable inputs obtained from various third-party data providers, including but not limited to, benchmark yields, interest rate curves, reported trades, broker/dealer quotes and reference data. The Company determines the fair value of its equity investments in Solid Biosciences, Inc., or Solid, by using the quoted market prices, which are Level 1 fair value measurements. F- 15 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The following tables set forth the fair value of the Company’s financial assets remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands): December 31, 2023 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 162,289 $ — $ — $ 162,289 Certificates of deposit and time deposits — 17,986 — 17,986 Corporate bonds — 215,166 — 215,166 Commercial paper — 20,620 — 20,620 Asset-backed securities — 2,712 — 2,712 U.S. Government Treasury and agency securities 57,437 259,605 — 317,042 Investment in Solid common stock 3,204 — — 3,204 Deferred compensation assets — 10,220 — 10,220 Total financial assets $ 222,930 $ 526,309 $ — $ 749,239 Financial Liabilities: Deferred compensation liabilities $ — $ 10,365 $ — $ 10,365 December 31, 2022 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 102,847 $ — $ — $ 102,847 Certificates of deposit and time deposits — 25,972 — 25,972 Corporate bonds — 427,598 — 427,598 Commercial paper — 135,393 — 135,393 Asset-backed securities — 11,980 — 11,980 U.S. Government Treasury and agency securities 27,645 129,345 — 156,990 Debt securities in government-sponsored entities — 15,855 — 15,855 Investment in Solid common stock 2,807 — — 2,807 Deferred compensation assets — 4,575 — 4,575 Total financial assets $ 133,299 $ 750,718 $ — $ 884,017 Financial Liabilities: Deferred compensation liabilities $ — $ 4,657 $ — $ 4,657 Deferred compensation assets are recorded at fair value in other non-current assets in the Consolidated Balance Sheets. There have been no significant gains or losses on deferred compensation assets for the periods presented. Deferred compensation liabilities consist of short-term liabilities of $ 0.2 million and nil as of December 31, 2023 and 2022 , respectively, included in accrued liabilities on the Consolidated Balance Sheets, and long-term liabilities of $ 10.1 million and $ 4.7 million as of December 31, 2023 and 2022 , respectively, included in other non-current liabilities on the Consolidated Balance Sheets. F- 16 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) 4. Balance Sheet Components Cash Equivalents and Marketable Debt Securities The fair values of cash equivalents and marketable debt securities classified as available-for-sale securities consisted of the following (in thousands): December 31, 2023 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 162,289 $ — $ — $ 162,289 Certificates of deposit and time deposits 17,986 — — 17,986 Corporate bonds 214,792 711 ( 337 ) 215,166 Commercial paper 20,620 — — 20,620 Asset-backed securities 2,715 — ( 3 ) 2,712 U.S. Government Treasury and agency securities 316,160 982 ( 100 ) 317,042 Total $ 734,562 $ 1,693 $ ( 440 ) $ 735,815 December 31, 2022 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 102,847 $ — $ — $ 102,847 Certificates of deposit and time deposits 25,972 — — 25,972 Corporate bonds 432,211 87 ( 4,700 ) 427,598 Commercial paper 135,393 — — 135,393 Asset-backed securities 12,002 — ( 22 ) 11,980 U.S. Government Treasury and agency securities 157,933 320 ( 1,263 ) 156,990 Debt securities in government-sponsored entities 16,005 — ( 150 ) 15,855 Total $ 882,363 $ 407 $ ( 6,135 ) $ 876,635 At December 31, 2023 , the remaining contractual maturities of available-for-sale securities were less than three years . There have been no significant realized gains or losses on available-for-sale securities for the periods presented. Inventory Inventory consists of the following (in thousands): December 31, 2023 2022 Work-in-process $ 18,859 $ 17,486 Finished goods 15,110 9,280 Total inventory $ 33,969 $ 26,766 F- 17 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Property, Plant, and Equipment, net Property, plant, and equipment, net consists of the following (in thousands): December 31, Useful life (years) 2023 2022 Building 20 - 30 $ 181,356 $ 2,798 Leasehold improvements Shorter of lease term or estimated useful life 58,683 43,941 Research and development equipment 5 56,347 50,291 Furniture and office equipment 5 6,419 5,540 Computer equipment and software 3 - 5 16,196 13,876 Manufacturing equipment 5 - 15 37,297 570 Land Not applicable 16,619 16,619 Construction-in-progress Not applicable 867 189,448 Other Varies by asset 183 24 Property, plant, and equipment, gross 373,967 323,107 Less: accumulated depreciation ( 83,401 ) ( 63,381 ) Property, plant, and equipment, net $ 290,566 $ 259,726 Depreciation expense for the years ended December 31, 2023, 2022, and 2021 was $ 22.2 million, $ 15.0 million and $ 12.9 million, respectively. Amortization of leasehold improvements and software is included in depreciation expense. Construction in progress reflects amounts incurred for construction or improvements of property or costs for equipment that has not been placed in service. The construction-in-progress balance as of December 31, 2022 is primarily the construction costs for the gene therapy manufacturing facility in Bedford, Massachusetts. Accrued Liabilities Accrued liabilities consists of the following (in thousands): December 31, 2023 2022 Research, clinical study, and manufacturing expenses $ 65,326 $ 73,558 Payroll and related expenses 82,936 78,938 Other 48,224 52,182 Total accrued liabilities $ 196,486 $ 204,678 5. Intangible Assets, net Indefinite-lived Intangibles The Company has IPR&D assets of $ 129.0 million as of December 31, 2023 and 2022. IPR&D assets represent the fair value of acquired programs to develop an AAV gene therapy for OTC deficiency and to develop an AAV gene therapy for glycogen storage disease type Ia. The fair value of IPR&D assets acquired was determined based on the discounted present value of each research project’s projected cash flows using an income approach, including the application of probability factors related to the likelihood of success of the program reaching final development and commercialization. Additionally, the projections consider the relevant market sizes and growth factors, estimated future cash flows from product sales resulting from completed products and in-process projects and timing and costs to complete the in-process projects. The rates utilized to discount the net cash flows to their present value are commensurate with the stage of development of the projects and uncertainties in the economic estimates used in the projections. IPR&D assets are considered to be indefinite-life until the completion or abandonment of the associated research and development efforts. Finite-lived Intangibles F- 18 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Subsequent to the FDA approval of Dojolvi for the treatment of LC-FAOD in 2020, the Company recorded $ 4.8 million for the attainment of various development and commercial milestones as finite-lived intangible assets which are amortized over a weighted-average useful life of 5.7 years. In January 2022, the Company announced a collaboration with Regeneron to commercialize Evkeeza for HoFH outside of the U.S. Upon closing of the transaction in January 2022, the Company paid Regeneron a $ 30.0 million upfront payment. During the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved. As both the upfront payment and the regulatory milestone are related to the Company’s use of intellectual property for Evkeeza for HoFH, these amounts were recorded as intangible assets, which are amortized over a weighted-average useful life of ten years . The Company's intangible assets were as follows: December 31, 2023 Gross Carrying Amount Weighted-Average Life (Years) Accumulated Amortization Net Carrying Amount Indefinite-lived intangibles $ 129,000 — $ — $ 129,000 Finite-lived intangibles 44,775 9.6 ( 7,504 ) 37,271 Total intangible assets $ 173,775 — $ ( 7,504 ) $ 166,271 December 31, 2022 Gross Carrying Amount Weighted-Average Life (Years) Accumulated Amortization Net Carrying Amount Indefinite-lived intangibles $ 129,000 — $ — $ 129,000 Finite-lived intangibles 34,775 9.9 ( 3,670 ) 31,105 Total intangible assets $ 163,775 — $ ( 3,670 ) $ 160,105 The Company recorded costs of sales of $ 3.8 million, $ 3.2 million and $ 0.3 million for the years ended December 31, 2023, 2022, and 2021, respectively, related to the amortization of the intangible assets. The expected amortization of the intangible assets, as of December 31, 2023, for each of the next five years and thereafter is as follows: 2024 $ 4,903 2025 4,903 2026 4,903 2027 4,462 2028 4,022 Thereafter 14,078 Total $ 37,271 F- 19 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) 6. Revenue The following table disaggregates total revenues from external customers by product sales, royalty revenue, and collaboration and license revenue (in thousands): Year Ended December 31, 2023 2022 2021 Product sales: Crysvita $ 75,697 $ 42,678 $ 21,422 Mepsevii 30,441 20,637 16,035 Dojolvi 70,633 55,612 39,560 Evkeeza 3,642 — — Total product sales 180,413 118,927 77,017 Crysvita royalty revenue 182,652 21,692 17,951 Collaboration and license revenue: Crysvita collaboration revenue in Profit-Share Territory 69,705 215,024 171,198 Crysvita royalty revenue in European Territory — — 244 Daiichi Sankyo 1,479 7,686 84,996 Total collaboration and license revenue 71,184 222,710 256,438 Total revenues $ 434,249 $ 363,329 $ 351,406 The following table disaggregates total revenues based on geographic location (in thousands): Year Ended December 31, 2023 2022 2021 North America $ 307,149 $ 281,088 $ 301,110 Latin America 77,342 44,711 23,636 Europe 47,534 36,369 26,660 Japan 2,224 1,161 — Total revenues $ 434,249 $ 363,329 $ 351,406 The following table presents the activity and ending balances for sales-related accruals and allowances (in thousands): Year Ended December 31, 2023 2022 2021 Balance of product sales reserve at beginning of year $ 11,487 $ 7,181 $ 3,913 Provisions 18,761 13,525 9,586 Payments ( 12,746 ) ( 9,613 ) ( 6,120 ) Adjustments ( 473 ) 394 ( 198 ) Balance of product sales reserve at end of year $ 17,029 $ 11,487 $ 7,181 The following table presents changes in the contract liabilities for the years ended December 31, 2023 and 2022 (in thousands): Year Ended December 31, 2023 2022 Balance of contract liabilities at beginning of period $ 1,479 $ 9,076 Additions — 89 Deductions ( 1,479 ) ( 7,686 ) Balance of contract liabilities at end of period, net $ — $ 1,479 F- 20 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) See Note 8 for additional details on contract liabilities activities. The Company’s largest accounts receivable balance was from a collaboration partner and was 53 % and 68 % of the total accounts receivable balance as of December 31, 2023 and 2022 , respectively. 7. GeneTx Acquisition In August 2019, the Company entered into a Program Agreement and a Unitholder Option Agreement with GeneTx Biotherapeutics LLC, or GeneTx, to collaborate on the development of GeneTx’s GTX-102, an ASO for the treatment of Angelman syndrome. In July 2022, pursuant to the terms of the Unitholder Option Agreement, as amended, the Company exercised the option to acquire GeneTx and entered into a Unit Purchase Agreement, or the Purchase Agreement, pursuant to which the Company purchased all the outstanding units of GeneTx. In accordance with the terms of the Purchase Agreement, the Company paid the option exercise price of $ 75.0 million and an additional $ 15.6 million to acquire the outstanding cash of GeneTx, and adjustments for working capital and transaction expenses of $ 0.6 million, for a total purchase consideration of $ 91.2 million. The Company may be required to make payments of up to $ 190.0 million upon the achievement of certain milestones, including up to $ 30.0 million in milestone payments upon achievement of the earlier of initiation of a Phase 3 clinical study or product approvals in Canada and the U.K., up to $ 85.0 million in additional regulatory approval milestones for the achievement of U.S. and EU product approvals, and up to $ 75.0 million in commercial milestone payments based on annual worldwide net product sales. The Company will also pay tiered mid- to high single-digit percentage royalties based on licensed product annual net sales. If the Company receives and resells an FDA priority review voucher, or PRV, in connection with a new drug application approval, GeneTx is entitled to receive a portion of proceeds from the sale or a cash payment from the Company if the Company choses to retain the PRV. As part of the Company's acquisition of GeneTx, the Company assumed a License Agreement with Texas A&M University, or TAMU. Under this agreement, TAMU is eligible to receive from the Company up to $ 23.5 million upon the achievement of various future milestones, a nominal annual license fee that may increase up to a maximum of $ 2.0 million, as well as royalties in the mid-single-digits of net sales. The transaction was accounted as an asset acquisition, as substantially all of the fair value of the gross assets acquired was concentrated in a single identifiable in-process research and development intangible asset. Prior to the achievement of certain development and regulatory milestones, the acquired in-process research and development intangible asset has not yet reached technological feasibility and has no alternative future use. Accordingly, the Company recorded the acquisition price of $ 75.0 million, net of cash and working capital acquired, as in-process research and development expense during the year ended December 31, 2022. 8. License and Research Agreements Kyowa Kirin Co., Ltd. In August 2013, the Company entered into a collaboration and license agreement with Kyowa Kirin Co., Ltd., or KKC. Under the terms of this collaboration and license agreement, as amended, the Company and KKC collaborate on the development and commercialization of Crysvita in the field of orphan diseases in the U.S. and Canada, or the Profit-Share Territory, and in the European Union, United Kingdom, and Switzerland, or the European Territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America. Development Activities In the field of orphan diseases, except for ongoing studies being conducted by KKC, the Company was the lead party for development activities in the Profit-Share Territory and in the European Territory until the applicable transition date. The Company shared the costs for development activities in the Profit-Share Territory and the European Territory conducted pursuant to the development plan before the applicable transition date equally with KKC. In April 2023, which was the transition date for the Profit-Share Territory, KKC became the lead party and became responsible for the costs of the subsequent development activities. However, the Company will continue to equally share in the costs of the studies with KKC that commenced prior to the applicable transition date. The collaboration and license agreements are within the scope of ASC 808, which provides guidance on the presentation and disclosure of collaborative arrangements. Collaboration and Royalty Revenue for Sales in the Profit-Share Territory The Company and KKC shared commercial responsibilities and profits in the Profit-Share Territory until April 2023. Under the collaboration agreement, KKC manufactured and supplied Crysvita for commercial use in the Profit-Share Territory and charged the Company a transfer price of 30 % of net sales in 2023, and 35 % prior to December 31, 2022. The remaining profit or loss after supply F- 21 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) costs from commercializing products in the Profit-Share Territory was shared between the Company and KKC on a 50 / 50 basis until April 2023. In April 2023, commercialization responsibilities for Crysvita in the Profit-Share Territory transitioned to KKC. Thereafter, the Company is entitled to receive a tiered double-digit revenue share from the mid- 20 % range up to a maximum rate of 30 %. In 2022, the Company entered into an amendment to the collaboration agreement which granted the Company the right to continue to support KKC in commercial field activities in the U.S. through April 2024, subject to the limitations and conditions set forth in the amendment. The parties subsequently mutually agreed to extend the Company's right to continue to support KKC in commercial field activities in the U.S. through December 31, 2024, and as a result, the Company will continue to support commercial field efforts in the U.S. through a cost share arrangement through December 2024. After December 31, 2024, the Company’s rights to promote Crysvita in the U.S. will be limited to medical geneticists and the Company will solely bear its expenses for the promotion of Crysvita in the Profit-Share Territory. As KKC was the principal in the sale transaction with the customer during the profit-share period, the Company recognized a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs. The Company concluded that its portion of KKC’s sales in the Profit-Share Territory prior to April 2023 was analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty. Starting in April 2023, the Company began to record the royalty revenue as the underlying sales occur. In July 2022, the Company sold to OMERS its right to receive 30 % of the future royalty payments due to the Company based on net sales of Crysvita in the U.S. and Canada, subject to a cap, beginning in April 2023, as further described in Note 10. The Company records this revenue as royalty revenue. Product Sales Revenue for Other Territories The Company is responsible for commercializing Crysvita in Latin America and Turkey. The Company is considered the principal in these territories as the Company controls the product before it is transferred to the customer. Accordingly, the Company records revenue on a gross basis for the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor. KKC has the option to assume responsibility for commercialization efforts in Turkey from the Company, after a certain minimum period. Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in Latin American territories and charges the Company a transfer price of 30 % of net sales. The transfer price on these sales was 35 % prior to December 31, 2022. The Company also pays to KKC a low single-digit royalty on net sales in Latin America. Total Crysvita revenue was as follows (in thousands): Year Ended December 31, 2023 2022 2021 Revenue in profit-share territory: Collaboration revenue $ 69,705 $ 215,024 $ 171,198 Royalty revenue 113,288 — — Non-cash royalty revenue 48,581 — — Total revenue in Profit-Share Territory 231,574 215,024 171,198 Product sales 75,697 42,678 21,422 Royalty revenue in European Territory — — 244 Non-cash royalty revenue in European Territories 20,783 21,692 17,951 Total Crysvita revenue $ 328,054 $ 279,394 $ 210,815 Royalty Revenue for Sales in the European Territory KKC has the commercial responsibility for Crysvita in the European Territory. In December 2019, the Company sold its right to receive royalty payments based on sales in the European Territory to Royalty Pharma, effective January 1, 2020, as further described in Note 10. Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10 % on net sales in the European Territory, which was recognized as the underlying sales occur. Beginning in 2020, the Company records the royalty revenue as non-cash royalty revenues. The Company records this revenue as royalty revenue. F- 22 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Collaboration Cost Sharing and Payments Under the collaboration agreement, KKC and the Company share certain development and commercialization costs and as a result, the Company was reimbursed for these costs and operating expenses were reduced. Additionally, KKC is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to KKC in cost of sales. These amounts were recognized in the Company’s Statements of Operations in connection with the collaboration agreement with KKC as follows (in thousands): Year Ended December 31, 2023 2022 2021 Research and development $ ( 6,510 ) $ ( 15,974 ) $ ( 21,657 ) Selling, general and administrative $ ( 17,199 ) $ ( 37,217 ) $ ( 32,629 ) Cost of sales $ 18,476 $ 13,250 $ 6,701 Collaboration Receivable and Payable The Company had accounts receivable from KKC in the amount of $ 39.2 million and $ 27.5 million from profit-share revenue and royalties and other receivables recorded in other current assets of $ 1.1 million and $ 6.4 million and accrued liabilities of $ 5.3 million and $ 3.1 million from commercial and development activity reimbursements, as of December 31, 2023 and 2022, respectively. Saint Louis University In November 2010, the Company entered into a license agreement with Saint Louis University, or SLU. Under the terms of this license agreement, SLU granted the Company an exclusive worldwide license to make, have made, use, import, offer for sale, and sell therapeutics related to SLU’s beta-glucuronidase product for use in the treatment of human diseases. The Company made a milestone payment of $ 0.1 million upon approval of Mepsevii for treatment of MPS 7. The Company is required to pay to SLU a low single-digit royalty on net sales of the licensed products in any country or region, upon reaching a certain level of cumulative worldwide sales of the product. Baylor Research Institute In September 2012, the Company entered into a license agreement with Baylor Research Institute, or BRI. Under the terms of this license agreement, as amended, BRI exclusively licensed to the Company its territories for certain intellectual property related to Dojolvi (triheptanoin) for the treatment of LC-FAOD. For the years ended December 31, 2023 and 2022 , the Company recorded nil and $ 2.5 million, respectively, for the attainment of various development and commercial milestones as finite-lived intangible assets. The Company is obligated to make additional future payments of up to $ 7.5 million contingent upon attainment of various development and commercial milestones. Additionally, the Company is paying BRI a mid- single-digit royalty on net sales of the licensed product in the licensed territories. REGENXBIO, Inc. The Company has a license agreement with REGENXBIO, Inc., or REGENX, for an exclusive, sublicensable, worldwide commercial license under certain intellectual property for preclinical and clinical research and development, and commercialization of drug therapies using REGENX's licensed patents for the treatment of hemophilia A, OTC deficiency, and GSD1a. The Company will pay an annual fee and certain milestone fees per disease indication, low to mid- single-digit royalty percentages on net sales of licensed products, and milestone and sublicense fees owed by REGENX to its licensors, contingent upon the attainment of certain development activities as outlined in the agreement. The Company also has an option and license agreement with REGENX under which the Company has an exclusive, sublicensable, worldwide license to make, have made, use, import, sell, and offer for sale licensed products to treat Wilson disease and CDKL5 deficiency. For each disease indication, the Company is obligated to pay an annual maintenance fee of $ 0.1 million and up to $ 9.0 million upon achievement of various milestones, as well as mid- to high single-digit royalties on net sales of licensed products and mid- single-digit to low double-digit percentage sublicenses fees, if any. In March 2020, the Company entered into a license agreement with REGENX, for an exclusive, sublicensable, worldwide license to REGENX’s NAV AAV8 and AAV9 vectors for the development and commercialization of gene therapy treatments for a rare metabolic disorder. In return for these rights, the Company made an upfront payment of $ 7.0 million. The Company will pay certain F- 23 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) annual fees of $ 0.1 million, milestone payments of up to $ 14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty. Bayer HealthCare LLC The Company previously had a collaboration and license agreement with Bayer Healthcare LLC, or Bayer, to research, develop and commercialize AAV gene therapy products for the treatment of hemophilia A, or DTX 201. Under this agreement, Bayer had been granted an exclusive license to develop and commercialize one or more novel gene therapies for hemophilia A. In October 2022, the Collaboration and License Agreement for DTX201 with Bayer was terminated and all licensed rights to DTX201 have reverted back to the Company. The Company also obtained rights to all necessary data and information to further develop DTX201 or another hemophilia A program through a royalty-free, worldwide, sublicensable, perpetual license. University of Pennsylvania The Company has a research, collaboration, and license agreement with University of Pennsylvania School of Medicine, or Penn, which provides the terms for the Company and Penn to collaborate with respect to the pre-clinical development of gene therapy products for the treatment of certain indications. Under the agreement, Penn granted the Company an exclusive, worldwide license to certain patent rights arising out of the research program, subject to certain retained rights, and a non-exclusive, worldwide license to certain Penn intellectual property, in each case to research, develop, make, have made, use, sell, offer for sale, commercialize and import licensed products in each indication for the term of the agreement. The Company will fund the cost of the research program in accordance with a mutually agreed-upon research budget and will be responsible for clinical development, manufacturing and commercialization of each indication. The Company may be obligated to make milestone payments of up to $ 5.0 million for each indication, if certain development milestones are achieved over time. The Company is also obligated to make milestone payments of up to $ 25.0 million per approved product if certain commercial milestones are achieved, as well as low to mid- single-digit royalties on net sales of each licensed product. Arcturus Therapeutics Holdings Inc. In October 2015, the Company entered into a Research Collaboration and License Agreement with Arcturus Therapeutics Holdings Inc., or Arcturus, to collaborate on the research and development of therapies for select rare diseases. Arcturus was responsible for conducting certain research services, funded by the Company, and the Company was responsible for development and commercialization costs. On a product-by-product basis, the Company is obligated to make development and regulatory milestone payments of up to $ 24.5 million, and commercial milestone payments of up to $ 45.0 million if certain milestones are achieved. For the year ended December 31, 2021, the Company achieved a $ 1.0 million development milestone, which was paid with a corresponding credit received from Arcturus for prior research and collaboration activities. The Company is also obligated to pay Arcturus royalties on any net sales of products incorporating the licensed intellectual property that may range from a mid- single-digit to low double-digit percentage. There were no material expenses for this arrangement during the years ended December 31, 2023, 2022, and 2021. In June 2019, the Company entered into an Equity Purchase Agreement and an amendment to the Research Collaboration and License Agreement, or License Agreement, to expand the field of use and increase the number of disease targets to include mRNA, DNA and siRNA therapeutics for up to 12 rare diseases. Pursuant to the agreements, the Company paid $ 6.0 million in cash upfront to Arcturus and purchased 2,400,000 shares of Arcturus’ common stock at a stated value of $ 10.00 per share, resulting in a total of $ 30.0 million of consideration paid at the close of the transaction. As a result, the Company received expanded license rights under the License Agreement, Arcturus common stock, and an option to purchase an additional 600,000 shares of Arcturus’ common stock at $ 16.00 per share. In May 2020, the Company exercised its option to purchase 600,000 shares of Arcturus common stock for a total purchase price of $ 9.6 million. The Company’s investment in Arcturus was accounted at fair value, as the fair value was readily determinable. During the year ended December 31, 2022, the Company sold 500,000 shares of Arcturus common stock, at a weighted-average price of $ 20.39 per share. As of December 31, 2022, the Company held no shares of Arcturus common stock. F- 24 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The changes in the fair value of the Company’s equity investment in Arcturus were as follows (in thousands): Arcturus Common Stock December 31, 2021 $ 18,505 Change in fair value ( 8,411 ) Sale of shares ( 10,094 ) December 31, 2022 $ — Daiichi Sankyo In March 2020, the Company executed a License and Technology Access Agreement, or the License Agreement, with Daiichi Sankyo Co., Ltd., or Daiichi Sankyo. Pursuant to the License Agreement, the Company granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to its Pinnacle PCL TM producer cell line platform, or Pinnacle PCL Platform, and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products. Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $ 125.0 million and an additional $ 25.0 million upon completion of the technology transfer of the Pinnacle PCL Platform and HEK293 platform. Daiichi Sankyo reimbursed the Company for all costs associated with the transfer of the manufacturing technology. The Company also entered into a Stock Purchase Agreement, or SPA, with Daiichi Sankyo, pursuant to which Daiichi Sankyo purchased 1,243,913 shares of the Company’s common stock in exchange for $ 75.0 million in cash during the first quarter of 2020. The fair market value of the common stock issued to Daiichi Sankyo was $ 55.3 million based on the stock price of $ 44.43 per share on the date of issuance, resulting in a $ 19.7 million premium on the SPA. In June 2020, the Company executed a subsequent license agreement, or the Sublicense Agreement, with Daiichi Sankyo for transfer of certain technology in consideration for an upfront payment of $ 8.0 million and annual maintenance fees, milestone payments, and royalties on any net sales of products incorporating the licensed intellectual property. The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its Pinnacle PCL Platform and HEK293 transient transfection manufacturing technology platform together with the initial technical assistance and technology transfer services, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer period. The Company allocated the total transaction price to the two performance obligations on a relative stand-alone selling price basis. Revenue allocated to the intellectual property and the technology transfer services was recognized over an initial period which was completed during the first quarter of 2022, measuring the progress toward complete satisfaction of the individual performance obligation using an input measure. Revenue for know-how and improvements after the completion of technology transfer was recognized on a straight-line basis over the remaining technology transfer period, which ended in March 2023, as it was expected that Daiichi Sankyo would receive and consume the benefits consistently throughout the period. The Company’s current obligations under the License Agreement and the Sublicense Agreement were completed following the conclusion of the technology transfer period. Total revenue recognized under the arrangement through December 31, 2023 was $ 183.3 million. The Company recognized $ 1.5 million, $ 7.7 million, and $ 85.0 million for the years ended December 31, 2023, 2022, and 2021 , respectively, in revenue related to this arrangement. Accordingly, the Company recorded contract liabilities of nil and $ 1.5 million, net, for this arrangement as of December 31, 2023 and 2022, respectively. Mereo In December 2020, the Company entered into a License and Collaboration Agreement with Mereo to collaborate on the development of setrusumab. Under the terms of the agreement, the Company will lead future global development of setrusumab in both pediatric and adult patients with OI. The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Turkey, and the rest of the world, excluding the European Economic Area, United Kingdom, and Switzerland, or the F- 25 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Mereo Territory, where Mereo retains commercial rights. Each party will be responsible for post-marketing commitments and commercial supply in their respective territories. Upon the closing of the transaction in January 2021, the Company made a payment of $ 50.0 million to Mereo and will be required to make payments of up to $ 254.0 million upon the achievement of certain clinical, regulatory, and commercial milestones. The Company will pay for all global development costs as well as tiered double-digit percentage royalties to Mereo on net sales in the U.S., Turkey, and the rest of the world (excluding the Mereo Territory), and Mereo will pay the Company a fixed double-digit percentage royalty on net sales in the Mereo Territory. Although Mereo is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Mereo. Prior to the achievement of certain development milestones, all consideration paid to Mereo represents rights to potential future benefits associated with Mereo’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. For the years ended December 31, 2023, 2022, and 2021 , the Company recorded research and development expense of $ 9.0 million for the achievement of a clinical milestone, nil , and $ 50.0 million for the upfront payment, respectively. Regeneron In January 2022, the Company announced a collaboration with Regeneron Pharmaceuticals, or Regeneron, to commercialize Evkeeza for HoFH outside of the U.S. Evkeeza is approved in the U.S., where it is marketed by Regeneron, and in the EU and U.K. as a first-in-class therapy for use together with diet and other low-density lipoprotein-cholesterol-lowering therapies to treat adults and adolescents aged 12 years and older with HoFH. Pursuant to the terms of the agreement, the Company received the rights to develop, commercialize and distribute the product for HoFH in countries outside of the U.S. The Company is obligated to pay up to $ 63.0 million in future milestone payments, contingent upon the achievement of certain regulatory and sales milestones. The Company may share in certain costs for global trials led by Regeneron and also received the right to opt into other potential indications. The collaboration agreement is within the scope of ASC 808 which provides guidance on the presentation and disclosure of collaborative arrangements. As the Company would be the principal in future sale transactions with the customer, the Company will recognize product sales and cost of sales in the period the related sales occur and the related revenue recognition criteria are met. Under the collaboration agreement, Regeneron supplies the product and charges the Company a transfer price from the low 20 % range up to 40 % on net sales, which is recognized as cost of sales in the Company’s Statement of Operations. The Company paid Regeneron a $ 30.0 million upfront payment upon the closing of the transaction in January 2022, and d uring the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved. As these payments are for the Company’s use of intellectual property for Evkeeza for HoFH, they were recorded as intangible assets. See Note 5 for additional details. Under the collaboration agreement, the Company reimbursed Regeneron for development costs of $ 7.6 million, $ 7.3 million, and nil for the years ended December 31, 2023, 2022, and 2021, respectively, which were recorded as research and development expense on the Consolidated Statements of Operations. The Company had collaboration payables for this arrangement included in accrued liabilities on the Consolidated Balance Sheets of $ 10.6 million and $ 6.8 million as of December 31, 2023 and December 31, 2022, respectively. A dditionally, Regeneron is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to Regeneron of $ 0.7 million in cost of sales on the Consolidated Statements of Operations for the year ended December 31, 2023. Abeona In May 2022, the Company announced an exclusive License Agreement for the AAV gene therapy for UX111 with Abeona for the treatment of MPS IIIA. Under the terms of the agreement, the Company assumed responsibility for the UX111 program and in return, Abeona is eligible to receive tiered royalties of up to 10 % on net sales and commercial milestone payments of up to $ 30.0 million following regulatory approval of the product. Additionally, the Company entered into an Assignment and Assumption Agreement with Abeona to transfer and assign to the Company the exclusive license agreement between Nationwide Children’s Hospital, or NCH, and Abeona for certain rights related to UX111. Under this agreement, NCH is eligible to receive from the Company up to $ 1.0 million in development and regulatory milestones as well as royalties in the low single-digits of net sales. F- 26 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The Company is obligated to pay Abeona certain prior development costs and other transition costs related to UX111. Prior to product regulatory approval, all consideration paid to Abeona represents rights to potential future benefits associated with Abeona’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, the value of the acquired intellectual property rights and clinical inventory as well as prior development costs and transition costs of $ 3.1 million, were recorded as research and development expense for the year ended December 31, 2022. The Company did no t incur any other material costs related to this agreement in the years presented. Solid Biosciences, Inc. In October 2020, the Company entered into a strategic Collaboration and License Agreement with Solid Biosciences Inc., or Solid, and received an exclusive license for any pharmaceutical product that expresses Solid’s proprietary microdystrophin construct from AAV8 and variants thereof in clade E for use in the treatment of Duchenne muscular dystrophy and other diseases resulting from lack of functional dystrophin, including Becker muscular dystrophy. The Company is collaborating to develop products that combine Solid’s differentiated microdystrophin construct, the Company’s Pinnacle PCL Platform, and the Company’s AAV8 variants. Solid is providing development support and was granted an exclusive option to co-invest in products the Company develops for profit-share participation in certain territories. On a product-by-product basis, the Company is obligated to make development milestone payments of up to $ 25.0 million, regulatory milestone payments of up to $ 65.0 million, and commercial milestone payments of up to $ 165.0 million, if such milestones are achieved, as well as royalties on any net sales of products incorporating the licensed intellectual property that range from a low to mid-double-digit percentage. The royalty rate changes to mid- to high double-digit percentage if Solid decides to co-invest in the product. The Company also entered into a Stock Purchase Agreement and the Investor Agreement with Solid, pursuant to which, the Company purchased 7,825,797 shares of Solid’s common stock for an aggregate purchase price of $ 40.0 million. In October 2022, Solid announced a 1 for 15 reverse stock split. After the split, the Company held 521,719 shares of Solid's common stock. The Company’s investment in Solid is being accounted at fair value, as the fair value is readily determinable. The Company recorded the common stock investment at $ 26.8 million on the transaction date, which was based on the quoted market price on the closing date. Although Solid is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Solid. Prior to the achievement of certain development milestones, all consideration paid to Solid represents rights to potential future benefits associated with Solid’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, the remaining $ 13.2 million of the total $ 40.0 million paid as consideration was attributed to the license rights obtained and was recorded as in-process research and development expense during the year ended December 31, 2020. The changes in the fair value of the Company’s investment in Solid’s common stock were as follows (in thousands): Solid Common Stock December 31, 2021 $ 13,695 Change in fair value ( 10,888 ) December 31, 2022 2,807 Change in fair value 397 December 31, 2023 $ 3,204 9. Leases The Company leases office space and research, testing and manufacturing laboratory space in various facilities in Novato and Brisbane, California, in Somerville, and Woburn, Massachusetts, and in certain foreign countries, under operating agreements expiring at various dates through 2029 . Certain lease agreements include options for the Company to extend the lease for multiple renewal periods and provide for annual minimum increases in rent, usually based on a consumer price index or annual minimum increases. None of these optional periods have been considered in the determination of the right-of-use lease asset or the lease liability for the leases as the Company did not consider it reasonably certain that it would exercise any such options. The Company recognizes lease expense on a straight-line basis over the non-cancelable term of its operating leases. The variable lease expense primarily consists of common area maintenance and other operating costs. F- 27 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The components of lease expense were as follows (in thousands): Year Ended December 31, 2023 2022 2021 Operating lease expense $ 12,883 $ 11,775 $ 11,209 Variable lease expense 5,272 4,785 4,142 Financing: Amortization 203 343 310 Interest expense — 37 58 Total $ 18,358 $ 16,940 $ 15,719 Cash paid for amounts included in the measurement of operating lease liabilities for the years ended December 31, 2023, 2022, and 2021 was $ 13.4 million, $ 13.1 million, and $ 11.8 million, respectively, and was included in net cash used in operating activities in the Consolidated Statements of Cash Flows. Right-of-use lease assets were $ 23.9 million and $ 26.0 million as of December 31, 2023 and 2022, respectively, and were included in other non-current assets on the Consolidated Balance Sheets. The following table summarizes maturities of lease liabilities and the reconciliation of lease liabilities as of December 31, 2023: Year Ending December 31, Operating 2024 $ 16,234 2025 11,932 2026 8,430 2027 5,867 2028 5,887 Thereafter 6,009 Total future lease payments 54,359 Less: Amount representing interest ( 11,190 ) Present value of future lease payments 43,169 Less: Lease liabilities, current ( 12,595 ) Lease liabilities , non-curre nt $ 30,574 Lease liabilities are based on the net present value of the remaining lease payments over the remaining lease term. For the years ended December 31, 2023 and 2022 , the weighted-average remaining operating lease terms were 4.5 years and 3.0 years, the weighted-average remaining financing lease terms were nil and 2.8 years, the weighted-average discount rates used to determine the lease liability for operating leases were 9.6 % and 6.7 %, and the weighted-average discount rates used to determine the lease liability for finance leases were nil and 5.1 % respectively. 10. Liabilities for Sales of Future Royalties In December 2019, the Company entered into a Royalty Purchase Agreement with RPI. Pursuant to the agreement, RPI paid $ 320.0 million to the Company in consideration for the right to receive royalty payments effective January 1, 2020, arising from the net sales of Crysvita in the EU, the U.K., and Switzerland under the terms of the Company’s Collaboration and License Agreement with KKC dated August 29, 2013, as amended, or the KKC Collaboration Agreement. The agreement with RPI will automatically terminate, and the payment of royalties to RPI will cease, in the event aggregate royalty payments received by RPI are equal to or greater than $ 608.0 million prior to December 31, 2030, or in the event aggregate royalty payments received by RPI are less than $ 608.0 million prior to December 31, 2030, or when aggregate royalty payments received by RPI are equal to $ 800.0 million. In July 2022, the Company entered into a Royalty Purchase Agreement with OMERS. Pursuant to the agreement, OMERS paid $ 500.0 million to the Company in consideration for the right to receive 30 % of the future royalty payments due to the Company from KKC based on net sales of Crysvita in the U.S. and Canada under the terms of the KKC Collaboration Agreement. The calculation of royalty payments to OMERS is based on net sales of Crysvita beginning in April 2023 and will expire upon the earlier of the date on which aggregate payments received by OMERS equals $ 725.0 million or the date the final royalty payment is made to the Company under the KKC Collaboration Agreement. Proceeds from these transactions were recorded as liabilities for sales of future royalties on the Consolidated Balance Sheets. Upon inception of the respective arrangements, the Company recorded $ 320.0 million and $ 500.0 million, net of transaction costs of $ 5.8 million and $ 9.1 million for RPI and OMERS, respectively, using the effective interest method over the estimated life of the applicable arrangement. In order to determine the amortization of the liabilities, the Company is required to estimate the total F- 28 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) amount of future royalty payments to be received by the Company and paid to RPI and OMERS, subject to the capped amount, over the life of the arrangements. The excess of future estimated royalty payments (subject to the capped amount) to RPI and OMERS, over the $ 314.2 million and $ 491.0 million, respectively, of net proceeds, is recorded as non-cash interest expense over the life of the arrangements. Consequently, the Company estimates an imputed interest on the unamortized portion of the liabilities and records interest expense relating to the transactions. The Company records the royalty revenue arising from the net sales of Crysvita in the applicable territories as royalty revenue in the Consolidated Statements of Operations over the term of the arrangements. Royalties earned under the RPI and OMERS arrangements from inception to December 31, 2023 have been $ 73.4 million and $4 8.6 million, respectively. The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources. To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company will prospectively adjust the amortization of the liabilities and the effective interest rate. The Company’s effective annual interest rates were 6.2 % and 7.8 %, for RPI and OMERS, respectively, as of December 31, 2023. There are a number of factors that could materially affect the amount and timing of royalty payments from KKC in the applicable territories, most of which are not within the Company’s control. Such factors include, but are not limited to, the success of KKC’s sales and promotion of Crysvita, changing standards of care, macroeconomic and inflationary pressures, the introduction of competing products, pricing for reimbursement in various territories, manufacturing or other delays, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of Crysvita, significant changes in foreign exchange rates as the royalty payments are made in U.S. dollars, or USD, while significant portions of the underlying sales of Crysvita are made in currencies other than USD, and other events or circumstances that could result in reduced royalty payments from sales of Crysvita, all of which would result in a reduction of royalty revenue and the non-cash interest expense over the life of the arrangement. Conversely, if sales of Crysvita in the relevant territories are more than expected, the royalty revenue and the non-cash interest expense recorded by the Company would be greater over the term of the arrangements. The following table shows the activity within the liability account (in thousands): Liabilities for Sales of Future Royalties RPI OMERS Total December 31, 2021 $ 351,786 $ — $ 351,786 Net proceeds from sale of future royalties — 490,950 490,950 Royalty revenue ( 21,692 ) — ( 21,692 ) Non-cash interest expense 35,095 19,300 54,395 December 31, 2022 365,189 510,250 875,439 Royalty revenue ( 20,783 ) ( 38,524 ) ( 59,307 ) Non-cash interest expense 32,235 43,200 75,435 December 31, 2023 $ 376,641 $ 514,926 $ 891,567 11. Equity At-the-Market Offerings In May 2021, the Company entered into an Open Market Sale Agreement with Jefferies LLC, or Jefferies, pursuant to which the Company may offer and sell shares of the Company’s common stock having an aggregate offering proceeds up to $ 350.0 million, from time to time, in at-the-market, or ATM, offerings through Jefferies. During the year ended December 31, 2023, there were 1,175,584 shares sold under the ATM resulting in net proceeds of $ 53.3 million. There were no shares sold under the ATM for year ended December 31, 2022. As of December 31, 2023 , the Company has sold a total of 2,225,956 shares under the ATM, resulting in net proceeds of $ 132.2 million. Underwritten Public Offering In October 2023, the Company completed an underwritten public offering in which 9,833,334 shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1,500,000 shares, at a public offering price of $ 30.00 per share. In connection with the offering, the Company sold to certain investors pre-funded warrants, in lieu of common stock, to purchase 1,666,722 shares of common stock at a purchase price of $ 29.999 per pre-funded warrant, which equals the public offering price per share of common stock less the $ 0.001 exercise price per share of each pre-funded warrant. The total F- 29 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) proceeds that the Company received from the offering were $ 326.5 million, net of underwriting discounts and commissions. As of December 31, 2023 , no ne of the pre-funded warrants had been exercised. The pre-funded warrants were classified as a component of permanent equity in the Company's Consolidated Balance Sheets as they are freestanding financial instruments that are immediately exercisable, do not embody an obligation for the Company to repurchase its own shares and permit the holders to receive a fixed number of shares of common stock upon exercise. All of the shares underlying the pre-funded warrants have been included in the weighted-average number of shares of common stock used to calculate net loss per share, basic and diluted, attributable to common stockholders because the shares may be issued for little or no consideration, are fully vested, and are exercisable after the original issuance date of the pre-funded warrants. 12. Stock-Based Awards Equity Plan Awards In 2014, the Company adopted the 2014 Incentive Plan, or the 2014 Plan, for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors. The 2014 Plan had 2,250,000 shares of common stock available for future issuance at the time of its inception. The 2014 Plan provided for automatic annual increases in shares available for grant, beginning on January 1, 2015 through June 7, 2023 . In June 2023, the Company adopted the 2023 Incentive Plan which had 4,500,000 shares of common stock available for future issuance at the time of its inception, plus the number of shares subject to the 2014 Plan cancelled after June 7, 2023. No further shares were granted under the 2014 Plan after June 7, 2023.In February 2021, the Company adopted the Employment Inducement Plan, or the Inducement Plan, which was subsequently amended in June 2023 to provide for a maximum of 850,000 shares available for grant under the plan. In 2014, the Company adopted the 2014 Incentive Plan, or the 2014 Plan, for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors. Under the terms of the 2023 Plan and Inducement Plan, awards may be granted at an exercise price not less than fair market value. The exercise price of an option may not be less than the fair market value. The term of an award granted under the 2023 Plan and Inducement Plan may not exceed ten years . Typically, the vesting schedule for option grants to the employees provides that ¼ of the grant vests upon the first anniversary of the date of grant, with the remainder of the shares vesting monthly thereafter at a rate of 1/48 of the total shares subject to the option. Typically, the vesting schedule for RSU grants provides that ¼ of the grant vests upon the annual anniversary of the date of grant over the period of four years . As of December 31, 2023 , an aggregate of 19,610,125 shares of common stock have been authorized for issuance under the 2014 Plan, the 2023 Plan, and the Inducement Plan. Stock Option Activity The following table summarizes activity under the Company’s stock option plans and related information: Options Outstanding Number of Options Weighted- Average Exercise Price Weighted-Average Remaining Contractual Term (Years) Aggregate Intrinsic Value (In thousands) Outstanding — December 31, 2022 7,773,367 $ 72.56 6.60 $ 8,476 Options granted 2,123,256 45.05 Options exercised ( 209,793 ) 13.07 Options cancelled ( 899,118 ) 71.56 Outstanding — December 31, 2023 8,787,712 67.43 6.39 7,558 Vested and exercisable — December 31, 2023 5,415,110 73.28 4.96 1,214 Vested and expected to vest — December 31, 2023 8,461,973 67.96 6.29 6,794 The aggregate intrinsic values of options outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the options and the fair value of the Company’s common stock. The total intrinsic value of options exercised during the years ended December 31, 2023, 2022, and 2021 was $ 4.9 million, $ 2.6 million, and $ 38.8 million, respectively. Cash received from the exercise of options was $ 2.7 million, $ 6.2 million, and $ 36.6 million for the years ended December 31, 2023, 2022, and 2021, respectively. F- 30 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The weighted-average estimated fair value of stock options granted was $ 25.53 , $ 34.77 , and $ 70.84 per share of the Company’s common stock during the years ended December 31, 2023, 2022, and 2021, respectively. The total estimated grant date fair value of options vested during the years ended December 31, 2023, 2022, and 2021 was $ 59.7 million, $ 58.7 million, and $ 48.1 million, respectively. Performance Stock Options The following table summarizes activity under the Company’s Performance Stock Option, or PSO, plans and related information: PSOs Outstanding Number of Options Weighted- Average Exercise Price Weighted-Average Remaining Contractual Term (Years) Aggregate Intrinsic Value Outstanding — December 31, 2022 1,624,599 $ 67.37 4.14 $ — PSOs cancelled ( 243,601 ) 67.37 Outstanding — December 31, 2023 1,380,998 67.37 3.15 — Vested and exercisable — December 31, 2023 117,865 67.37 3.09 — Vested and expected to vest — December 31, 2023 983,173 67.37 3.14 — During the year ended December 31, 2022, PSOs were granted to certain nonexecutive employees. PSOs are subject to vest only if specified operational milestones are achieved and the employees’ continued service with the Company. The Company uses the Black-Scholes method to calculate the fair value at the grant date and is recognizing stock-based compensation expense for the PSOs that are expected to vest. Stock-based compensation for PSOs is recognized over the service period, beginning in the period the Company determines it is probable that a milestone will be achieved. Forfeitures of PSOs are recognized as they occur. The Company reassesses the probability of the performance condition at each reporting period and adjusts the compensation cost based on the probability assessment. As of December 31, 2023, certain operational milestones were deemed probable of achievement. The aggregate intrinsic values of PSOs outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the PSOs and the fair value of the Company’s common stock. The total estimated grant date fair value of PSOs vested during the year ended December 31, 2023 , was $ 3.4 million. No PSOs were granted or were exercised during the year ended December 31, 2023. The weighted-average estimated fair value of PSOs granted was $ 28.76 during the year ended December 31, 2022. Restricted Stock Units The following table summarizes activity under the Company’s Restricted Stock Units, or RSU, plans and related information: RSUs Outstanding Number of Shares Weighted- Average Grant Date Fair Value Unvested — December 31, 2022 2,129,153 $ 75.11 RSUs granted 2,447,170 44.52 RSUs vested ( 738,130 ) 73.99 RSUs cancelled ( 394,081 ) 61.22 Unvested — December 31, 2023 3,444,112 55.21 The fair value of the RSUs is determined on the grant date based on the fair value of the Company’s common stock. The fair value of the RSUs is recognized as expense ratably over the vesting period of one to four years . The total grant date fair value of the RSUs vested during the years ended December 31, 2023, 2022, and 2021 was $ 54.6 million, $ 47.1 million, and $ 35.5 million, respectively. The aggregate intrinsic value of the shares of the RSUs vested during the years ended December 31, 2023, 2022, and 2021 was $ 33.0 million, $ 37.8 million, and $ 69.9 million, respectively. F- 31 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Performance Stock Units The following table summarizes activity under the Company’s Performance Stock Units, or PSUs and related information: PSUs Outstanding Number of Shares Weighted- Average Grant Date Fair Value Unvested — December 31, 2022 209,230 $ 98.09 PSUs granted 362,470 50.29 PSUs vested ( 27,581 ) 141.86 PSUs cancelled ( 38,013 ) 106.80 Unvested — December 31, 2023 506,106 60.82 The fair value of the PSUs is determined on the grant date based on the fair value of the Company’s common stock, except for certain PSUs with a market vesting condition, for which fair value is estimated using a Monte Carlo simulation model. PSUs are subject to vest only if certain specified criteria are achieved and the employees’ continued service with the Company. For certain PSUs, the number of PSUs that may vest are also subject to the achievement of certain specified criteria, including both performance conditions and market conditions. As of December 31, 2023, certain specified criteria were deemed probable of achievement or already achieved. Stock-based compensation for PSUs is recognized over the service period beginning in the period the Company determines it is probable that the performance criteria will be achieved. The total grant date fair value of the PSUs vested during the years ended December 31, 2023, 2022, and 2021 was $ 3.9 million, $ 1.6 million, and $ 9.2 million, respectively, with an aggregate intrinsic value of the shares of $ 1.3 million, $ 2.0 million and $ 18.9 million, respectively. Employee Stock Purchase Plan In January 2014, the Company adopted the 2014 Employee Stock Purchase Plan, or ESPP, which was amended and restated in June 2023. Under the ESPP, eligible employees may purchase common stock at 85 % of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature. ESPP purchases are settled with common stock from the ESPP’s previously authorized and available pool of shares. During the year ended December 31, 2023 , the Company issued 195,462 shares of common stock under the ESPP. As of December 31, 2023 , an aggregate of 6,609,795 shares of common stock have been authorized for future issuance on the ESPP. Stock-Based Compensation Expense Total stock-based compensation recognized was as follows (in thousands): Year Ended December 31, 2023 2022 2021 Cost of sales $ 1,166 $ 902 $ 871 Research and development 74,531 74,464 59,097 Selling, general and administrative 59,516 55,002 45,011 Total stock-based compensation expense $ 135,213 $ 130,368 $ 104,979 Stock-based compensation of $ 1.9 million, $ 2.2 million, and $ 1.7 million was capitalized into inventory for the years ended December 31, 2023, 2022, and 2021, respectively. Capitalized stock-based compensation is recognized as cost of sales when the related product is sold. As of December 31, 2023 , the total unrecognized compensation expense related to unvested equity awards, net of estimated forfeitures, was $ 219.8 million, which the Company expects to recognize over an estimated weighted-average period of 2.2 years. In determining the estimated fair value of the stock options, PSOs and ESPP, the Company uses the Black-Scholes option-pricing model and assumptions discussed below. Each of these inputs is subjective and generally requires significant judgment to determine. Expected Term —The Company’s expected term represents the period that the Company’s stock-based awards are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). Expected Volatility —The Company’s expected volatility is based on historical volatility over the look-back period corresponding to the expected term. F- 32 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Risk-Free Interest Rate —The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of option. Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero. Strike price for options awards and PSOs is equal to the closing market value of our common stock on the date of grant. The fair value of stock option awards granted was estimated at the date of grant using a Black-Scholes option-pricing model with the following weighted-average assumptions: Year Ended December 31, 2023 2022 2021 Expected term (years) 6.07 6.07 6.06 Expected volatility 55 % 56 % 60 % Risk-free interest rate 4.2 % 2.0 % 1.0 % Expected dividend rate 0.0 % 0.0 % 0.0 % The fair value of PSOs granted was estimated at the date of grant using a Black-Scholes option-pricing model with the following weighted-average assumptions: Year Ended December 31, 2022 Expected term in years 3.60 Expected volatility 57 % Risk-free interest rate 1.5 % Expected dividend rate 0.0 % 13. Defined Contribution Plan The Company sponsors a retirement plan in which substantially all of its full-time employees in the U.S. and certain other foreign countries are eligible to participate. Eligible participants may contribute a percentage of their annual compensation to this plan, subject to statutory limitations. The Company recorded $ 9.7 million, $ 9.0 million, and $ 5.5 million as expense related to the plan for the years ended December 31, 2023, 2022, and 2021 , respectively. 14. Income Taxes The components of the Company’s loss before income taxes were as follows (in thousands): Year Ended December 31, 2023 2022 2021 Domestic $ 608,166 $ 703,411 $ 455,314 Foreign 298 ( 1,686 ) ( 2,333 ) Total loss before income taxes $ 608,464 $ 701,725 $ 452,981 F- 33 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The components of the Company’s income tax provision were as follows (in thousands): Year Ended December 31, 2023 2022 2021 Current provision for income taxes: Federal $ — $ — $ — State ( 3,187 ) 6,062 ( 14 ) International 3,127 1,274 1,058 Total current tax provision ( 60 ) 7,336 1,044 Deferred tax provision: Federal — — — State ( 1,608 ) ( 1,640 ) — International ( 157 ) — — Total deferred tax provision ( 1,765 ) ( 1,640 ) — Total (benefit from) provision for income taxes $ ( 1,825 ) $ 5,696 $ 1,044 The Company has incurred net operating losses since inception. The Company has not reflected any benefit of such net operating loss carryforwards in the accompanying financial statements. The Company has established a full valuation allowance against its deferred tax assets due to the uncertainty surrounding the realization of such assets. Beginning in 2022, the Tax Cuts and Jobs Act of 2017 eliminated the right to deduct research and development expenditures for tax purposes in the period the expenses were incurred and instead requires all U.S. and foreign research and development expenditures to be amortized over five and fifteen tax years, respectively. Due to this required capitalization of research and development expenditures and the significant taxable income generated as a result of our sale of royalties in July 2022, the Company has recorded current state income tax expense of $ 6.1 million for the year ended December 31, 2022. For the year ended December 31, 2023, the Company recognized an income tax benefit of $ 4.8 million attributable to modifications in its state apportionment methodology. The Company realized no benefit for current year losses due to a full valuation allowance against the U.S. net deferred tax assets. The benefit was offset by an income tax expense of $ 3.0 million from foreign jurisdictions. The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows: Year Ended December 31, 2023 2022 2021 Federal statutory income tax rate 21.0 % 21.0 % 21.0 % State income taxes, net of federal benefit 0.8 ( 0.4 ) — Federal tax credits 7.3 5.9 7.2 Other ( 0.7 ) ( 0.1 ) 0.5 Nondeductible permanent items ( 0.3 ) ( 0.6 ) ( 0.8 ) Stock-based compensation ( 1.8 ) ( 1.2 ) 1.3 Uncertain tax positions ( 1.4 ) ( 1.2 ) ( 1.4 ) Change in valuation allowance ( 24.1 ) ( 24.0 ) ( 27.9 ) Foreign rate differential ( 0.5 ) ( 0.2 ) ( 0.1 ) Provision for income taxes 0.3 % ( 0.8 ) % ( 0.2 ) % F- 34 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The tax effect of temporary differences that give rise to significant portions of the deferred tax assets is presented below (in thousands): Year Ended December 31, 2023 2022 Deferred tax assets: Loss carryforwards $ 266,253 $ 231,835 Tax credits 305,198 260,546 Stock options 44,795 39,784 Accruals and reserves 27,694 27,029 Fixed assets and intangibles 33,853 39,233 Liabilities for sales of future royalties 205,400 214,900 Basis difference in equity investments 8,423 8,971 Capitalized research and development costs 149,898 75,335 Other 281 3,028 Gross deferred tax assets 1,041,795 900,661 Valuation allowance ( 1,035,836 ) ( 894,518 ) Total deferred tax assets 5,959 6,143 Deferred tax liabilities: In-process research and development ( 30,688 ) ( 31,667 ) Right-of-use lease assets ( 5,329 ) ( 6,143 ) Gross deferred tax liabilities ( 36,017 ) ( 37,810 ) Net deferred tax liabilities $ ( 30,058 ) $ ( 31,667 ) As of December 31, 2023 and 2022 , the Company had approximately $ 1,004.8 million and $ 756.6 million, respectively, of federal net operating loss carryforwards available to reduce future taxable income that will begin to expire in 2031 . As of December 31, 2023 and 2022 , the Company had approximately $ 659.9 million and $ 710.0 million, respectively, of state net operating loss carryforwards available to reduce future taxable income that will begin to expire in 2031 . As of December 31, 2023 and 2022 , the Company had federal research tax credit carryforwards of approximately $ 46.9 million and $ 32.6 million, respectively, available to reduce future tax liabilities that will begin to expire in 2030 . As of December 31, 2023 and 2022 , the Company had state research credit carryforwards of $ 74.4 million and $ 59.9 million, respectively, available to reduce future tax liabilities that will be carried forward indefinitely. As of December 31, 2023 and 2022 , the Company had federal Orphan Drug Credits of $ 269.6 million and $ 239.3 million, respectively, available to reduce future tax liabilities that will begin to expire in 2031 . The Company’s ability to use net operating loss and tax credit carryforwards to reduce future taxable income and liabilities may be subject to annual limitations pursuant to Internal Revenue Code Sections 382 and 383 as a result of ownership changes in the past and future. As a result of ownership changes in 2012 and 2011, $ 3.6 million of federal net operating loss carryforwards, $ 3.6 million of state net operating loss carryforwards, and $ 0.2 million of federal tax credits are permanently limited. Deferred tax assets for net operating losses and tax credits have been reduced and a corresponding adjustment to the valuation allowance has been recorded. The valuation allowance increased by $ 141.3 million and $ 193.8 million during the years ended December 31, 2023 and 2022, respectively. Due to a change in the state tax rates, the Company recorded a net decrease to the deferred tax liability of $ 1.6 million with a corresponding deferred income tax benefit of $ 1.6 million for the year ended December 31, 2023. F- 35 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) The Company recorded unrecognized tax benefits for uncertainties in income taxes. A reconciliation of the Company’s unrecognized tax benefits follows (in thousands): December 31, 2023 2022 2021 Balance at beginning of year $ 66,794 $ 55,360 $ 46,662 Additions based on tax positions related to current year 12,562 11,316 8,542 Additions for tax positions of prior years 642 377 356 Reductions for tax positions of prior years — ( 259 ) ( 200 ) Balance at end of year $ 79,998 $ 66,794 $ 55,360 Approximately $ 1.3 million in unrecognized tax benefits would impact the Company’s effective tax rate if recognized. The Company has elected to include interest and penalties as a component of tax expense. For the year ended December 31, 2023, the Company recognized accrued interest and penalties of $ 0.2 million as a component of income tax expense. No accrued interest and penalties were recognized as a component of income tax expense during the years ended December 31, 2022 and 2021. The Company does not anticipate that the amount of existing unrecognized tax benefits will significantly increase or decrease during the next year. It is the Company’s intention to reinvest the earnings of its non-U.S. subsidiaries in their operations. As of December 31, 2023 , the Company had not made a provision for any incremental foreign withholding taxes on approximately $ 10.8 million of the excess of the amount of net income for financial reporting over the tax basis of investments in foreign subsidiaries that are essentially permanent in duration. If these earnings were repatriated to the U.S., the deferred tax liability associated with these temporary differences would result in a nominal amount of withholding taxes. The Company files income tax returns in the U.S. federal, 40 state tax jurisdictions, and ten foreign countries. The federal and state income tax returns from inception to December 31, 2023 remain subject to examination. 15. Commitments and Contingencies The Company has various manufacturing, construction, clinical, research, and other contracts with vendors in the conduct of the normal course of its business. Other than as noted below, contracts are terminable, with varying provisions regarding termination. If a contract with a specific vendor were to be terminated, the Company would only be obligated for the products or services that the Company had received at the time the termination became effective. Manufacturing and service contract obligations primarily relate to the manufacture of inventory for our approved products, the majority of which are due in the next 12 months . As of December 31, 2023, the aggregate payments under contractually-binding manufacturing and service agreements are as follows (in thousands): Year Ended December 31, 2024 2025 Total Manufacturing and Services $ 27,899 $ 5,718 $ 33,617 The terms of certain of the Company’s licenses, royalties, development and collaboration agreements, as well as other research and development activities, require the Company to pay potential future milestone payments based on product development success. The amount and timing of such obligations are unknown or uncertain. These potential obligations are further described in “Note 8. License and Research Agreements.” See “Note 9. Leases” for lease commitments. Contingencies While there are no material legal proceedings the Company is aware of, the Company may become party to various claims and complaints arising in the ordinary course of business. Management does not believe that any ultimate liability resulting from any of these potential claims will have a material adverse effect on its results of operations, financial position, or liquidity. However, management cannot give any assurance regarding the ultimate outcome of these claims, and their resolution could be material to operating results for any particular period, depending upon the level of income for the period. F- 36 ULTRAGENYX PHARMACEUTICAL INC. Notes to Consolidated Financial Statements (continued) Guarantees and Indemnifications The Company indemnifies each of its directors and officers for certain events or occurrences, subject to certain limits, while the director or officer is or was serving at the Company’s request in such capacity, as permitted under Delaware law and in accordance with its certificate of incorporation and bylaws. The term of the indemnification period lasts as long as a director or officer may be subject to any proceeding arising out of acts or omissions of such director and officer in such capacity. The maximum amount of potential future indemnification is unlimited; however, the Company currently holds director liability insurance. This insurance allows the transfer of risk associated with the Company’s exposure and may enable it to recover a portion of any future amounts paid. The Company believes that the fair value of these indemnification obligations is minimal. Accordingly, it has not recognized any liabilities relating to these obligations for any period presented. 16. Related Party Transaction In July 2022, the Company entered into an agreement with a non-profit foundation in which two members of the Company’s board of directors, including the Company’s Chief Executive Officer, also serve as board members of the foundation, whereby an aggregate $ 1.0 million contribution is being paid to the foundation over a four-year period, beginning in the third quarter of 2022, to support rare disease education and awareness. As a result, the Company recorded $ 0.3 million and $ 0.3 million as research and development expense for this agreement for the years ended December 31, 2023 and 2022 , respectively. 17. Net Loss per Share The following table sets forth the computation of the basic and diluted net loss per share during the years ended December 31, 2023, 2022, and 2021 (in thousands, except share and per share data): Year Ended December 31, 2023 2022 2021 Numerator: Net loss $ ( 606,639 ) $ ( 707,421 ) $ ( 454,025 ) Denominator: Weighted-average shares used to compute net loss per share, basic and diluted 73,543,862 69,914,225 67,795,540 Net loss per share, basic and diluted $ ( 8.25 ) $ ( 10.12 ) $ ( 6.70 ) The following weighted-average outstanding common stock equivalents were excluded from the computation of diluted net loss per share for the periods presented because including them would have been antidilutive: Year Ended December 31, 2023 2022 2021 Options to purchase common stock, restricted stock units, and performance stock units 14,152,286 11,290,935 8,214,063 Employee stock purchase plan 8,450 7,581 3,511 14,160,736 11,298,516 8,217,574 18. Accumulated Other Comprehensive Income (Loss) Total accumulated other comprehensive income (loss) consisted of the following (in thousands): Year Ended December 31, 2023 2022 Cumulative foreign currency translation adjustment $ ( 606 ) $ ( 845 ) Unrealized gain (loss) on securities available-for-sale 1,253 ( 5,728 ) Total accumulated other comprehensive income (loss) $ 647 $ ( 6,573 ) F- 37