UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) For the transition period from to . ULTRAGENYX PHARMACEUTICAL INC. (Exact name of registrant as specified in its charter) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934. For the quarterly period ended June 30, 2021 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934. Delaware 27-2546083 (State or other jurisdiction of incorporation or ...

Commercial Performance & Financial Position - Ultragenyx reported total revenue of $99.4 million in Q1 2021[21] - Crysvita in Ultragenyx territories contributed $42.1 million in revenue[21] - Dojolvi generated $7.0 million in revenue[21] - The company's cash balance as of Q1 2021 was approximately $1.0 billion[21] - Ultragenyx anticipates Crysvita revenue in Ultragenyx territories to be between $180 million and $190 million for 2021[21] Clinical Development & Pipeline - Ultragenyx plans to initiate four pivotal clinical studies, including three gene therapy programs[6, 22] - A Phase 3 study for DTX401 in GSDIa is expected to begin in early 2H21[22] - A Phase 1/2/3 study for UX701 in Wilson Disease is expected to begin in early 2H21[22] - A Phase 2/3 study for Setrusumab in pediatric Osteogenesis Imperfecta is planned for late 2021[22, 28] Therapeutic Focus & Market Potential - Ultragenyx is targeting three therapeutic areas with the potential to generate $1 billion in product revenue within the next five years[11] - Setrusumab for Osteogenesis Imperfecta targets a worldwide prevalence of approximately 60,000 patients[19, 25] - GTX-102 for Angelman Syndrome targets a worldwide prevalence of approximately 60,000 patients[19, 31]

Ultragenyx Pharmaceutical Inc. (NASDAQ:RARE) Q1 2021 Earnings Conference Call May 4, 2021 5:00 PM ET Company Participants Joshua Higa - Director, Investor Relations Emil Kakkis - President and CEO Camille Bedrosian - Chief Medical Officer Erik Harris - Chief Commercial Officer Mardi Dier - Chief Financial Officer Conference Call Participants Gena Wang - Barclays Tazeen Ahmad - Bank of America Yaron Werber - Cowen Dae Gon Ha - Stifel Yigal Nochomovitz - Citigroup Cory Kasimov - JPMorgan Maury Raycroft - Jeff ...

Part I – Financial Information [Financial Statements](index=4&type=section&id=Item%201.%20Financial%20Statements) The company's Q1 2021 revenue grew significantly while net loss widened due to higher operating expenses Condensed Consolidated Balance Sheet Highlights (in thousands) | Account | March 31, 2021 | December 31, 2020 | | :--- | :--- | :--- | | Cash and cash equivalents | $383,794 | $713,526 | | Marketable debt securities | $663,238 | $498,513 | | Total current assets | $1,070,936 | $1,295,304 | | Total assets | $1,597,763 | $1,759,555 | | Total current liabilities | $127,044 | $189,609 | | Total liabilities | $543,181 | $605,180 | | Total stockholders' equity | $1,054,582 | $1,154,375 | Condensed Consolidated Statement of Operations Highlights (in thousands, except per share data) | Account | Q1 2021 | Q1 2020 | | :--- | :--- | :--- | | Total revenues | $99,395 | $36,309 | | Research and development | $147,518 | $112,961 | | Selling, general and administrative | $53,258 | $47,516 | | Loss from operations | ($106,569) | ($120,665) | | Change in fair value of equity investments | ($20,619) | $7,668 | | Net loss | ($136,141) | ($119,025) | | Net loss per share, basic and diluted | ($2.03) | ($2.05) | Condensed Consolidated Statement of Cash Flows Highlights (in thousands) | Account | Q1 2021 | Q1 2020 | | :--- | :--- | :--- | | Net cash used in operating activities | ($159,346) | ($95,152) | | Net cash used in investing activities | ($182,424) | ($95,125) | | Net cash provided by financing activities | $12,649 | $55,615 | | Net decrease in cash, cash equivalents and restricted cash | ($329,892) | ($135,285) | [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=21&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Revenue grew 174% driven by collaborations and product sales, while higher R&D and investment losses increased the net loss [Overview and Pipeline](index=21&type=section&id=Overview%20and%20Pipeline) The company advances a diversified pipeline for rare diseases despite some COVID-19 related delays - The company's pipeline is diversified across four product categories: **biologics, small molecules, gene therapy, and nucleic acid product candidates**[106](index=106&type=chunk) - The COVID-19 pandemic has caused interruptions to clinical trial activities, including patient enrollment and dosing, and has delayed some regulatory interactions and data reporting[104](index=104&type=chunk) Key Upcoming Clinical Milestones in 2021 | Product Candidate | Indication | Milestone | Expected Timing | | :--- | :--- | :--- | :--- | | UX143 (setrusumab) | OI | Pediatric Ph2/3 Initiation | 2H 2021 | | DTX401 | GSDIa | Ph3 Initiation | Early 2H 2021 | | DTX301 | OTC | Ph3 Initiation | 2H 2021 | | UX701 | Wilson Disease | Ph1/2/3 Initiation | Early 2H 2021 | | GTX-102 | Angelman Syndrome | Resume Ph1/2 Study | 2021 | | UX053 | GSDIII | Ph1/2 Initiation | 2H 2021 | [Results of Operations](index=25&type=section&id=Results%20of%20Operations) Q1 2021 revenue surged 174% due to collaboration and product sales, while R&D expenses rose 31% Revenue Breakdown (in thousands) | Revenue Source | Q1 2021 | Q1 2020 | % Change | | :--- | :--- | :--- | :--- | | Crysvita collaboration revenue | $36,260 | $27,215 | 33% | | Daiichi Sankyo | $42,750 | $0 | N/A | | Total Product Sales | $16,513 | $6,479 | 155% | | *Dojolvi Product Sales* | *$7,034* | *$1,444* | *387%* | | Crysvita non-cash royalty revenue | $3,872 | $2,615 | 48% | | **Total Revenues** | **$99,395** | **$36,309** | **174%** | Research & Development Expenses Breakdown (in thousands) | Expense Category | Q1 2021 | Q1 2020 | % Change | | :--- | :--- | :--- | :--- | | Commercial programs | $13,661 | $5,857 | 133% | | Gene therapy programs | $21,362 | $13,200 | 62% | | Upfront license and milestone fees | $50,000 | $32,000 | 56% | | **Total R&D Expenses** | **$147,518** | **$112,961** | **31%** | - The increase in upfront license fees was primarily due to a **$50.0 million payment to Mereo** in January 2021, partially offset by a $25.0 million payment to GeneTx and a $7.0 million payment to REGENXBIO in Q1 2020[137](index=137&type=chunk) - The fair value of equity investments in Arcturus and Solid Biosciences **decreased by $20.6 million** in Q1 2021, compared to a $7.7 million increase in Q1 2020, causing significant volatility in net loss[142](index=142&type=chunk) [Liquidity and Capital Resources](index=28&type=section&id=Liquidity%20and%20Capital%20Resources) The company maintains over $1 billion in liquidity, sufficient for operations despite increased cash usage - The company holds **$1.047 billion in available cash**, cash equivalents, and marketable debt securities as of March 31, 2021[148](index=148&type=chunk) - Cash used in operating activities increased to **$159.3 million in Q1 2021** from $95.2 million in Q1 2020, reflecting a higher net loss and unfavorable changes in working capital, including a decrease in contract liabilities related to the Daiichi Sankyo agreement[150](index=150&type=chunk)[152](index=152&type=chunk)[154](index=154&type=chunk) Contractual Obligations (in thousands) | Obligation | Less than 1 year | 1 to 3 years | 3 to 5 years | More than 5 years | Total | | :--- | :--- | :--- | :--- | :--- | :--- | | Operating and finance leases | $12,140 | $24,224 | $15,058 | $2,410 | $53,832 | | Manufacturing and service contracts | $7,760 | $1,033 | $0 | $0 | $8,793 | | Building construction agreement | $17,744 | $141 | $0 | $0 | $17,885 | | **Total** | **$37,644** | **$25,398** | **$15,058** | **$2,410** | **$80,510** | [Quantitative and Qualitative Disclosures About Market Risk](index=30&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) The company's primary market risks stem from volatile equity investments, with minor interest rate and currency exposures - The company has **significant equity risk** from its investments in Arcturus and Solid, with the fair value of these investments decreasing by **$20.6 million in Q1 2021**[164](index=164&type=chunk) - A hypothetical **10% decrease** in the market price of its equity investments in Arcturus and Solid as of March 31, 2021 would decrease their fair value by **$13.4 million**[164](index=164&type=chunk) - Interest rate risk is managed through a low-risk, investment-grade debt instrument policy, and a hypothetical **100 basis point change** in interest rates would not have a material impact[165](index=165&type=chunk) [Controls and Procedures](index=31&type=section&id=Item%204.%20Controls%20and%20Procedures) Management confirmed the effectiveness of disclosure controls and procedures with no material changes in internal controls - The CEO and CFO concluded that the company's disclosure controls and procedures were **effective** as of March 31, 2021[167](index=167&type=chunk) - **No material changes** to internal control over financial reporting occurred during the quarter ended March 31, 2021[168](index=168&type=chunk) Part II – Other Information [Legal Proceedings](index=31&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently involved in any material legal proceedings - As of the filing date, the company is **not a party to any material legal proceedings**[169](index=169&type=chunk) [Risk Factors](index=31&type=section&id=Item%201A.%20Risk%20Factors) Key risks include a history of losses, clinical development uncertainties, and reliance on third-party partners - The company has a history of operating losses and expects to continue incurring them for the foreseeable future due to **high R&D and commercialization costs**[176](index=176&type=chunk) - Clinical drug development is a lengthy, expensive, and uncertain process, with **gene therapy candidates** in particular posing risks of undesirable side effects[186](index=186&type=chunk)[198](index=198&type=chunk) - The company is **dependent on its partner KKC** for the clinical and commercial supply of Crysvita and for its commercialization in key markets[215](index=215&type=chunk)[233](index=233&type=chunk) - The ongoing **COVID-19 pandemic** has impacted and could continue to materially adversely affect business operations, including clinical trials, regulatory timelines, and the supply chain[282](index=282&type=chunk)[283](index=283&type=chunk)[284](index=284&type=chunk) [Unregistered Sales of Equity Securities and Use of Proceeds](index=66&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) No unregistered sales of equity securities occurred during the reporting period - None[326](index=326&type=chunk) [Exhibits](index=68&type=section&id=Item%206.%20Exhibits) This section lists all exhibits filed with the report, including required certifications and XBRL data - The exhibits include the CEO and CFO certifications required under the Sarbanes-Oxley Act and Inline XBRL documents[332](index=332&type=chunk)

ultrageny? Corporate Deck February 2021 Legal Warning Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but not limited to, statements regarding our expectations and projections regarding our future operating results and financial performance, anticipated cost or expense reductions, plans with respect to commercializing our product and product candidates, our translational research program, expectations regarding our manufacturing capabil ...

ultrageny? Corporate Deck February 2021 Legal Warning Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but not limited to, statements regarding our expectations and projections regarding our future operating results and financial performance, anticipated cost or expense reductions, plans with respect to commercializing our product and product candidates, our translational research program, expectations regarding our manufacturing capabil ...

Ultragenyx Pharmaceutical Inc. (NASDAQ:RARE) Q4 2020 Earnings Conference Call February 11, 2021 5:00 PM ET Company Participants Joshua Higa - Director, Investor Relations Emil Kakkis - Chief Executive Officer and President Camille Bedrosian - Chief Medical Officer Erik Harris - Chief Commercial Officer Mardi Dier - Chief Financial Officer Conference Call Participants Yaron Werber - Cowen Gena Wang - Barclays Cory Kasimov - JPMorgan Joon Lee - Truist Securities Yigal Nochomovitz - Citigroup Liisa Bayko - Eve ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Form 10-K ☑ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2020 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-36276 Ultragenyx Pharmaceutical Inc. (Exact name of registrant as specified in its charter) (415) 483-8800 (Registrant's telephone number, includin ...

January 2021 Corporate Deck Legal Warning Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but not limited to, statements regarding our expectations and projections regarding our future operating results and financial performance, anticipated cost or expense reductions, plans with respect to commercializing our product and product candidates, our translational research program, expectations regarding our manufacturing capabilities, the e ...

November 2020 Corporate Presentation Legal Warning Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but not limited to, statements regarding our expectations and projections regarding our future operating results and financial performance, anticipated cost or expense reductions, plans with respect to commercializing our product and product candidates, our translational research program, expectations regarding our manufacturing capabiliti ...