What changed in this filing

/stocks — the workspaceLOADING

Item 9A. Controls and Procedures

2026-02-18 compared with 2025-02-19 · 294 added, 350 removed, 1140 unchanged (36% of the section changed)

42 unchanged sentences

Other Information

During the three months ended December 31, 2024, the following directors and officers adopted a Rule 10b5-1 trading arrangement intended to satisfy the affirmative defense conditions of Rule 10b5-1(c).

Name and Title

Aggregate Number of Shares of Common Stock to be Sold (Subject to Certain Conditions)

Plan End Date

Shehnaaz Suliman , M.D., Ph.D.

November 8, 2024

Up to 27,110 shares, all of which are shares to be acquired upon the exercise of stock options

November 7, 2025

Corsee Sanders , Ph.D.,

November 15, 2024

Up to 2,405 shares

June 26, 2025

Matthew Fust ,

November 22, 2024

Up to 15,000 shares, all of which are shares to be acquired upon the exercise of stock options

November 21, 2025

Eric Crombez , M.D.

EVP, Chief Medical Officer

December 3, 2024

Up to 64,235 shares, 28,500 of which are shares to be acquired upon the exercise of stock options

December 3, 2025

Howard Horn ,

EVP, Chief Financial Officer

December 9, 2024

Up to 17,477 shares

December 9, 2025

During the three months ended December 31, 2025, none of our directors and officers adopted a Rule 10b5-1 trading arrangement intended to satisfy the affirmative defense conditions of Rule 10b5-1(c).

Disclosure Regarding Foreign Jurisdictions that Prevent Inspections

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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 2025 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 “2025 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,” “Executive Officers,” ““Board of Directors and Committees,” “Corporate Governance” and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.” We have adopted a Global Code of Conduct 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.

Except as set forth below, the information required by this Item is incorporated herein by reference to information in the proxy statement for our 2026 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 “2026 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,” “Executive Officers,” ““Board of Directors and Committees,” “Corporate Governance” and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.”

We have adopted a Global Code of Conduct 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.

Our Global Code of Conduct is posted on our website located at https://ir.ultragenyx.com/ under “Corporate Governance”.

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Principal Accountant Fees and Services

The information required by this Item is incorporated herein by reference to information in the 2025 Proxy Statement, including under the heading “Proposal No.

3—Ratification of the Selection of Independent Registered Public Accounting Firm.”

The information required by this Item is incorporated herein by reference to information in the 2026 Proxy Statement, including under the heading “Ratification of the Selection of Independent Registered Public Accounting Firm.”

Ex hibits and Financial Statement Schedules

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and OCM LS23 Holdings LP

Royalty Purchase Agreement, dated as of November 3, 2025, by and among Rare Delaware Inc., Ultragenyx Pharmaceutical Inc.

and OCM LS23 Holding LP

2014 Incentive Plan (as amended)

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Second Amendment to Employment Inducement Plan

Third Amendment to Employment Inducement Plan

Form of Non Statutory Stock Option Agreement (Inducement Plan)

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Kakkis, M.D., Ph.D.

Offer Letter, dated as of October 31, 2011, between Ultragenyx Pharmaceutical Inc.

and Thomas Kassberg

Amendment No.

1 to Offer Letter, dated as of August 8, 2014, between Ultragenyx Pharmaceutical Inc.

and Thomas Kassberg

Amendment No.

2, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc.

and Thomas Kassberg

Offer Letter, dated as of April 26, 2016, between Ultragenyx Pharmaceutical Inc.

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and Woburn MCB II, LLC

Commercial Lease, dated July 2, 2018, between Ultragenyx Pharmaceutical Inc.

and 32 Leveroni LLC

First Amendment, dated December 9, 2025, to the Lease Agreement between Ultragenyx Pharmaceutical Inc.

and Woburn MCB II, LLC

Lease, dated August 18, 2022, between Ultragenyx Pharmaceutical Inc.

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and Brickbottom I QOZB L.P.

Commercial Lease, dated July 2, 2018, between Ultragenyx Pharmaceutical Inc.

and 32 Leveroni LLC

Ultragenyx Insider Trading Policy

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Consolidated Statements of Comprehensive Loss

Consolidated Statements of Stockholders’ Equity

Consolidated Statements of Stockholders’ Equity (Deficit)

Consolidated Statements of Cash Flows

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Description of the Matter

As discussed in Note 11, 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.

As discussed in Note 10, the Company has entered into three 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, $500 million and $400 million.

The proceeds from each transaction were recorded as liabilities and are being amortized using the effective interest method over the estimated lives of the respective arrangements.

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 counterparties, subject to capped amount.

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.

How We Addressed the Matter

Auditing the Company’s liabilities related to the sale of future royalties was challenging because it required significant judgment to evaluate management’s forecasts of expected royalty payments, which are dependent on forward-looking assumptions.

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 amount of imputed effective interest rates, we performed audit procedures that included, among others, evaluating the reasonableness of management’s assumptions related to the forecasted revenue growth rates, including 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.

To test management’s estimates of 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 forecasted royalty growth rates.

We compared management’s forecasted royalty payments to historical trends and to analyst expectations for underlying Crysvita sales.

We also performed a sensitivity analysis over the estimated future royalties to assess the impact of changes in key assumptions on the interest expense recorded for the year ended December 31, 2025.

/s/ Ernst & Young LLP

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CONSOLIDATED BA LANCE SHEETS

(In thousands, except share and per share amounts)

(in millions, except per share amounts)

Current assets:

Cash and cash equivalents

Marketable debt securities

Marketable securities

Accounts receivable, net

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Property, plant, and equipment, net

Marketable debt securities

Marketable securities

Intangible assets, net

LIABILITIES AND STOCKHOLDERS' EQUITY

LIABILITIES AND STOCKHOLDERS' EQUITY (DEFICIT)

Current liabilities:

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Noncontrolling interest

Stockholders’ equity:

Stockholders’ equity (deficit):

Preferred stock, par value of $ 0.001 per share— 25.0 shares authorized;

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outstanding— 96.6 in 2025 and 92.5 in 2024

Treasury stock, at cost, 69,757 in 2024 and 9,559 in 2023

Treasury stock, at cost, 0.2 shares in 2025 and 0.1 shares in 2024

Deferred compensation obligation

Additional paid-in capital

Accumulated other comprehensive (loss) income

Accumulated other comprehensive income (loss)

Accumulated deficit

Total stockholders’ equity

Total liabilities, noncontrolling interest and stockholders’ equity

Total stockholders’ equity (deficit)

Total liabilities, noncontrolling interest and stockholders’ equity (deficit)

See accompanying notes.

(1) The Company's Consolidated Balance Sheet as of December 31, 2024 includes $ 13.5 million in cash and cash equivalents that can be used only to settle obligations of the consolidated variable interest entity.

Investment in Amlogenyx Inc."

ULTRAGENYX PHARMACEUTICAL INC.

CONSOLIDATED ST ATEMENTS OF OPERATIONS

(In thousands, except share and per share amounts)

(in millions, except per share amounts)

Year Ended December 31,

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Interest income

Change in fair value of equity investments

Non-cash interest expense on liabilities for sales of future royalties

Other expense

Other income (expense)

Loss before income taxes

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CONSOLIDATED STATEM ENTS OF COMPREHENSIVE LOSS

(In thousands)

(in millions)

Year Ended December 31,

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Foreign currency translation adjustments

Changes in unrealized gain (loss) on available-for-sale securities

Change in unrealized gain (loss) on available-for-sale securities

Other comprehensive income (loss):

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ULTRAGENYX PHARMACEUTICAL INC.

CONSOLIDATED STATE MENTS OF STOCKHOLDERS’ EQUITY

(In thousands, except share amounts)

CONSOLIDATED STATE MENTS OF STOCKHOLDERS’ EQUITY (DEFICIT)

(In millions)

Comprehensive

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Income (Loss)

Balance as of December 31, 2021

Stock-based compensation

Issuance of common stock under

equity plan awards, net of tax

Other comprehensive loss

Equity (Deficit)

Balance as of December 31, 2022

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equity plan awards, net of tax

Deferred compensation

Other comprehensive income

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Balance as of December 31, 2024

Issuance of common stock in connection with

at-the-market offering, net

Stock-based compensation

Issuance of common stock under

equity plan awards, net of tax

Deferred compensation

Other comprehensive income

Balance as of December 31, 2025

See accompanying notes.

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CONSOLIDATED STA TEMENTS OF CASH FLOWS

(In thousands)

(in millions)

Year Ended December 31,

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Stock-based compensation

Acquired in-process research and development

Amortization of premium (discount) on marketable debt securities, net

Amortization of discount on marketable securities, net

Depreciation and amortization

Change in fair value of equity investments

Non-cash collaboration royalty revenue

Non-cash royalty revenue

Non-cash interest expense on liabilities for sales of future royalties

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Accounts payable, accrued, and other liabilities

Deferred tax liabilities

Net cash used in operating activities

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Purchase of property, plant, and equipment

Acquisition, net of cash acquired

Purchase of marketable debt securities

Proceeds from sale of marketable debt securities

Proceeds from sale of equity investments

Proceeds from maturities of marketable debt securities

Payment for intangible asset

Net cash (used in) provided by investing activities

Purchase of marketable securities

Proceeds from sale of marketable securities

Proceeds from maturities of marketable securities

Payments for intangible asset

Net cash provided by (used in) investing activities

Financing activities:

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Proceeds from the issuance of common stock and pre-funded warrants in connection with underwritten

public offerings, net of issuance costs

public offerings, net

Proceeds from the issuance of common stock in connection with at-the-market

offering, net of issuances costs

Proceeds from the issuance of common stock from exercise of equity

plan awards, net

Proceeds from issuance of equity interest in noncontrolling interest

offering, net

Proceeds from the issuance of common stock under equity plans, net

Proceeds from issuance of equity from noncontrolling interest

Net cash provided by financing activities

Effect of exchange rate changes on cash

Net (decrease) increase in cash, cash equivalents, and restricted cash

Net increase (decrease) in cash, cash equivalents, and restricted cash

Cash, cash equivalents, and restricted cash at beginning of year

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CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

(in millions)

Year Ended December 31,

Supplemental disclosures of non-cash investing and financing information:

Supplemental disclosures of non-cash information:

Acquired lease liabilities arising from obtaining right-of-use assets and property, plant, and equipment

Costs of property, plant and equipment included in accounts payable, accrued, and other liabilities

Non-cash interest expense on liabilities for sales of future royalties capitalized during the year into ending property, plant and equipment

Costs of intangible assets included in accounts payable, accrued and other liabilities

See accompanying notes.

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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 is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultra-rare genetic diseases.

The Company operates as one reportable segment and has four commercially approved products.

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• 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 Imperfecta, 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;

• 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;

• 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;

• UX143 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 Imperfecta, or OI.

The Company has sustained operating losses and expects such annual losses to continue in the near term.

The Company’s ultimate success depends on the outcome of its research and development and commercialization activities.

Through December 31, 2024 , 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.

Through December 31, 2025 , the Company has relied primarily on the sale of equity securities, revenues from commercial products, the sale of certain 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.

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The Consolidated Financial Statements include the accounts of the Company and its wholly-owned subsidiaries.

The Company consolidates any variable interest entity, or VIE, for which it is the primary beneficiary.

The Company cons olidates any variable interest entity, or VIE, for which it is the primary beneficiary.

Certain reclassifications have been made to prior periods in the consolidated financial statements and accompanying notes to conform with the current presentation.

ULTRAGENYX PHARMACEUTICAL INC.

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The segment derives its current revenues from its four commercially approved products.

The Company’s Chief Operating Decision Maker, or CODM, its Chief Executive Officer and the executive leadership team, manage the Company’s operations on an integrated basis for the purposes of allocating resources.

When evaluating the Company’s financial performance, the CODM regularly reviews total revenues and total expenses and makes decisions using this information on a global basis.

The Company’s Chief Operating Decision Maker, or CODM, is the Company's Chief Executive Officer .

The CODM manages the Company’s operations on an integrated basis for the purpose of allocating resources.

When evaluating the Company’s financial performance, the CODM regularly reviews total revenues and total expenses and makes decisions using this information on a consolidated basis.

Use of Estimates

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Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility leases and to guarantee the fulfillment of certain sales orders to certain government-sponsored customers.

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):

Cash and cash equivalents

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shown in the statements of cash flows

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.

Marketable Securities

All marketable 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.

Investments with a maturity of one year or less from the balance sheet date are reported as current marketable securities and investments with a maturity of greater than one year from the balance sheet date are reported as non-current marketable securities.

Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive loss.

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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 were no material credit losses recorded for receivables and available-for-sale debt securities which were attributable to credit risk for the years ended December 31, 2025 and 2024.

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.

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Intangible Assets

Finite-lived intangibles consist of contractual payments made for certain milestones achieved with collaboration partners.

Finite-lived intangibles consist of contractual payments made in conjunction with license agreements and collaboration agreements.

The contractual payments are recorded as intangible assets and are amortized over their estimated useful lives.

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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 recorded the liabilities at inception based upon estimated future cash flows discounted at a market rate.

The liabilities are being amortized 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 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 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.

Liabilities for Sales of Future Royalties.” At inception, the Company recorded a liability based upon estimated future cash flows discounted at a market rate.

The liability is amortized using the effective interest method over the estimated life of the applicable arrangement.

To determine the amortization of the liability, the Company estimates the total amount of future royalty payments to be received by the Company and paid to RPI and OMERS.

Any estimated royalty payments in excess of the initial liability are recorded as non-cash interest expense.

Consequently, the Company estimates imputed interest on the unamortized portion of the liabilities and records interest expense based on the estimated term of the arrangements.

ULTRAGENYX PHARMACEUTICAL INC.

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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.

The Company’s estimates of government mandated rebates, chargebacks, estimated product returns, and other deductions depend 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.

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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 also records royalty revenues under certain of the Company’s license or collaboration agreements in exchange for the license of intellectual property.

As described in “Note 10.

Liabilities for Sales of Future Royalties”, for certain royalty payments from net sales of Crysvita in applicable territories that were sold to RPI and OMERS, the Company records the royalty revenue on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the applicable arrangement.

Liabilities for Sales of Future Royalties”, for certain royalty payments from net sales of Crysvita in applicable territories that were sold to RPI and OMERS, the Company records the non-cash royalty revenue on a prospective basis as 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.

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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.

These awards are recorded as treasury stock and deferred compensation obligation within stockholders’ equity (deficit).

Lease agreements are evaluated to determine whether an arrangement is or contains a lease in accordance with ASC 842, Leases .

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The Company has elected to not separate lease and non-lease components.

See “Note 10.

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.

Comprehensive loss is the change in stockholders’ equity (deficit) 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.

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The Company is currently evaluating the impact of adopting ASU 2024-03.

In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280):

Improvements to Reportable Segment Disclosures , requiring public entities to disclose information about their reportable segments’ significant expenses and other segment items on an interim and annual basis.

Public entities with a single reportable segment are required to apply the disclosure requirements in ASU 2023-07, as well as all existing segment disclosures and reconciliation requirements in ASC 280 on an interim and annual basis.

In December 2023, the FASB issued ASU 2023-09, Income Taxes (Topic 740):

Improvements to Income Tax Disclosures requiring public entities to disclose disaggregated information about their effective tax rate reconciliation and additional information about income taxes paid.

Disclosure requirements will be applied on a prospective basis.

ASU 2023-09 is effective for fiscal years beginning after December 15, 2024.

The Company adopted ASU 2023-09 during the year ended December 31, 2025.

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The Company determines the fair value of its equity investment in Solid Biosciences, Inc., or Solid, by using the quoted market prices, which are Level 1 fair value measurements.

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):

The following tables set forth the fair value of the Company’s financial assets and liabilities remeasured on a recurring basis based on the three-tier fair value hierarchy (in millions):

December 31, 2025

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Commercial paper

Asset-backed securities

Government Treasury and agency securities

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Money market funds

Certificates of deposit and time deposits

Time deposits

Corporate bonds

Commercial paper

Asset-backed securities

Government Treasury and agency securities

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Deferred compensation liabilities consist of short-term liabilities of $ 1 million and $ 1 million as of December 31, 2025 and 2024 , respectively, included in accrued liabilities on the Consolidated Balance Sheets, and long-term liabilities of $ 18 million and $ 15 million as of December 31, 2025 and 2024, respectively, included in other non-current liabilities on the Consolidated Balance Sheets.

There have been no significant net gains or losses on deferred compensation assets or liabilities for the periods presented.

There have been no material net gains or losses on deferred compensation assets or liabilities for the periods presented.

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):

Cash Equivalents and Marketable Securities

The fair values of cash equivalents and marketable securities classified as available-for-sale securities consist of the following (in millions):

December 31, 2025

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Commercial paper

Asset-backed securities

Government Treasury and agency securities

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Money market funds

Certificates of deposit and time deposits

Time deposits

Corporate bonds

Commercial paper

Asset-backed securities

Government Treasury and agency securities

At December 31, 2024 , the remaining contractual maturities of available-for-sale securities were less than three years .

At December 31, 2025 , the remaining contractual maturities of available-for-sale securities were less than two years .

The cost of securities sold is based on the specific-identification method.

There have been no significant realized gains or losses on available-for-sale securities for the periods presented.

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Notes to Consolidated Financial Statements (continued)

Inventory consists of the following (in thousands):

Inventory consists of the following (in millions):

Work-in-process

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Property, Plant, and Equipment, net

Property, plant, and equipment, net consists of the following (in thousands):

Property, plant, and equipment, net consists of the following (in millions):

Useful life (years)

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Accrued Liabilities

Accrued liabilities consists of the following (in thousands):

Research, clinical study, and manufacturing expenses

Accrued liabilities consist of the following (in millions):

Research and clinical study expenses

Payroll and related expenses

Revenue related reserves

Manufacturing and related expenses

Commercial and development milestones

Total accrued liabilities

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IPR&D assets are considered to be indefinite-life until the completion or abandonment of the associated research and development efforts.

Finite-lived Intangibles

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Finite-lived Intangibles

Subsequent to the FDA approval of Dojolvi for the treatment of LC-FAOD in 2020, the Company recorded $ 5 million for the attainment of various development and commercial milestones as finite-lived intangible assets which are amortized over a weighted-average total useful life of 6 years.

In January 2022, the Company announced a collaboration with Regeneron to commercialize Evkeeza for HoFH outside of the U.S.

In January 2022, the Company entered into a collaboration with Regeneron to commercialize Evkeeza for HoFH outside of the U.S.

Pursuant to the collaboration agreement, the Company has incurred an upfront payment and regulatory and sales milestones to date totaling $ 63 million.

As these payments are for the Company’s use of intellectual property for Evkeeza for HoFH, they were recorded as intangible assets , which are amortized over a weighted-average total useful life of 9 years.

The Company's intangible assets were as follows:

The Company's intangible assets were as follows (in millions, except for years):

December 31, 2025

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Total intangible assets

The Company recorded costs of sales of $ 5.5 million, $ 3.8 million and $ 3.2 million for the years ended December 31, 2024, 2023, and 2022, respectively, related to the amortization of the intangible assets.

The expected amortization of the intangible assets, as of December 31, 2024, for each of the next five years and thereafter is as follows:

The Company recorded costs of sales of $ 8 million, $ 6 million and $ 4 million for the years ended December 31, 2025, 2024, and 2023, respectively, related to the amortization of intangible assets.

The expected amortization of intangible assets, as of December 31, 2025, for each of the next five years and thereafter is as follows (in millions):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The following table disaggregates total revenues from external customers by product sales, royalty revenue, and collaboration and license revenue (in thousands):

The following table disaggregates total revenues from external customers by product sales, royalty revenue, and collaboration and license revenue (in millions):

Year Ended December 31,

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Total revenues

The following table disaggregates total revenues based on geographic location (in thousands):

The following table disaggregates total revenues based on geographic location (in millions):

Year Ended December 31,

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Total revenues

The following table presents the activity and ending balances for product sales related accruals and allowances (in thousands):

The following table presents the activity and ending balances for product sales related accruals and allowances (in millions):

Year Ended December 31,

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Balance of product sales reserve at end of year

The following table presents changes in the contract liabilities for the years ended December 31, 2023 (in thousands):

Balance of contract liabilities at beginning of period

Balance of contract liabilities at end of period, net

License and Research Agreements” for additional details on contract liabilities activities.

The Company’s largest accounts receivable balance was from a collaboration partner, KKC, and was 62 % and 70 % of the total accounts receivable balance as of December 31, 2025 and 2024 , respectively.

Investment in Amlogenyx.

Investment in Amlogenyx Inc.

In July 2024, the Company contributed certain intellectual property rights to Amlogenyx Inc., or Amlogenyx, a subsidiary of the Company, and received 9.0 million shares of common stock of Amlogenyx.

A third-party investor along with one of its affiliated entities, and the Company, each contributed $ 7.0 million to Amlogenyx and in exchange, each received approximately 1.6 million

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

shares of series seed preferred stock of Amlogenyx.

A third-party investor along with one of its affiliated entities, and the Company, each contributed $ 7 million to Amlogenyx and in exchange, each received approximately 1.6 million shares of series seed preferred stock of Amlogenyx.

The purpose of Amlogenyx is to pursue the application of the Company’s novel adeno-associated virus, or AAV, gene therapy to treat beta-amyloid disorders and related neurodegenerative diseases.

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Upon initial consolidation, the non-controlling interest of the third-party investor was recorded at its estimated fair value of $ 7.0 million, which is equal to their original investment.

As of December 31, 2024 , total assets and liabilities included on the Consolidated Balance Sheets for Amlogenyx were $ 13.5 million and $ 0.1 million, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

As of December 31, 2025 and 2024 , total assets included on the Consolidated Balance Sheets for Amlogenyx were $ 5 million and $ 14 million, respectively.

The assets primarily consisted of cash and cash equivalents which may only be used to settle obligations of Amlogenyx.

Noncontrolling interest related to the third-party investment in Amlogenyx is reported on the Consolidated Balance Sheets in mezzanine equity.

Changes in the carrying value of noncontrolling interest for the year ended December 31, 2024, were as follows:

Changes in the carrying value of noncontrolling interest for the year ended December 31, 2025, were as follows (in millions):

Noncontrolling Interest

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As of December 31, 2024

In October 2024, Amlogenyx granted 778,500 stock options to its employees from its 2024 Equity Incentive Plan, which authorizes 1,358,060 shares for issuance.

For the year ended December 31, 2024 , stock-based compensation related to these awards was immaterial.

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.

During the year ended December 31, 2024, the Company achieved a $ 30.0 million regulatory milestone upon the initiation of the Phase 3 Aspire clinical study for GTX-102.

The Company is obligated to pay 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, contingent upon the achievement of the milestones.

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 unitholders are 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.

To date, the Company recognized an aggregate of $ 0.5 million for clinical milestones under the TAMU agreement, and have in aggregate up to $ 23.0 million of future obligations for various future milestones and a nominal annual license fee that may increase up to a maximum of $ 2.0 million.

The Company will also pay mid-single-digit percentage royalties based on licensed product annual net sales.

As of December 31, 2024 and 2023, the Company had $ 0.5 million and nil , respectively, in collaboration payables under this arrangement.

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, to date, amounts paid to acquire GeneTx, net of cash and working capital acquired, were classified as in-process research and development expense.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Changes and adjustments

As of December 31, 2025

License and Research Agreements

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The collaboration and license agreements are within the scope of ASC 808, which provides guidance on the presentation and disclosure of collaborative arrangements.

Product Sales Revenue for Latin America and Turkey

The Company is responsible for commercializing Crysvita in Latin America and Turkey.

Product Sales Revenue for Latin America and Türkiye

The Company is responsible for commercializing Crysvita in Latin America and Türkiye.

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.

In Turkey, KKC has the option to assume responsibility for commercialization efforts.

In Türkiye, KKC has the option to assume responsibility for commercialization efforts.

Transfer Price and Royalties on Product Sales Revenue

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in Latin America and Turkey, 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.

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in Latin America and Türkiye.

KKC charges the Company a transfer price of 30 % of net sales for supply of product to Latin America.

The Company also pays to KKC a low single-digit royalty on net sales in Latin America.

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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.

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.

The remaining profit or loss after supply costs from commercializing products in the Profit-Share Territory was shared between the Company and KKC on a 50 / 50 basis until April 2023.

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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 %.

The parties subsequently agreed that the Company would have the right to continue to support KKC in commercial field activities in the U.S.

through January 31, 2025, as amended.

After January 31, 2025, the Company’s rights to promote Crysvita in the U.S.

are limited to medical geneticists and the Company solely bears its expenses for the promotion of Crysvita in the Profit-Share Territory.

During the prior profit-share period, as KKC was the principal in the sale transaction with the customer, the Company recognized a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurred.

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Starting in April 2023, the Company began to record as royalty revenue in the period the underlying sales occurred.

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 11.

Liabilities for Sales of Future Royalties.”

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 11.

Liabilities for Sales of Future Royalties.” 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.

Total Crysvita revenue was as follows (in thousands):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

In July 2022, the Company sold to OMERS its right to receive 30 % of the future royalty payments, beginning in April 2023, that are due to the Company based on net sales of Crysvita in the U.S.

and Canada, subject to a cap.

In November 2025, the Company sold to OMERS its right to an additional 25 % of the future royalty payments, beginning in January 2028, that are due to the Company based on net sales of Crysvita in the U.S.

and Canada, subject to a cap.

These agreements are further described in “Note 10.

Liabilities for Sales of Future Royalties.”

Royalty Revenue for Sales in the European Territory

KKC has commercial responsibility for Crysvita in the European Territory.

Under the collaboration agreement, the Company is entitled to receive royalties of up to 10 % of net sales in the European Territory, which are recorded as royalty revenue as the underlying sales occur.

In December 2019, the Company sold its right to receive these royalty payments to Royalty Pharma, effective January 1, 2020, as further described in “Note 10.

Liabilities for Sales of Future Royalties.”

Total Crysvita revenue was as follows (in millions):

Year Ended December 31,

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Total Crysvita revenue

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.

Collaboration Cost Sharing and Payments

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KKC also receives a transfer price and royalty on net product sales revenue which is recorded 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):

These amounts were recognized in the Company’s Consolidated Statements of Operations in connection with the collaboration agreement with KKC as follows (in millions):

Year Ended December 31,

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Collaboration Receivable and Payable

The Company had accounts receivable from KKC in the amount of $ 85.4 million and $ 39.2 million from profit-share revenue and royalties and other receivables recorded in other current assets of $ 1.8 million and $ 1.1 million and accrued liabilities of $ 7.1 million and $ 5.3 million from amounts owed for transfer price and royalties as well as commercial and development activity reimbursements, as of December 31, 2024 and 2023, respectively.

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 for the treatment of LC-FAOD.

During the year ended December 31, 2022, the Company recorded $ 2.5 million for the attainment of a commercial milestone as a finite-lived intangible asset.

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 pays BRI a mid- single-digit royalty on net sales of the licensed product in the licensed territories.

In January 2022, the Company announced a collaboration with Regeneron to commercialize Evkeeza for HoFH outside of the U.S.

The Company had accounts receivable from KKC in the amount of $ 98 million and $ 85 million from royalties, other receivables of $ 1 million and $ 2 million recorded in other current assets, and accrued liabilities of $ 12 million and $ 7 million from amounts owed for transfer price and royalties as well as commercial and development activity reimbursements, as of December 31, 2025 and 2024, respectively.

In January 2022, the Company entered into a collaboration with Regeneron to commercialize Evkeeza for HoFH outside of the U.S.

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 paid Regeneron a $ 30 million upfront payment.

As of December 31, 2024 the Company has recognized an aggregate of $ 27.5 million for regulatory and sales milestones under the agreement, of which $ 15.0

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

million was achieved during the year ended December 31, 2024.

As of December 31, 2025 , the Company has recognized an aggregate of $ 33 million for regulatory and sales milestones under the agreement.

As these payments are for the Company’s use of intellectual property for Evkeeza for HoFH, they were recorded as intangible assets.

Intangible Assets, net" for additional details.

Going forward, the Company is obligated to pay Regeneron up to an aggregate of $ 35.5 million of future obligations for additional regulatory and sales milestones, if achieved.

The Company may share in certain costs for global trials led by Regeneron and also received the right to opt into other potential indications.

Additionally, the Company pays Regeneron a transfer price fee and royalties on certain revenues.

The Company is required to pay up to an aggregate of $ 31 million in the future contingent upon the achievement of certain regulatory and sales milestones.

The Company may share in certain costs for global trials led by Regeneron.

Additionally, the Company pays Regeneron a product purchase price and royalties on certain revenues.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The collaboration agreement is within the scope of ASC 808 which provides guidance on the presentation and disclosure of collaborative arrangements.

As the Company is the principal in sales transactions with the customer, the Company recognizes 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.

Under the collaboration agreement, Regeneron supplies the product and charges the Company a product purchase price from the low 20 % range up to 40 % on net sales, which is recognized as cost of sales in the Company’s Consolidated Statement of Operations.

Under the collaboration agreement, Regeneron and the Company share certain development and commercialization costs.

Regeneron also receives a transfer price and royalty on net product sales revenue which is recorded in cost of sales.

These amounts were recognized in the Company’s Statements of Operations in connection with the collaboration agreement with Regeneron as follows (in thousands):

Regeneron also receives a product purchase price and royalty on net product sales revenue which is recorded in cost of sales.

These amounts were recognized in the Company’s Consolidated Statements of Operations in connection with the collaboration agreement with Regeneron as follows (in millions):

Year Ended December 31,

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Cost of sales

The Company had collaboration payables for this arrangement included in accrued liabilities on the Consolidated Balance Sheets of $ 17.8 million and $ 10.6 million as of December 31, 2024 and December 31, 2023, respectively.

The Company had collaboration payables for this arrangement included in accrued liabilities on the Consolidated Balance Sheets of $ 9 million and $ 18 million as of December 31, 2025 and 2024, respectively.

Saint Louis University

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Under this agreement, the Company is obligated to pay up to $ 1 million contingent upon achievement of development and regulatory milestones as well as royalties in the low single-digits of net sales.

The Company paid Abeona $ 3.1 million for prior development and transition costs which were recorded as research and development expense for the year ended December 31, 2022.

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, as amended, 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, or the Ultragenyx Territory, excluding the EEA, UK, and Switzerland, or the Mereo Territory, where Mereo retains commercial rights.

The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Türkiye, and the rest of the world, or the Ultragenyx Territory, excluding the EEA, UK, and Switzerland, or the Mereo Territory, where Mereo retains commercial rights.

Each party will be responsible for post-marketing

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Upon the closing of the transactions under the License and Collaboration Agreement with Mereo in January 2021, the Company made a payment of $ 50 million to Mereo.

To date, the Company has made payments totaling $ 9.0 million for regulatory milestones achieved.

As of December 31, 2025, the Company has made payments totaling $ 9 million for regulatory milestones achieved.

The Company is obligated to pay Mereo up to $ 245 million in future milestone payments, contingent upon the achievement of certain regulatory and commercial milestones.

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Mereo will pay the Company a fixed double-digit percentage royalty on net sales in the Mereo Territory.

If the Company receives and resells an FDA PRV in connection with a new drug application approval, Mereo is entitled to receive a portion of proceeds from the sale of the PRV or a cash payment from the Company, in the event the Company chooses to retain the PRV.

If the Company receives and resells an FDA priority review voucher, or PRV, in connection with a new drug application approval, Mereo is entitled to receive a portion of proceeds from the sale of the PRV or a cash payment from the Company, in the event the Company chooses to retain the PRV.

In December 2024, the Company entered into a manufacturing and supply agreement with Mereo where it is responsible for the supply of setrusumab to Mereo in the Mereo Territory.

Mereo is responsible to reimburse us for a portion of the manufacturing process development costs as well as future commercial supply costs.

Mereo is responsible for reimbursing us for a portion of the manufacturing process development costs as well as future commercial supply costs.

Although Mereo is a VIE, 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.

F or the year ended December 31, 2024, the Company recorded an offset to research and development expense of $ 0.9 million.

For the years ended December 31, 2025 and 2024 , the Company recorded offsets to research and development expense of $ 5 million and $ 1 million, respectively.

For the year ended December 31, 2023, the Company recorded development costs of $ 9 million for the achievement of a clinical milestone recorded in research and development expense.

As of December 31, 2025 and 2024, t he Company had receivables from Mereo in the amount of $ 1 million and $ 1 million, respectively, recorded in other current assets for development activity reimbursements.

GeneTx Biotherapeutics LLC

In August 2019, the Company entered into a Program Agreement and a Unitholder Option Agreement with GeneTx Biotherapeutics LLC, or GeneTx, as subsequently amended, or the Option Agreement, to collaborate on the development of GeneTx’s GTX-102, an ASO for the treatment of Angelman syndrome.

In July 2022, the Company exercised its option to acquire GeneTx, pursuant to the terms of the Option Agreement.

During the year ended December 31, 2024, the Company achieved a $ 30 million regulatory milestone upon the initiation of the Phase 3 Aspire clinical study for GTX-102.

The Company is obligated to pay up to $ 85 million in additional regulatory approval milestones for the achievement of U.S.

and EU product approvals, and up to $ 75 million in commercial milestone payments based on annual worldwide net product sales, contingent upon the achievement of the milestones.

The Company will also pay tiered mid- to high single-digit percentage royalties based on licensed product annual net sales.

As part of the Company's acquisition of GeneTx, the Company assumed a License Agreement with Texas A&M University, or TAMU.

The Company recognized an aggregate of $ 1 million for clinical milestones under the TAMU agreement, and has future obligations up to $ 23 million for various milestones and a nominal annual license fee that may increase up to a maximum of $ 2 million.

The Company will also pay mid-single-digit percentage royalties based on licensed product annual net sales.

As of December 31, 2025 and 2024 , the Company had nil and $ 1 million, respectively, in collaboration payables under this arrangement.

Prior to the achievement of certain development and regulatory milestones, amounts paid towards the milestones are classified as in-process research and development expense, as the acquired in-process research and development intangible asset has not yet reached technological feasibility and has no alternative future use.

University of Pennsylvania

1 unchanged sentence

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 will fund the cost of the research program in accordance with a mutually agreed-upon research budget and will be responsible for clinical development,

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

manufacturing and commercialization of each indication.

The Company is obligated to make milestone payments of up to $ 5 million for each indication, if certain development milestones are achieved.

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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, which are 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 a nominal annual maintenance fee 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 is obligated to pay nominal annual fees, milestone payments of up to $ 14.0 million contingent upon achievement, 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.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

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 holds 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 VIE, 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, 2022

Change in fair value

December 31, 2023

Change in fair value

December 31, 2024

Arcturus Therapeutics Holdings Inc.

The Company previously held an investment in shares of common stock from Arcturus Therapeutics Holdings Inc., or Arcturus, which 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, 2024 and 2023, the Company held no shares of Arcturus common stock.

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

Change in fair value

Sale of shares

December 31, 2022

This license agreement was terminated for certain indications in November 2025.

The Company also had an option and license agreement with REGENX under which the Company had 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 .

This option and license agreement was terminated in November 2025.

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 2031 .

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The variable lease expense primarily consists of common area maintenance and other operating costs.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The components of lease expense were as follows (in thousands):

The components of lease expense were as follows (in millions):

Year Ended December 31,

1 unchanged sentence

Variable lease expense

Interest expense

Cash paid for amounts included in the measurement of operating lease liabilities for the years ended December 31, 2025, 2024, and 2023 was $ 14 million, $ 16 million, and $ 13 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 million and $ 26 million as of December 31, 2025 and 2024, 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, 2024:

The following table summarizes maturities of lease liabilities and the reconciliation of lease liabilities as of December 31, 2025 (in millions):

Year Ending December 31,

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Lease liabilities, non-current

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, 2024 and 2023 , the weighted-average remaining operating lease terms were 4 years and 5 years, respectively, the weighted-average discount rates used to determine the lease liability for operating leases were 10.1 % and 9.6 %, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

For the years ended December 31, 2025 and 2024, the weighted-average remaining operating lease terms and the weighted-average discount rates used to determine the lease liability were as follows:

Year Ended December 31,

Weighted-average remaining lease term (in years)

Weighted-average discount rate

Liabilities for Sales of Future Royalties

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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 million prior to December 31, 2030, or when aggregate royalty payments received by RPI are equal to $ 800 million.

In July 2022, the Company entered into a Royalty Purchase Agreement with OMERS.

In July 2022, the Company entered into a Royalty Purchase Agreement with OMERS, or the 2022 OMERS Agreement.

Pursuant to the agreement, OMERS paid $ 500 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.

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 million or on the date the final royalty payment is made to the Company under the KKC Collaboration Agreement.

In November 2025, the Company entered into a second Royalty Purchase Agreement with OMERS, or the 2025 OMERS Agreement.

Pursuant to the agreement, OMERS paid $ 400 million to the Company in exchange for the right to receive an additional 25 % of future royalty payments, starting on January 1, 2028, on net sales of Crysvita in the U.S.

OMERS will also continue to receive 30 % of Crysvita net sales in the U.S.

and Canada following the achievement of $ 725 million in aggregate payments under the 2022 OMERS Agreement.

The 2025 OMERS Agreement will expire upon the earlier of the date on which aggregate payments received by OMERS under this transaction equal $ 620 million or on the date the final royalty payment is made to the Company under the KKC Collaboration Agreeme nt.

Under the agreement, OMERS granted the Company an option to repurchase the entire purchased interest, that expires in November 2027 , for 1.35 times the purchase price, or $ 540 million .

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.

Upon inception of the respective arrangements, the Company recorded liabilities of $ 320 million, $ 500 million, and $ 400 million, net of transaction costs of $ 6 million, $ 9 million, and $ 8 million, for the RPI Agreement, the 2022 OMERS Agreement, and the 2025 OMERS Agreement, respectively.

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, 2024

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

have been $ 99.3 million and $ 123.3 million, respectively.

The Company’s effective annual interest rates were 6.2 % and 7.5 %, for RPI and OMERS, respectively, as of December 31, 2024.

Royalties earned under the RPI Agreement, the 2022 OMERS Agreement, and the 2025 OMERS Agreement from inception to December 31, 2025 have been $ 128 million, $ 206 million, and nil , respectively.

The Company’s effective annual interest rates were 5.5 %, 7.3 %, and 9 .2 % for the RPI Agreement, the 2022 OMERS Agreement, and the 2025 OMERS Agreement, respectively, as of December 31, 2025.

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.

2 unchanged sentences

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):

The following table shows the activity within the liability account (in millions):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Liabilities for Sales of Future Royalties

3 unchanged sentences

December 31, 2024

Net proceeds from sale of future royalties

Royalty revenue

2 unchanged sentences

At-the-Market Offerings

In February 2024, the Company entered into a Sales Agreement with Cowen and Company, LLC, or Cowen, 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 Cowen.

No shares were sold under this agreement during the year ended December 31, 2024.

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 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.

In February 2024, the Company entered into a Sales Agreement with Cowen and Company, LLC, or Cowen, pursuant to which the Company may offer and sell shares of the Company’s common stock having an aggregate offering proceeds of up to $ 350 million, from time to time, in at-the-market, or ATM, offerings through Cowen.

The Company sold 2.2 million shares under the ATM for net proceeds of $ 80 million during the year ended December 31, 2025.

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 of up to $ 350 million, from time to time, in ATM offerings through Jefferies.

During the year ended December 31, 2023 , there were 1.2 million shares sold under the ATM resulting in net proceeds of $ 53 million.

Underwritten Public Offering

In June 2024, the Company completed an underwritten public offering in which 8,782,051 shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1,346,153 shares, at a public offering price of $ 39.00 per share.

In connection with the offering, the Company sold to certain investors pre-funded warrants, in lieu of common stock, to purchase 1,538,501 shares of common stock at a purchase price of $ 38.999 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.

In June 2024, the Company completed an underwritten public offering in which 8.8 million shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1.3 million shares, at a public offering price of $ 39.00 per share.

In connection with the offering, the Company sold to certain investors pre-funded warrants, in lieu of common stock, to purchase 1.5 million shares of common stock at a purchase price of $ 38.999 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 proceeds that the Company received from the offering were $ 381 million, net of underwriting discounts and commissions.

In October 2023, the Company completed an underwritten public offering in which 9.8 million shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1.5 million 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 1.7 million 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 proceeds that the Company received from the offering were $ 327 million, net of underwriting discounts and commissions.

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

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

consideration, are fully vested, and are exercisable after the original issuance date of the pre-funded warrants.

As of December 31, 2024 , no ne of the pre-funded warrants had been exercised.

As of December 31, 2025 , no pre-funded warrants had been exercised.

The table below summarizes pre-funded warrants activity:

3 unchanged sentences

As of December 31, 2024

Issuance of pre-funded warrants

Changes and adjustments

As of December 31, 2025

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 proceeds that the Company received from the offering were $ 326.5 million, net of underwriting discounts and commissions.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Stock-Based Awards

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ESPP purchases are settled with common stock from the ESPP’s previously authorized and available pool of shares.

During the year ended December 31, 2024 , the Company issued 200,539 shares of common stock under the ESPP.

During the year ended December 31, 2025 , the Company issued 0.2 million shares of common stock under the ESPP.

The table below summarizes the Company's equity plans as of December 31, 2025:

7 unchanged sentences

2014 Employee Stock Purchase Plan

(1) Maximum number of shares authorized and shares available for future issuance under the 2023 Incentive Plan include 1,975,837 shares subject to the 2014 Incentive Plan cancelled after June 7, 2023 .

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

(1) Maximum number of shares authorized and shares available for future issuance under the 2023 Incentive Plan includes 4.0 million shares subject to the 2014 Incentive Plan cancelled after June 7, 2023 .

Stock Option Activity

5 unchanged sentences

Aggregate Intrinsic Value

(In thousands)

(In millions)

Outstanding — December 31, 2024

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Vested and expected to vest — December 31, 2025

The following table summarizes the Company's options exercised and vested for each of the periods indicated (in thousands except for weighted-average estimated fair value of options granted):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The following table summarizes the Company's options exercised and vested for each of the periods indicated (in millions except for weighted-average estimated fair value of options granted):

Year Ended December 31,

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Vested and expected to vest — December 31, 2025

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

During the year ended December 31, 2022, PSOs were granted to certain nonexecutive employees.

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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, 2024, certain operational milestones were deemed probable of achievement.

As of December 31, 2025, certain operational milestones had been achieved.

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 years ended December 31, 2024 and 2023, was $ 9.9 million and $ 3.4 million, respectively.

No PSOs were granted or exercised during the years ended December 31, 2024 and 2023.

The weighted-average estimated fair value of PSOs granted was $ 28.76 during the year ended December 31, 2022.

The total estimated grant date fair value of PSOs vested during the years ended December 31, 2025, 2024, and 2023 was $ 14 million, $ 10 million, and $ 3 million, respectively.

Restricted Stock Units

1 unchanged sentence

RSUs Outstanding

Number of Shares

Weighted-Average Grant Date Fair Value

2 unchanged sentences

Unvested — December 31, 2025

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The fair value of the RSUs is determined on the grant date based on the fair value of the Company’s common stock.

5 unchanged sentences

PSUs Outstanding

Number of Shares

Weighted-Average Grant Date Fair Value

8 unchanged sentences

The total grant date fair value of the PSUs vested during the years ended December 31, 2025, 2024, and 2023 was $ 12 million, $ 3 million, and $ 4 million, respectively, with an aggregate intrinsic value of the shares of $ 9 million, $ 2 million and $ 1 million, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Stock-Based Compensation Expense

Total stock-based compensation expense recognized was as follows (in thousands):

Total stock-based compensation expense recognized was as follows (in millions):

Year Ended December 31,

14 unchanged sentences

Therefore, the Company used an expected dividend yield of zero.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Strike price for options awards and PSOs is equal to the closing market value of our common stock on the date of grant.

5 unchanged sentences

Expected dividend rate

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,

Expected term in years

Expected volatility

Risk-free interest rate

Expected dividend rate

Defined Contribution Plan

3 unchanged sentences

The Company recorded $ 10 million, $ 10 million, and $ 10 million as expense related to the plan for the years ended December 31, 2025, 2024, and 2023 , respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The components of the Company’s loss (income) before income taxes were as follows (in thousands):

The components of the Company’s loss before income taxes were as follows (in millions):

Year Ended December 31,

Total loss before income taxes

The components of the Company’s income tax provision were as follows (in thousands):

The components of the Company’s income tax provision (benefit) were as follows (in millions):

Year Ended December 31,

4 unchanged sentences

International

Total deferred tax provision

Total deferred tax benefit

Total provision for (benefit from) income taxes

2 unchanged sentences

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 15 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, and then offset by an income tax expense of $ 3.0 million from foreign jurisdictions.

For the year ended December 31, 2024, the Company recognized an income tax expense of $ 0.2 million for state tax, and income tax expense of $ 1.4 million from foreign jurisdictions.

The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows:

For the year ended December 31, 2023, the Company recognized an income tax benefit of $ 5 million attributable to modifications in its state apportionment methodology, offset by an income tax expense of $ 3 million from foreign jurisdictions.

For the year ended December 31, 2024, the Company recognized income tax expense of $ 1 million from foreign jurisdictions alongside a nominal amount of state tax.

For the year ended December 31, 2025, the Company recognized income tax expense of $ 4 million from foreign jurisdictions and a nominal amount of state tax.

The Company realized no benefit for current year losses due to a full valuation allowance against the U.S.

net deferred tax assets.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The table below provides the updated requirements of ASU 2023-09 for the year ended December 31, 2025.

The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows (in millions except percentage amounts):

Year Ended December 31,

1 unchanged sentence

State income taxes, net of federal benefit (1)

Foreign tax effects

Effect of changes in tax laws or rates enacted in the current period

Effect of cross-border tax laws

Research tax credit

Orphan drug credit

Change in valuation allowance

Nontaxable or nondeductible items

Share-based payment awards

Uncertain tax positions

Other Adjustments

Provision for income taxes

(1) Includes a nominal amount of state tax.

Illinois State tax made up the majority (greater than 50 percent) of the tax effect in this category.

As previously disclosed for the years ended December 31, 2024 and 2023, prior to the adoption of ASU 2023-09, the effective income tax rate differs from the statutory federal income tax rate as follows:

Year Ended December 31,

Federal statutory income tax

State income taxes, net of federal benefit

Federal tax credits

7 unchanged sentences

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):

Income taxes paid ( net of refunds) for the year ended December 31, 2025 is disaggregated as follows (in millions):

Year Ended December 31,

Federal income taxes paid (net of refunds)

State income taxes paid (net of refunds)

Foreign income taxes paid (net of refunds)

Total income taxes paid (net of refunds)

(1) There was a nominal amount of foreign taxes paid (net of refunds) to Canada, Switzerland, France, Japan, and the Netherlands.

The tax effect of temporary differences that give rise to significant portions of the deferred tax assets is presented below (in millions):

Year Ended December 31,

Deferred tax assets:

17 unchanged sentences

As of December 31, 2025 and 2024 , the Company had federal research tax credit carryforwards of approximately $ 60 million and $ 45 million, respectively, available to reduce future tax liabilities that will begin to expire in 2031 .

As of December 31, 2024 and 2023 , the Company had state research credit carryforwards of $ 92.0 million and $ 74.4 million, respectively, available to reduce future tax liabilities that will be carried forward indefinitely.

As of December 31, 2024 and 2023 , the Company had federal Orphan Drug Credits of $ 338.5 million and $ 269.6 million, respectively, available to reduce future tax liabilities that will begin to expire in 2031 .

As of December 31, 2025 and 2024 , the Company had state research credit carryforwards of $ 110 million and $ 92 million, respectively, available to reduce future tax liabilities.

The majority of these credits will be carried forward indefinitely, and others will expire at various dates in the future.

As of December 31, 2025 and 2024 , the Company had federal Orphan Drug Credits of approximately $ 379 million and $ 339 million, respectively, available to reduce future tax liabilities that will begin to expire in 2031 .

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

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.

As a result of ownership changes in 2012 and 2011, $ 4 million of federal net operating loss carryforwards, $ 4 million of state net operating loss carryforwards, and a nominal amount 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.

1 unchanged sentence

The Company recorded unrecognized tax benefits for uncertainties in income taxes.

A reconciliation of the Company’s unrecognized tax benefits follows (in thousands):

A reconciliation of the Company’s unrecognized tax benefits follows (in millions):

Balance at beginning of year

3 unchanged sentences

Balance at end of year

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Approximately $ 1 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 years ended December 31, 2024 and 2023, the Company recognized accrued interest and penalties of $ 0.1 million and $ 0.2 million, respectively, as a component of income tax expense.

No accrued interest and penalties were recognized as a component of income tax expense during the year ended December 31, 2022.

For the years ended December 31, 2025, 2024 and 2023, the Company recognized nominal amounts for accrued interest and penalties as a component of income tax expense.

The Company does not anticipate that the amount of existing unrecognized tax benefits will significantly increase or decrease during the next year.

7 unchanged sentences

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.

The Company has various manufacturing, 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, 2024, the aggregate payments under contractually-binding manufacturing and service agreements are as follows (in thousands):

Year Ended December 31,

Manufacturing and Services

Manufacturing and service contract obligations primarily relate to manufacturing of product for our clinical stage pipeline, the majority of which are due in the next 12 month s .

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.

2 unchanged sentences

License and Research Agreements.”

See “Note 10.

Leases” for lease commitments.

3 unchanged sentences

The process of resolving matters through litigation or other means is inherently uncertain, however 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.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Guarantees and Indemnifications

6 unchanged sentences

Accordingly, it has not recognized any liabilities relating to these obligations for any period presented.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

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, at the time also served as board members of the foundation, whereby an aggregate $ 1 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, $ 0.3 million, and $ 0.3 million as research and development expense for this agreement for the years ended December 31, 2024, 2023, and 2022 , respectively.

A total of $ 1 million has been recorded as research and development expense for this agreement to date.

There are no further obligations under this agreement.

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, 2024, 2023, and 2022 (in thousands, except share and per share data):

The following table sets forth the computation of the basic and diluted net loss per share during the years ended December 31, 2025, 2024, and 2023 (in millions, except per share data):

Year Ended December 31,

2 unchanged sentences

Net loss per share, basic and diluted

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,

1 unchanged sentence

restricted stock units, and performance stock units

Employee stock purchase plan

Accumulated Other Comprehensive (Loss) Income

Total accumulated other comprehensive (loss) income consisted of the following (in thousands):

Accumulated Other Comprehensive Income (Loss)

Total accumulated other comprehensive income (loss) consisted of the following (in millions):

Year Ended December 31,

Cumulative foreign currency translation adjustment

Unrealized gain (loss) on securities available-for-sale

Total accumulated other comprehensive (loss) income

Unrealized gain on securities available-for-sale

Total accumulated other comprehensive income (loss)

Subsequent Events

In February 2026, the Company’s Board of Directors approved a strategic restructuring plan that includes a reduction of approximately 10 % of the Company’s workforce, or the Restructuring Plan.

As a result of this reduction in force, the Company estimates that it will incur restructuring charges of approximately $ 50 million in total in connection with employee related termination and severance costs, charges for the termination of UX143 manufacturing agreements, and other related activities,

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

substantially all of which are expected to be recognized during the first half of 2026.

Cash payments related to these costs are expected to be made over the same period.

The Restructuring Plan is intended to reduce the Company's headcount and expenses by focusing resources on the Company’s largest value drivers.

Management’s estimates are based on information available as of the approval date of the Restructuring Plan and are subject to change as the plan is implemented.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures