What changed in this filing

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Item 9A. Controls and Procedures

2025-02-19 compared with 2024-02-21 · 366 added, 317 removed, 1124 unchanged (38% of the section changed)

18 unchanged sentences

Opinion on Internal Control Over Financial Reporting

We have audited Ultragenyx Pharmaceutical Inc.’s internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the

Treadway Commission ( 2013 framework) (the COSO criteria).

We have audited Ultragenyx Pharmaceutical Inc.’s internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission ( 2013 framework) (the COSO criteria).

In our opinion, Ultragenyx Pharmaceutical Inc.

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Other Information

On November 10, 2023 , Corsee Sanders , Ph.D., a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 2,322 shares of the Company’s common stock through July 12, 2024, subject to certain conditions.

On December 7, 2023 , Matthew Fust , a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 12,195 shares of the Company’s common stock through December 6, 2024, subject to certain conditions.

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

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 2024 Annual Meeting of Stockholders, which we will file with the SEC within 120 days of the end of the fiscal year to which this Annual Report relates, or the “2024 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,” “Executive Officers,” ““Board of Directors and Committees,” and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.” We have adopted a code of ethics that applies to all of our directors, officers and employees, including our principal executive, principal financial and principal accounting officers, or persons performing similar functions, or Code of Ethics.

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

We intend to disclose future amendments to certain provisions of the Code of Ethics, and waivers of the Code of Ethics granted to executive officers and directors, on the website within four business days following the date of the amendment or waiver.

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.

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

We intend to disclose future amendments to certain provisions of the Global Code of Conduct, and waivers of the Global Code of Conduct granted to executive officers and directors, on the website within four business days following the date of the amendment or waiver.

Executive Compensation

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Form of Pre-Funded Warrant

Description of Common Stock

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and Kyowa Kirin Co., Ltd.

Supply Agreement, effective as of November 18, 2020, between Ultragenyx Pharmaceutical Inc.

and Kyowa Kirin Inc.

Amendment No.

1, effective as of September 13, 2024, to the Supply Agreement between Ultragenyx Pharmaceutical Inc.

and Kyowa Kirin, Inc.

Unit Purchase Agreement, dated as of July 15, 2022, by and among Ultragenyx Pharmaceutical Inc., GeneTx Biotherapeutics LLC, the Unitholders and Deborah A.

Commercial Supply and Services Agreement – Drug Substance, effective December 7, 2017, between Ultragenyx Europe GmbH and Rentschler Biopharma SE

Commercial Master Service Agreement – Drug Product, effective February 22, 2021, between Ultragenyx Pharmaceutical Inc.

and BSP Pharmaceuticals S.p.A

Commercial Supply Agreement, dated June 19, 2023, between Ultragenyx Pharmaceutical Inc.

and IOI Oleo GmbH

Royalty Purchase Agreement, dated as of December 17, 2019, between Ultragenyx Pharmaceutical Inc.

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Form of Restricted Stock Unit Agreement (Grant for New Directors) (2014 Plan)

2023 Incentive Plan

Amended and Restated 2023 Incentive Plan

Form of Incentive Stock Option Agreement (2023 Plan)

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Form of Performance Stock Unit Agreement (2023)

Form of Performance Stock Unit Agreement (2024)

Amended and Restated 2014 Employee Stock Purchase Plan

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First Amendment to Employment Inducement Plan

Second Amendment to Employment Inducement Plan

Form of Non Statutory Stock Option Agreement (Inducement Plan)

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and Condiotti Enterprises, Inc.

Addendum #7 to Standard Lease, effective as of November 22, 2024, between Ultragenyx Pharmaceutical Inc.

and Condiotti Enterprises, Inc.

Lease Agreement, dated as of December 8, 2015, between Marina Boulevard Property, LLC and Ultragenyx Pharmaceutical Inc.

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and ARE-MA Region No., LLC.

Fifth Amendment, dated November 25, 2024, to the Lease Agreement between Ultragenyx Pharmaceutical Inc.

and ARE-MA Region No.

Lease Agreement, dated December 15, 2019, between Ultragenyx Pharmaceutical Inc.

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and ARE-San Francisco No.

Fourth Amendment, dated December 13, 2024, to the Lease Agreement between Ultragenyx Pharmaceutical Inc.

and GI ETS Shoreline LLC (as successor-in-interest to ARE-San Francisco No.

Office Lease, dated April 19, 2019, between Ultragenyx Pharmaceutical Inc.

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and Brickbottom I QOZB L.P.

First Amendment, dated March 12, 2024, between Ultragenyx Pharmaceutical Inc.

and Brickbottom I QOZB L.P.

Ultragenyx Insider Trading Policy

Subsidiaries of Ultragenyx Pharmaceutical Inc.

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(1) relates to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective or complex judgments.

The communication of the critical audit matter does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing a separate opinion on the critical audit matter or on the accounts or disclosures to which it relates.

Liabilities for sales of future royalties

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Specifically, the forecasted revenues of Crysvita involve significant estimation uncertainty given the limited historical Crysvita sales data.

How We Addressed the Matter in Our Audit

How We Addressed the Matter

We obtained an understanding, evaluated the design and tested the operating effectiveness of controls over the Company’s process of accounting for the liabilities related to the sale of future royalties, including controls over the Company’s estimates of projected sales of Crysvita in the European and North American markets.

To test management’s estimates of the future royalties and the imputed effective interest rates, we performed audit procedures that included, among others, evaluating the reasonableness of management’s assumptions related to the treatable patient populations, estimated pricing and reimbursement, and the rate of adoption.

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.

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Accounts receivable, net

Prepaid expenses and other assets

Total current assets

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Accrued liabilities

Contract liabilities

Lease liabilities

Liabilities for sales of future royalties

Other liabilities

Total current liabilities

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Total liabilities

Commitments and contingencies (Notes 9 and 15)

Commitments and contingencies (Note 16)

Noncontrolling interest

Stockholders’ equity:

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outstanding— 92,484,330 in 2024 and 82,315,590 in 2023

Treasury stock, at cost, 9,559 in 2023 and nil in 2022

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

Deferred compensation obligation

Additional paid-in capital

Accumulated other comprehensive income (loss)

Accumulated other comprehensive (loss) income

Accumulated deficit

Total stockholders’ equity

Total liabilities and stockholders’ equity

Total liabilities, noncontrolling interest and stockholders’ equity

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.

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Loss before income taxes

Benefit from (provision for) income taxes

(Provision for) benefit from income taxes

Net loss per share, basic and diluted

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Foreign currency translation adjustments

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

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

Other comprehensive income (loss):

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Balance as of December 31, 2021

Issuance of common stock in connection with at-the-market

offering, net of issuance costs

Stock-based compensation

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Balance as of December 31, 2022

Issuance of common stock and pre-funded warrants in connection with underwritten

public offering, net of issuance costs

Issuance of common stock in connection with

at-the-market offering, net of issuance costs

Stock-based compensation

1 unchanged sentence

equity plan awards, net of tax

Other comprehensive loss

Deferred compensation

Other comprehensive income

Balance as of December 31, 2023

1 unchanged sentence

public offering, net of issuance costs

Issuance of common stock in connection with

at-the-market offering, net of issuance costs

Stock-based compensation

2 unchanged sentences

Deferred compensation

Other comprehensive income

Other comprehensive loss

Balance as of December 31, 2024

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Accounts receivable

Prepaid expenses and other assets

Accounts payable, accrued, and other liabilities

Contract liabilities, net

Deferred tax liabilities

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Payment for intangible asset

Net cash provided by (used in) investing activities

Net cash (used in) provided by investing activities

Financing activities:

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offering, net of issuances costs

Proceeds from the issuance of common stock from exercise of warrants and equity

Proceeds from the issuance of common stock from exercise of equity

plan awards, net

Proceeds from issuance of equity interest in noncontrolling interest

Net cash provided by financing activities

Effect of exchange rate changes on cash

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

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

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

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Evkeeza® (evinacumab) is approved in the U.S.

and the European Economic Area, or EEA, for the treatment of homozygous familial hypercholesterolemia, or HoFH.

and the European Economic Area, or EEA, and Japan for the treatment of homozygous familial hypercholesterolemia, or HoFH.

The Company has exclusive rights to commercialize Evkeeza® (evinacumab) outside of the U.S.

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• DTX301 is an AAV8 gene therapy product candidate in development for the treatment of patients with ornithine transcarbamylase, or OTC deficiency, the most common urea cycle disorder;

• UX143 (setrusumab), which is subject to the Company ’ s collaboration agreement with Mereo BioPharma 3, or Mereo, is a fully human monoclonal antibody that inhibits sclerostin, a protein that acts on a key bone-signaling pathway and inhibits the activity of bone-forming cells for the treatment of patients with osteogenesis imperfect, or OI;

• GTX-102 is an antisense oligonucleotide, or ASO for the treatment of Angelman syndrome, a debilitating and rare neurogenetic disorder caused by loss-of-function of the maternally inherited allele of the UBE3A gene;

• UX701 is an adeno-associated virus 9, or AAV9, gene therapy designed to deliver stable expression of a truncated version of the ATP7B copper transporter following a single intravenous infusion to improve copper distribution and excretion from the body and reverse pathological findings of Wilson liver disease.

The Company has sustained operating losses and expects such annual losses to continue over the next several years.

The Company 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.

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Basis of Consolidation

The Consolidated Financial Statements include the accounts of Ultragenyx Pharmaceutical Inc.

and its wholly owned subsidiaries.

All intercompany balances and transactions have been eliminated.

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.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Segment Reporting

The Company operates as one reportable segment relating to the research, development and commercialization of its products.

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.

Use of Estimates

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Cash equivalents consist primarily of amounts invested in money market accounts.

Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility leases and the gene therapy building construction project.

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):

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

Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in other income (expense).

Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in other expense.

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

1 unchanged sentence

Equity Investments

The Company records investments in equity securities, other than equity method investments, at fair market value, if the fair value is readily determinable.

The Company records investments in equity securities, other than equity method investments, at fair market value, using market quotes when readily determinable.

Equity securities with no readily determinable fair values are recorded using the measurement alternative of cost adjusted for observable price changes in orderly transactions for identical or similar investments of the same issuer less impairment, if any.

Investments in equity securities are recorded in Equity investments on the Company's Consolidated Balance Sheets.

Investments in equity securities are recorded in other assets on the Company's Consolidated Balance Sheets.

Unrealized gains and losses are reported in change in fair value of equity investments on the Company’s Consolidated Statements of Operations.

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The Company is exposed to credit losses primarily through receivables from customers and collaborators and through its available-for-sale debt securities.

For trade receivables and other instruments, the Company uses a forward-looking expected loss model that generally results in the earlier recognition of allowances for losses.

For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities.

For trade receivables and other financial instruments, the Company uses a forward-looking expected loss model that recognizes a current period charge for losses that are expected to be incurred over the life of the financial instrument.

The Company’s expected loss allowance methodology for the receivables is developed using historical collection experience, current and future economic market conditions, a review of the current aging status and financial condition of the entities.

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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.

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.

There was no allowance for losses on available-for-sale debt securities which were attributable to credit risk for the years ended December 31, 2024 and 2023.

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Balance Sheet Components” for further disclosure on the useful lives of property, plant, and equipment.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Intangible Assets

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The Company measures fair value based on the estimated future undiscounted cash flows associated with these assets in addition to other assumptions and projections that the Company deems to be reasonable and supportable.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Indefinite-lived intangibles consist of acquired in-process research and development, or IPR&D.

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The Company determines the actual costs through obtaining information from external service providers as to the progress or stage of completion of the services and the agreed-upon fee to be paid for such services.

Liabilities for Sales of Future Royalties

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 11.

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.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources.

To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company employs the prospective method to adjust the amortization of the liabilities and the effective interest rate.

Revenue Recognition

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The Company sells its approved products through a limited number of distributors.

Under ASC 606, revenue from product sales is recognized at the point in time when control is transferred to these distributors.

Under Accounting Standards Codification, or ASC, 606, Revenue from Contracts with Customers, revenue from product sales is recognized at the point in time when control is transferred to these distributors.

The Company also recognizes revenue from sales of certain products on a “named patient” basis, which are allowed in certain countries prior to the commercial approval of the product.

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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.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Collaboration, License, and Royalty Revenue

The Company has certain license and collaboration agreements that are within the scope of Accounting Standards Codification, or ASC, 808, Collaborative Agreements , which provides guidance on the presentation and disclosure of collaborative arrangements.

The Company has certain license and collaboration agreements that are within the scope of ASC 808, Collaborative Agreements , which provides guidance on the presentation and disclosure of collaborative arrangements.

Generally, the classification of the transactions under the collaborative arrangements is determined based on the nature of contractual terms of the arrangement, along with the nature of the operations of the participants.

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

Liabilities for Sales of Future Royalties.” The Company records the royalty revenue from the net sales of Crysvita in the applicable territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the applicable arrangement.

As described in “Note 11.

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.

The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities.

The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers, or ASC 606, to determine the distinct performance obligations.

The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers , to determine the distinct performance obligations.

The Company analogizes to ASC 606 for the accounting for distinct performance obligations for which there is a customer relationship.

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Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved.

Total consideration may include nonrefundable upfront license fees, payments for research and development activities, reimbursement of certain third-party costs, payments based upon the achievement of specified milestones, and royalty payments based on product sales derived from the collaboration.

Total consideration may include nonrefundable upfront license fees, payments for research and

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

development activities, reimbursement of certain third-party costs, payments based upon the achievement of specified milestones, and royalty payments based on product sales derived from the collaboration.

If there are multiple distinct performance obligations, the Company allocates the transaction price to each distinct performance obligation based on its relative standalone selling price.

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The Company maintains a nonqualified deferred compensation plan whereby certain employees and members of the board of directors are able to defer certain equity awards and other compensation.

Amounts deferred are invested into shares of the Company's common stock, mutual funds, and other investment options.

Amounts deferred are invested into shares of the Company's common stock and corporate-owned life insurance.

The plan complies with the provisions of Section 409A of the Internal Revenue Code.

All of the various mutual funds held in the plan are classified as trading securities and recorded at fair value in other non-current assets in the Consolidated Balance Sheets with changes in fair value recognized as earnings in the period they occur.

All the investments held in the plan are recorded in other non-current assets in the Consolidated Balance Sheets.

The short-term portion of the corresponding liability for the plan is included in accrued expenses.

The long-term portion of the liability is included in other non-current liabilities in the Consolidated Balance Sheets.

Changes in the value of the deferred compensation assets and liabilities are recorded in earnings as they occur.

Certain equity awards deferred under the plan are required to be settled through the issuance of Company stock.

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The Company determines if an arrangement includes a lease at inception.

Right-of-use lease assets and lease liabilities are

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

recognized based on the present value of the future minimum lease payments over the lease term at the commencement date.

Right-of-use lease assets and lease liabilities are recognized based on the present value of the future minimum lease payments over the lease term at the commencement date.

The right-of-use lease asset includes any lease payments made and excludes lease incentives.

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

See “Note 10.

Leases” for further disclosure.

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Stock compensation expense on awards expected to vest is recognized net of estimated forfeitures.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company uses the liability method of accounting for income taxes.

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To date, there have been no interest or penalties charged in relation to the unrecognized tax benefits.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Foreign Currency

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Income and expense accounts are translated at average exchange rates for the period.

Transactions which are not in the functional currency of the entity are remeasured into the functional currency and gains or losses resulting from the remeasurement recorded in other income (expense).

Transactions which are not in the functional currency of the entity are remeasured into the functional currency and gains or losses resulting from the remeasurement recorded in other expense.

Net Loss per Share

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In periods when we have incurred a net loss, options and warrants to purchase common stock are considered common stock equivalents, but have been excluded from the calculation of diluted net loss per share, as their effect is antidilutive.

Recent Accounting Pronouncements

In November 2024, the FASB issued ASU 2024-03, Income Statement-Reporting Comprehensive Income-Expense Disaggregation Disclosures (Subtopic 220-40):

Disaggregation of Income Statement Expenses , requiring public entities to disclose additional information about specific expense categories in the notes to the financial statements on an interim and annual basis.

ASU 2024-03 is effective for fiscal years beginning after December 15, 2026, and for interim periods beginning after December 15, 2027, with early adoption permitted.

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.

The Company adopted ASU 2023-07 during the year ended December 31, 2024.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Fair Value Measurements

Financial assets and liabilities are recorded at fair value.

Certain financial assets and liabilities are recorded at fair value.

The carrying amount of certain financial instruments, including cash and cash equivalents, accounts receivable, accounts payable and accrued liabilities approximate fair value due to their relatively short maturities.

The carrying amounts of liabilities for the sales of future royalties also approximate their fair value.

Assets and liabilities recorded at fair value on a recurring basis in the balance sheets are categorized based upon the level of judgment associated with the inputs used to measure their fair values.

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Where applicable these models project future cash flows and discount the future amounts to a present value using market-based observable inputs obtained from various third-party data providers, including but not limited to, benchmark yields, interest rate curves, reported trades, broker/dealer quotes and reference data.

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

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

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):

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Money market funds

Certificates of deposit and time deposits

Time deposits

Corporate bonds

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Deferred compensation liabilities

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

December 31, 2023

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Government Treasury and agency securities

Debt securities in government-sponsored entities

Investment in Solid common stock

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Deferred compensation liabilities

Deferred compensation assets are recorded at fair value in other non-current assets in the Consolidated Balance Sheets.

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

Deferred compensation liabilities consist of short-term liabilities of $ 0.2 million and nil as of December 31, 2023 and 2022 , respectively, included in accrued liabilities on the Consolidated Balance Sheets, and long-term liabilities of $ 10.1 million and $ 4.7 million as of December 31, 2023 and 2022 , respectively, included in other non-current liabilities on the Consolidated Balance Sheets.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Deferred compensation liabilities consist of short-term liabilities of $ 0.6 million and $ 0.2 million as of December 31, 2024 and 2023 , respectively, included in accrued liabilities on the Consolidated Balance Sheets, and long-term liabilities of $ 15.2 million and $ 10.1 million as of December 31, 2024 and 2023, 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.

Balance Sheet Components

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Money market funds

Certificates of deposit and time deposits

Time deposits

Corporate bonds

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Gross Unrealized

Amortized Cost

Money market funds

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Government Treasury and agency securities

Debt securities in government-sponsored entities

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

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

All marketable securities with unrealized losses at December 31, 2024 have been in a loss position for less than 12 months or the loss is not material and is temporary in nature.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Inventory consists of the following (in thousands):

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Total inventory

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Property, Plant, and Equipment, net

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Leasehold improvements

Shorter of lease term or

estimated useful life

Shorter of lease term or estimated useful life

Research and development equipment

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Not applicable

Construction-in-progress

Not applicable

Varies by asset

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Amortization of leasehold improvements and software is included in depreciation expense.

Construction in progress reflects amounts incurred for construction or improvements of property or costs for equipment that has not been placed in service.

The construction-in-progress balance as of December 31, 2022 is primarily the construction costs for the gene therapy manufacturing facility in Bedford, Massachusetts.

Accrued Liabilities

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Payroll and related expenses

Revenue related reserves

Total accrued liabilities

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Indefinite-lived Intangibles

The Company has IPR&D assets of $ 129.0 million as of December 31, 2023 and 2022.

As a result of the accounting for our acquisition of Dimension Therapeutics, Inc.

in November 2017, the Company has IPR&D assets of $ 129.0 million as of December 31, 2024 and 2023.

IPR&D assets represent the fair value of acquired programs to develop an AAV gene therapy for OTC deficiency and to develop an AAV gene therapy for glycogen storage disease type Ia.

The fair value of IPR&D assets acquired was determined based on the discounted present value of each research project’s projected cash flows using an income approach, including the application of probability factors related to the likelihood of success of the program reaching final development and commercialization.

Additionally, the projections consider the relevant market sizes and growth factors, estimated future cash flows from product sales resulting from completed products and in-process projects and timing and costs to complete the in-process projects.

The rates utilized to discount the net cash flows to their present value are commensurate with the stage of development of the projects and uncertainties in the economic estimates used in the projections.

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

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Notes to Consolidated Financial Statements (continued)

Subsequent to the FDA approval of Dojolvi for the treatment of LC-FAOD in 2020, the Company recorded $ 4.8 million for the attainment of various development and commercial milestones as finite-lived intangible assets which are amortized over a weighted-average useful life of 5.7 years.

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

Upon closing of the transaction in January 2022, the Company paid Regeneron a $ 30.0 million upfront payment.

During the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved.

As both the upfront payment and the regulatory milestone are related to the Company’s use of intellectual property for Evkeeza for HoFH, these amounts were recorded as intangible assets, which are amortized over a weighted-average useful life of ten years .

Pursuant to the collaboration agreement, the Company has incurred an upfront payment and regulatory and sales milestones to date totaling $ 57.5 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:

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Crysvita collaboration revenue in Profit-Share Territory

Crysvita royalty revenue in European Territory

Daiichi Sankyo

Total collaboration and license revenue

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Latin America

Europe, Middle East, and Africa

Total revenues

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

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

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 and 2022 (in thousands):

Year Ended December 31,

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 70 % and 53 % of the total accounts receivable balance as of December 31, 2024 and 2023 , respectively.

Investment in Amlogenyx.

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)

See Note 8 for additional details on contract liabilities activities.

The Company’s largest accounts receivable balance was from a collaboration partner and was 53 % and 68 % of the total accounts receivable balance as of December 31, 2023 and 2022 , respectively.

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.

Amlogenyx was determined to be a VIE and the Company is the primary beneficiary as it has the power to direct the activities that would most significantly impact the economic performance of Amlogenyx, including the performance of R&D activities relating to its sole product candidate.

As the primary beneficiary, the Company has consolidated the financial position, results of operations and cash flows of Amlogenyx in its financial statements and all intercompany balances have been eliminated in consolidation.

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.

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:

Noncontrolling Interest

As of December 31, 2023

Issuance of equity from noncontrolling interest

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

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In accordance with the terms of the Purchase Agreement, the Company paid the option exercise price of $ 75.0 million and an additional $ 15.6 million to acquire the outstanding cash of GeneTx, and adjustments for working capital and transaction expenses of $ 0.6 million, for a total purchase consideration of $ 91.2 million.

The Company may be required to make payments of up to $ 190.0 million upon the achievement of certain milestones, including up to $ 30.0 million in milestone payments upon achievement of the earlier of initiation of a Phase 3 clinical study or product approvals in Canada and the U.K., up to $ 85.0 million in additional regulatory approval milestones for the achievement of U.S.

and EU product approvals, and up to $ 75.0 million in commercial milestone payments based on annual worldwide net product sales.

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 is entitled to receive a portion of proceeds from the sale or a cash payment from the Company if the Company choses to retain the PRV.

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.

Under this agreement, TAMU is eligible to receive from the Company up to $ 23.5 million upon the achievement of various future milestones, a nominal annual license fee that may increase up to a maximum of $ 2.0 million, as well as royalties in the mid-single-digits of net sales.

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, the Company recorded the acquisition price of $ 75.0 million, net of cash and working capital acquired, as in-process research and development expense during the year ended December 31, 2022.

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)

License and Research Agreements

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Under the terms of this collaboration and license agreement, as amended, the Company and KKC collaborate on the development and commercialization of Crysvita in the field of orphan diseases in the U.S.

and Canada, or the Profit-Share Territory, and in the European Union, United Kingdom, and Switzerland, or the European Territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America.

Development Activities

In the field of orphan diseases, except for ongoing studies being conducted by KKC, the Company was the lead party for development activities in the Profit-Share Territory and in the European Territory until the applicable transition date.

The Company shared the costs for development activities in the Profit-Share Territory and the European Territory conducted pursuant to the development plan before the applicable transition date equally with KKC.

In April 2023, which was the transition date for the Profit-Share Territory, KKC became the lead party and became responsible for the costs of the subsequent development activities.

However, the Company will continue to equally share in the costs of the studies with KKC that commenced prior to the applicable transition date.

and Canada, or the Profit-Share Territory, and in the European Union, UK, and Switzerland, or the European Territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America.

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.

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.

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.

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

Collaboration and Royalty Revenue for Sales in the Profit-Share Territory

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Under the collaboration agreement, KKC manufactured and supplied Crysvita for commercial use in the Profit-Share Territory and charged the Company a transfer price of 30 % of net sales in 2023, and 35 % prior to December 31, 2022.

The remaining profit or loss after supply

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

costs from commercializing products in the Profit-Share Territory was shared between the Company and KKC on a 50 / 50 basis until April 2023.

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.

In April 2023, commercialization responsibilities for Crysvita in the Profit-Share Territory transitioned to KKC.

Thereafter, the Company is entitled to receive a tiered double-digit revenue share from the mid- 20 % range up to a maximum rate of 30 %.

In 2022, the Company entered into an amendment to the collaboration agreement which granted the Company the right to continue to support KKC in commercial field activities in the U.S.

through April 2024, subject to the limitations and conditions set forth in the amendment.

The parties subsequently mutually agreed to extend the Company's right to continue to support KKC in commercial field activities in the U.S.

through December 31, 2024, and as a result, the Company will continue to support commercial field efforts in the U.S.

through a cost share arrangement through December 2024.

After December 31, 2024, the Company’s rights to promote Crysvita in the U.S.

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

As KKC was the principal in the sale transaction with the customer during the profit-share period, the Company recognized a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs.

The 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.

The Company concluded that its portion of KKC’s sales in the Profit-Share Territory prior to April 2023 was analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty.

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

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.

Product Sales Revenue for Other Territories

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

The Company is considered the principal in these territories as the Company controls the product before it is transferred to the customer.

Accordingly, the Company records revenue on a gross basis for the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor.

KKC has the option to assume responsibility for commercialization efforts in Turkey from the Company, after a certain minimum period.

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in Latin American territories and charges the Company a transfer price of 30 % of net sales.

The transfer price on these sales was 35 % prior to December 31, 2022.

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

Total Crysvita revenue was as follows (in thousands):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Year Ended December 31,

Product sales

Revenue in profit-share territory:

Collaboration revenue

Royalty revenue

Non-cash royalty revenue

Collaboration revenue

Total revenue in Profit-Share Territory

Product sales

Royalty revenue in European Territory

Non-cash royalty revenue in European Territories

Non-cash royalty revenue in European Territory

Total Crysvita revenue

Royalty Revenue for Sales in the European Territory

KKC has the commercial responsibility for Crysvita in the European Territory.

In December 2019, the Company sold its right to receive royalty payments based on sales in the European Territory to Royalty Pharma, effective January 1, 2020, as further described in Note 10.

Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10 % on net sales in the European Territory, which was recognized as the underlying sales occur.

Beginning in 2020, the Company records the royalty revenue as non-cash royalty revenues.

The Company records this revenue as royalty revenue.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Development Activities

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

Under the collaboration agreement, KKC and the Company share certain development and commercialization costs, and as a result, the Company was reimbursed for these costs and operating expenses were reduced.

Additionally, KKC is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to KKC in cost of sales.

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):

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Collaboration Receivable and Payable

The Company had accounts receivable from KKC in the amount of $ 39.2 million and $ 27.5 million from profit-share revenue and royalties and other receivables recorded in other current assets of $ 1.1 million and $ 6.4 million and accrued liabilities of $ 5.3 million and $ 3.1 million from commercial and development activity reimbursements, as of December 31, 2023 and 2022, respectively.

Saint Louis University

In November 2010, the Company entered into a license agreement with Saint Louis University, or SLU.

Under the terms of this license agreement, SLU granted the Company an exclusive worldwide license to make, have made, use, import, offer for sale, and sell therapeutics related to SLU’s beta-glucuronidase product for use in the treatment of human diseases.

The Company made a milestone payment of $ 0.1 million upon approval of Mepsevii for treatment of MPS 7.

The Company is required to pay to SLU a low single-digit royalty on net sales of the licensed products in any country or region, upon reaching a certain level of cumulative worldwide sales of the product.

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 (triheptanoin) for the treatment of LC-FAOD.

For the years ended December 31, 2023 and 2022 , the Company recorded nil and $ 2.5 million, respectively, for the attainment of various development and commercial milestones as finite-lived intangible assets.

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

REGENXBIO, Inc.

The Company has a license agreement with REGENXBIO, Inc., or REGENX, for an exclusive, sublicensable, worldwide commercial license under certain intellectual property for preclinical and clinical research and development, and commercialization of drug therapies using REGENX's licensed patents for the treatment of hemophilia A, OTC deficiency, and GSD1a.

The Company will pay an annual fee and certain milestone fees per disease indication, low to mid- single-digit royalty percentages on net sales of licensed products, and milestone and sublicense fees owed by REGENX to its licensors, contingent upon the attainment of certain development activities as outlined in the agreement.

The Company also has an option and license agreement with REGENX under which the Company has an exclusive, sublicensable, worldwide license to make, have made, use, import, sell, and offer for sale licensed products to treat Wilson disease and CDKL5 deficiency.

For each disease indication, the Company is obligated to pay an annual maintenance fee of $ 0.1 million and up to $ 9.0 million upon achievement of various milestones, as well as mid- to high single-digit royalties on net sales of licensed products and mid- single-digit to low double-digit percentage sublicenses fees, if any.

In March 2020, the Company entered into a license agreement with REGENX, for an exclusive, sublicensable, worldwide license to REGENX’s NAV AAV8 and AAV9 vectors for the development and commercialization of gene therapy treatments for a rare metabolic disorder.

In return for these rights, the Company made an upfront payment of $ 7.0 million.

The Company will pay certain

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

annual fees of $ 0.1 million, milestone payments of up to $ 14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty.

Bayer HealthCare LLC

The Company previously had a collaboration and license agreement with Bayer Healthcare LLC, or Bayer, to research, develop and commercialize AAV gene therapy products for the treatment of hemophilia A, or DTX 201.

Under this agreement, Bayer had been granted an exclusive license to develop and commercialize one or more novel gene therapies for hemophilia A.

In October 2022, the Collaboration and License Agreement for DTX201 with Bayer was terminated and all licensed rights to DTX201 have reverted back to the Company.

The Company also obtained rights to all necessary data and information to further develop DTX201 or another hemophilia A program through a royalty-free, worldwide, sublicensable, perpetual license.

University of Pennsylvania

The Company has a research, collaboration, and license agreement with University of Pennsylvania School of Medicine, or Penn, which provides the terms for the Company and Penn to collaborate with respect to the pre-clinical development of gene therapy products for the treatment of certain indications.

Under the agreement, Penn granted the Company an exclusive, worldwide license to certain patent rights arising out of the research program, subject to certain retained rights, and a non-exclusive, worldwide license to certain Penn intellectual property, in each case to research, develop, make, have made, use, sell, offer for sale, commercialize and import licensed products in each indication for the term of the agreement.

The Company will fund the cost of the research program in accordance with a mutually agreed-upon research budget and will be responsible for clinical development, manufacturing and commercialization of each indication.

The Company may be obligated to make milestone payments of up to $ 5.0 million for each indication, if certain development milestones are achieved over time.

The Company is also obligated to make milestone payments of up to $ 25.0 million per approved product if certain commercial milestones are achieved, as well as low to mid- single-digit royalties on net sales of each licensed product.

Arcturus Therapeutics Holdings Inc.

In October 2015, the Company entered into a Research Collaboration and License Agreement with Arcturus Therapeutics Holdings Inc., or Arcturus, to collaborate on the research and development of therapies for select rare diseases.

Arcturus was responsible for conducting certain research services, funded by the Company, and the Company was responsible for development and commercialization costs.

On a product-by-product basis, the Company is obligated to make development and regulatory milestone payments of up to $ 24.5 million, and commercial milestone payments of up to $ 45.0 million if certain milestones are achieved.

For the year ended December 31, 2021, the Company achieved a $ 1.0 million development milestone, which was paid with a corresponding credit received from Arcturus for prior research and collaboration activities.

The Company is also obligated to pay Arcturus royalties on any net sales of products incorporating the licensed intellectual property that may range from a mid- single-digit to low double-digit percentage.

There were no material expenses for this arrangement during the years ended December 31, 2023, 2022, and 2021.

In June 2019, the Company entered into an Equity Purchase Agreement and an amendment to the Research Collaboration and License Agreement, or License Agreement, to expand the field of use and increase the number of disease targets to include mRNA, DNA and siRNA therapeutics for up to 12 rare diseases.

Pursuant to the agreements, the Company paid $ 6.0 million in cash upfront to Arcturus and purchased 2,400,000 shares of Arcturus’ common stock at a stated value of $ 10.00 per share, resulting in a total of $ 30.0 million of consideration paid at the close of the transaction.

As a result, the Company received expanded license rights under the License Agreement, Arcturus common stock, and an option to purchase an additional 600,000 shares of Arcturus’ common stock at $ 16.00 per share.

In May 2020, the Company exercised its option to purchase 600,000 shares of Arcturus common stock for a total purchase price of $ 9.6 million.

The Company’s investment in Arcturus was accounted at fair value, as the fair value was readily determinable.

During the year ended December 31, 2022, the Company sold 500,000 shares of Arcturus common stock, at a weighted-average price of $ 20.39 per share.

As of December 31, 2022, the Company held no shares of Arcturus common stock.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The changes in the fair value of the Company’s equity investment in Arcturus were as follows (in thousands):

Arcturus Common Stock

December 31, 2021

Change in fair value

Sale of shares

December 31, 2022

Daiichi Sankyo

In March 2020, the Company executed a License and Technology Access Agreement, or the License Agreement, with Daiichi Sankyo Co., Ltd., or Daiichi Sankyo.

Pursuant to the License Agreement, the Company granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to its Pinnacle PCL TM producer cell line platform, or Pinnacle PCL Platform, and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products.

Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $ 125.0 million and an additional $ 25.0 million upon completion of the technology transfer of the Pinnacle PCL Platform and HEK293 platform.

Daiichi Sankyo reimbursed the Company for all costs associated with the transfer of the manufacturing technology.

The Company also entered into a Stock Purchase Agreement, or SPA, with Daiichi Sankyo, pursuant to which Daiichi Sankyo purchased 1,243,913 shares of the Company’s common stock in exchange for $ 75.0 million in cash during the first quarter of 2020.

The fair market value of the common stock issued to Daiichi Sankyo was $ 55.3 million based on the stock price of $ 44.43 per share on the date of issuance, resulting in a $ 19.7 million premium on the SPA.

In June 2020, the Company executed a subsequent license agreement, or the Sublicense Agreement, with Daiichi Sankyo for transfer of certain technology in consideration for an upfront payment of $ 8.0 million and annual maintenance fees, milestone payments, and royalties on any net sales of products incorporating the licensed intellectual property.

The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its Pinnacle PCL Platform and HEK293 transient transfection manufacturing technology platform together with the initial technical assistance and technology transfer services, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer period.

The Company allocated the total transaction price to the two performance obligations on a relative stand-alone selling price basis.

Revenue allocated to the intellectual property and the technology transfer services was recognized over an initial period which was completed during the first quarter of 2022, measuring the progress toward complete satisfaction of the individual performance obligation using an input measure.

Revenue for know-how and improvements after the completion of technology transfer was recognized on a straight-line basis over the remaining technology transfer period, which ended in March 2023, as it was expected that Daiichi Sankyo would receive and consume the benefits consistently throughout the period.

The Company’s current obligations under the License Agreement and the Sublicense Agreement were completed following the conclusion of the technology transfer period.

Total revenue recognized under the arrangement through December 31, 2023 was $ 183.3 million.

The Company recognized $ 1.5 million, $ 7.7 million, and $ 85.0 million for the years ended December 31, 2023, 2022, and 2021 , respectively, in revenue related to this arrangement.

Accordingly, the Company recorded contract liabilities of nil and $ 1.5 million, net, for this arrangement as of December 31, 2023 and 2022, respectively.

In December 2020, the Company entered into a License and Collaboration Agreement with Mereo to collaborate on the development of setrusumab.

Under the terms of the agreement, the Company will lead future global development of setrusumab in both pediatric and adult patients with OI.

The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Turkey, and the rest of the world, excluding the European Economic Area, United Kingdom, and Switzerland, or the

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.

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 $ 30.0 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)

Mereo Territory, where Mereo retains commercial rights.

Each party will be responsible for post-marketing commitments and commercial supply in their respective territories.

Upon the closing of the transaction in January 2021, the Company made a payment of $ 50.0 million to Mereo and will be required to make payments of up to $ 254.0 million upon the achievement of certain clinical, regulatory, and commercial milestones.

The Company will pay for all global development costs as well as tiered double-digit percentage royalties to Mereo on net sales in the U.S., Turkey, and the rest of the world (excluding the Mereo Territory), and Mereo will pay the Company a fixed double-digit percentage royalty on net sales in the Mereo Territory.

Although Mereo is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Mereo.

Prior to the achievement of certain development milestones, all consideration paid to Mereo represents rights to potential future benefits associated with Mereo’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use.

For the years ended December 31, 2023, 2022, and 2021 , the Company recorded research and development expense of $ 9.0 million for the achievement of a clinical milestone, nil , and $ 50.0 million for the upfront payment, respectively.

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

Evkeeza is approved in the U.S., where it is marketed by Regeneron, and in the EU and U.K.

as a first-in-class therapy for use together with diet and other low-density lipoprotein-cholesterol-lowering therapies to treat adults and adolescents aged 12 years and older with HoFH.

Pursuant to the terms of the agreement, the Company received the rights to develop, commercialize and distribute the product for HoFH in countries outside of the U.S.

The Company is obligated to pay up to $ 63.0 million in future milestone payments, contingent upon the achievement of certain regulatory and sales milestones.

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

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

As the Company would be the principal in future sale transactions with the customer, the Company will recognize product sales and cost of sales in the period the related sales occur and the related revenue recognition criteria are met.

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.

The Company paid Regeneron a $ 30.0 million upfront payment upon the closing of the transaction in January 2022, and d uring the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved.

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

See Note 5 for additional details.

Under the collaboration agreement, the Company reimbursed Regeneron for development costs of $ 7.6 million, $ 7.3 million, and nil for the years ended December 31, 2023, 2022, and 2021, respectively, which were recorded as research and development expense on the Consolidated Statements of Operations.

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):

Year Ended December 31,

Research and development

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.

A dditionally, Regeneron is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to Regeneron of $ 0.7 million in cost of sales on the Consolidated Statements of Operations for the year ended December 31, 2023.

Saint Louis University

In November 2010, the Company entered into a license agreement with Saint Louis University, or SLU.

Under the license agreement, the Company is obligated to pay to SLU a low single-digit royalty on net sales of the licensed products in Europe and Japan, subject to certain potential deductions.

The Company's obligation to pay royalties to SLU in these territories continues until the expiration of any orphan drug exclusivity.

In May 2022, the Company announced an exclusive License Agreement for the AAV gene therapy for UX111 with Abeona for the treatment of MPS IIIA.

Under the terms of the agreement, the Company assumed responsibility for the UX111 program and in return, Abeona is eligible to receive tiered royalties of up to 10 % on net sales and commercial milestone payments of up to $ 30.0 million following regulatory approval of the product.

Under the terms of the agreement, the Company assumed responsibility for the UX111 program and in return, the Company is obligated to pay tiered royalties of up to 10 % on net sales and commercial milestone payments of up to $ 30.0 million contingent upon regulatory approval of the product.

Additionally, the Company entered into an Assignment and Assumption Agreement with Abeona to transfer and assign to the Company the exclusive license agreement between Nationwide Children’s Hospital, or NCH, and Abeona for certain rights related to UX111.

Under this agreement, NCH is eligible to receive from the Company up to $ 1.0 million in development and regulatory milestones as well as royalties in the low single-digits of net sales.

Under this agreement, the Company is obligated to pay up to $ 1.0 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.

Each party will be responsible for post-marketing

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company is obligated to pay Abeona certain prior development costs and other transition costs related to UX111.

Prior to product regulatory approval, all consideration paid to Abeona represents rights to potential future benefits associated with Abeona’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use.

Accordingly, the value of the acquired intellectual property rights and clinical inventory as well as prior development costs and transition costs of $ 3.1 million, were recorded as research and development expense for the year ended December 31, 2022.

The Company did no t incur any other material costs related to this agreement in the years presented.

commitments in their respective territories and Ultragenyx will be responsible for commercial supply in both the Ultragenyx Territory and Mereo Territory.

Upon the closing of the transactions under the License and Collaboration Agreement with Mereo in January 2021, the Company made a payment of $ 50.0 million to Mereo.

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

The Company is obligated to pay Mereo up to $ 245.0 million in future milestone payments, contingent upon the achievement of certain regulatory and commercial milestones.

The Company pays for all global development costs and will pay a tiered double-digit percentage royalties to Mereo on net sales in the Ultragenyx Territory.

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.

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.

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.

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

For the year ended December 31, 2023, the Company recorded development costs of $ 9.0 million for the achievement of a clinical milestone recorded in research and development expense.

University of Pennsylvania

The Company is obligated to make milestone payments of up to $ 5.0 million for each indication, if certain development milestones are achieved.

The Company is also obligated to make milestone payments of up to $ 25.0 million per approved product, if certain commercial milestones are achieved, as well as low to mid- single-digit royalties on net sales of each licensed product.

REGENXBIO, Inc.

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.

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 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.

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The royalty rate changes to mid- to high double-digit percentage if Solid decides to co-invest in the product.

The Company also entered into a Stock Purchase Agreement and the Investor Agreement with Solid, pursuant to which, the Company purchased 7,825,797 shares of Solid’s common stock for an aggregate purchase price of $ 40.0 million.

In October 2022, Solid announced a 1 for 15 reverse stock split.

After the split, the Company held 521,719 shares of Solid's common stock.

The Company 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 variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Solid.

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.

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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

The Company leases office space and research, testing and manufacturing laboratory space in various facilities in Novato and Brisbane, California, in Somerville and Woburn, Massachusetts, and in certain foreign countries, under operating agreements expiring at various dates through 2029 .

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Lease liabilities, current

Lease liabilities , non-curre nt

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, 2023 and 2022 , the weighted-average remaining operating lease terms were 4.5 years and 3.0 years, the weighted-average remaining financing lease terms were nil and 2.8 years, the weighted-average discount rates used to determine the lease liability for operating leases were 9.6 % and 6.7 %, and the weighted-average discount rates used to determine the lease liability for finance leases were nil and 5.1 % respectively.

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.

Liabilities for Sales of Future Royalties

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Proceeds from these transactions were recorded as liabilities for sales of future royalties on the Consolidated Balance Sheets.

Upon inception of the respective arrangements, the Company recorded $ 320.0 million and $ 500.0 million, net of transaction costs of $ 5.8 million and $ 9.1 million for RPI and OMERS, respectively, using the effective interest method over the estimated life of the applicable arrangement.

In order to determine the amortization of the liabilities, the Company is required to estimate the total

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.

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)

amount of future royalty payments to be received by the Company and paid to RPI and OMERS, subject to the capped amount, over the life of the arrangements.

The excess of future estimated royalty payments (subject to the capped amount) to RPI and OMERS, over the $ 314.2 million and $ 491.0 million, respectively, of net proceeds, is recorded as non-cash interest expense over the life of the arrangements.

Consequently, the Company estimates an imputed interest on the unamortized portion of the liabilities and records interest expense relating to the transactions.

Royalties earned under the RPI and OMERS arrangements from inception to December 31, 2023 have been $ 73.4 million and $4 8.6 million, respectively.

The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources.

To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company will prospectively adjust the amortization of the liabilities and the effective interest rate.

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.

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December 31, 2022

Net proceeds from sale of future

Royalty revenue

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At-the-Market Offerings

In May 2021, the Company entered into an Open Market Sale Agreement with Jefferies LLC, or Jefferies, pursuant to which the Company may offer and sell shares of the Company’s common stock having an aggregate offering proceeds up to $ 350.0 million, from time to time, in at-the-market, or ATM, offerings through Jefferies.

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.

During the year ended December 31, 2023 , there were 1,175,584 shares sold under the ATM resulting in net proceeds of $ 53.3 million.

There were no shares sold under the ATM for year ended December 31, 2022.

As of December 31, 2023 , the Company has sold a total of 2,225,956 shares under the ATM, resulting in net proceeds of $ 132.2 million.

Underwritten Public Offering

In October 2023, the Company completed an underwritten public offering in which 9,833,334 shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1,500,000 shares, at a public offering price of $ 30.00 per share.

In 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.

The total proceeds that the Company received from the offering were $ 381.0 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)

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

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.

The table below summarizes pre-funded warrants activity:

Pre-funded warrants

As of December 31, 2022

Issuance of pre-funded warrants

As of December 31, 2023

Issuance of pre-funded warrants

As of December 31, 2024

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.

Stock-Based Awards

Equity Plan Awards

In 2014, the Company adopted the 2014 Incentive Plan, or the 2014 Plan, for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors.

The 2014 Plan had 2,250,000 shares of common stock available for future issuance at the time of its inception.

The 2014 Plan provided for automatic annual increases in shares available for grant, beginning on January 1, 2015 through June 7, 2023 .

In June 2023, the Company adopted the 2023 Incentive Plan which had 4,500,000 shares of common stock available for future issuance at the time of its inception, plus the number of shares subject to the 2014 Plan cancelled after June 7, 2023.

No further shares were granted under the 2014 Plan after June 7, 2023.In February 2021, the Company adopted the Employment Inducement Plan, or the Inducement Plan, which was subsequently amended in June 2023 to provide for a maximum of 850,000 shares available for grant under the plan.

Under the terms of the 2023 Plan and Inducement Plan, awards may be granted at an exercise price not less than fair market value.

Under the terms of the Company's 2023 Incentive Plan, or 2023 Plan, and Employment Inducement Plan, or Inducement Plan, awards may be granted at an exercise price not less than fair market value.

The exercise price of an option may not be less than the fair market value.

The term of an award granted under the 2023 Plan and Inducement Plan may not exceed ten years .

Typically, the vesting schedule for option grants to the employees provides that ¼ of the grant vests upon the first anniversary of the date of grant, with the remainder of the shares vesting monthly thereafter at a rate of 1/48 of the total shares subject to the option.

Typically, the vesting schedule for option grants to employees provides that 1/4 of the grant vests upon the first anniversary of the date of grant, with the remainder of the shares vesting monthly thereafter at a rate of 1/48 of the total shares subject to the option.

Typically, the vesting schedule for RSU grants provides that 1/4 of the grant vests upon the annual anniversary of the date of grant over the period of four years .

As of December 31, 2023 , an aggregate of 19,610,125 shares of common stock have been authorized for issuance under the 2014 Plan, the 2023 Plan, and the Inducement Plan.

Under the 2014 Employee Stock Purchase Plan, or ESPP, eligible employees may purchase common stock at 85 % of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature.

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

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

The table below summarizes the Company's equity plans as of December 31, 2024:

Year of Adoption

Expiration Date, as Amended

Maximum Number of Shares Authorized

Shares Available for Future Issuance

Employment Inducement Plan

February 3, 2031

2023 Incentive Plan (1)

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)

Stock Option Activity

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Vested and expected to vest — December 31, 2024

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):

Year Ended December 31,

Intrinsic value of options exercised

Cash received from the exercise of options

Weighted-average estimated fair value of options granted

Estimated fair value of options vested

The aggregate intrinsic values of options outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the options and the fair value of the Company’s common stock.

The total intrinsic value of options exercised during the years ended December 31, 2023, 2022, and 2021 was $ 4.9 million, $ 2.6 million, and $ 38.8 million, respectively.

Cash received from the exercise of options was $ 2.7 million, $ 6.2 million, and $ 36.6 million for the years ended December 31, 2023, 2022, and 2021, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The weighted-average estimated fair value of stock options granted was $ 25.53 , $ 34.77 , and $ 70.84 per share of the Company’s common stock during the years ended December 31, 2023, 2022, and 2021, respectively.

The total estimated grant date fair value of options vested during the years ended December 31, 2023, 2022, and 2021 was $ 59.7 million, $ 58.7 million, and $ 48.1 million, respectively.

Performance Stock Options

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Vested and expected to vest — December 31, 2024

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 aggregate intrinsic values of PSOs outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the PSOs and the fair value of the Company’s common stock.

The total estimated grant date fair value of PSOs vested during the year ended December 31, 2023 , was $ 3.4 million.

No PSOs were granted or were exercised during the year ended December 31, 2023.

The 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.

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The aggregate intrinsic value of the shares of the RSUs vested during the years ended December 31, 2024, 2023, and 2022 was $ 54.0 million, $ 33.0 million, and $ 37.8 million, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Performance Stock Units

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The total grant date fair value of the PSUs vested during the years ended December 31, 2024, 2023, and 2022 was $ 3.4 million, $ 3.9 million, and $ 1.6 million, respectively, with an aggregate intrinsic value of the shares of $ 2.1 million, $ 1.3 million and $ 2.0 million, respectively.

Employee Stock Purchase Plan

In January 2014, the Company adopted the 2014 Employee Stock Purchase Plan, or ESPP, which was amended and restated in June 2023.

Under the ESPP, eligible employees may purchase common stock at 85 % of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature.

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

During the year ended December 31, 2023 , the Company issued 195,462 shares of common stock under the ESPP.

As of December 31, 2023 , an aggregate of 6,609,795 shares of common stock have been authorized for future issuance on the ESPP.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Stock-Based Compensation Expense

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

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

Year Ended December 31,

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Expected Volatility —The Company’s expected volatility is based on historical volatility over the look-back period corresponding to the expected term.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Risk-Free Interest Rate —The risk-free interest rate is based on the U.S.

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The Company recorded $ 9.8 million, $ 9.7 million, and $ 9.0 million as expense related to the plan for the years ended December 31, 2024, 2023, and 2022 , respectively.

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

Year Ended December 31,

Total loss before income taxes

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):

Year Ended December 31,

Total loss before income taxes

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

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Total deferred tax provision

Total (benefit from) provision for income taxes

Total provision for (benefit from) income taxes

The Company has incurred net operating losses since inception.

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Beginning in 2022, the Tax Cuts and Jobs Act of 2017 eliminated the right to deduct research and development expenditures for tax purposes in the period the expenses were incurred and instead requires all U.S.

and foreign research and development expenditures to be amortized over five and fifteen tax years, respectively.

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.

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

net deferred tax assets.

The benefit was offset by an income tax expense of $ 3.0 million from foreign jurisdictions.

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:

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The valuation allowance increased by $ 170.7 million and $ 141.3 million during the years ended December 31, 2024 and 2023, respectively.

Due to a change in the state tax rates, the Company recorded a net decrease to the deferred tax liability of $ 1.6 million with a corresponding deferred income tax benefit of $ 1.6 million for the year ended December 31, 2023.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

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

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Balance at end of year

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Approximately $ 1.3 million in unrecognized tax benefits would impact the Company’s effective tax rate if recognized.

The Company has elected to include interest and penalties as a component of tax expense.

For the year ended December 31, 2023, the Company recognized accrued interest and penalties of $ 0.2 million as a component of income tax expense.

No accrued interest and penalties were recognized as a component of income tax expense during the years ended December 31, 2022 and 2021.

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.

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

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License and Research Agreements.”

See “Note 10.

Leases” for lease commitments.

Contingencies

While there are no material legal proceedings the Company is aware of, the Company may become party to various claims and complaints arising in the ordinary course of business.

Management does not believe that any ultimate liability resulting from any of these potential claims will have a material adverse effect on its results of operations, financial position, or liquidity.

However, management cannot give any assurance regarding the ultimate outcome of these claims, and their resolution could be material to operating results for any particular period, depending upon the level of income for the period.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

In the ordinary course of business, the Company may become party to various claims and complaints.

Legal Proceedings” for material legal proceedings the Company is aware of.

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.

Guarantees and Indemnifications

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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, also serve as board members of the foundation, whereby an aggregate $ 1.0 million contribution is being paid to the foundation over a four-year period, beginning in the third quarter of 2022, to support rare disease education and awareness.

As a result, the Company recorded $ 0.3 million and $ 0.3 million as research and development expense for this agreement for the years ended December 31, 2023 and 2022 , respectively.

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 $ 1.0 million contribution is being paid to the foundation over a four-year period, beginning in the third quarter of 2022, to support rare disease education and awareness.

As a result, the Company recorded $ 0.3 million, $ 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.

Net Loss per Share

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Employee stock purchase plan

Accumulated Other Comprehensive Income (Loss)

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

Accumulated Other Comprehensive (Loss) Income

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

Year Ended December 31,

1 unchanged sentence

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

Total accumulated other comprehensive income (loss)

Total accumulated other comprehensive (loss) income

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