UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from __________ to ____________ Commission File Number: 001-38938 Stoke Therapeutics, Inc. (Mark One) ☒ 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 Not applicable (Former name, former address and former fiscal year, if chan ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 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 Number: 001-38938 Stoke Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) (State or other jur ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ 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 Number 001-38938 Stoke Therapeutics, Inc. (Exact name of Registrant as specified in its Charter) (State or other jurisdiction of incorporation o ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 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 Number: 001-38938 Stoke Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 47-114 ...

SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2020 OR Commission File Number: 001-38938 Stoke Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 47-1144582 (State or other jurisdiction of incorporation or organization) 45 Wiggins Ave Bedford, Massachusetts 01730 (Address of principal executive offices) (Zip Code) (I.R ...

SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 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 Number: 001-38938 Stoke Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 47-1144582 (State or oth ...

FORM 10-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2019 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 Number 001-38938 Stoke Therapeutics, Inc. (Exact name of Registrant as specified in its Charter) Delaware 47-1144582 (State or other jurisdictio ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2019 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 WASHINGTON, DC 20549 FORM 10-Q For the transition period from __________ to ____________ Commission File Number: 001-38938 Stoke Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) (State or other ...

PART I. FINANCIAL INFORMATION [Financial Statements (Unaudited)](index=4&type=section&id=Item%201.%20Financial%20Statements%20(Unaudited)) The unaudited financial statements reflect a significant increase in cash to $242.7 million due to the June 2019 IPO, alongside a net loss of $13.6 million for the first half of 2019 [Condensed Consolidated Balance Sheets](index=4&type=section&id=Condensed%20Consolidated%20Balance%20Sheets) Total assets increased to $246.4 million by June 30, 2019, primarily due to a rise in cash and cash equivalents following the IPO Condensed Consolidated Balance Sheet Highlights (in thousands) | Account | June 30, 2019 (unaudited) | December 31, 2018 (audited) | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $242,680 | $105,399 | | Total current assets | $244,445 | $106,143 | | Total assets | $246,372 | $107,539 | | **Liabilities & Stockholders' Equity** | | | | Total liabilities | $4,836 | $2,471 | | Total stockholders' equity | $241,536 | $105,068 | | Total liabilities and stockholders' equity | $246,372 | $107,539 | - Upon the closing of the IPO on June 21, 2019, all outstanding convertible preferred stock was **automatically converted** into common stock[27](index=27&type=chunk) [Condensed Consolidated Statements of Operations and Comprehensive Loss](index=5&type=section&id=Condensed%20Consolidated%20Statements%20of%20Operations%20and%20Comprehensive%20Loss) The company reported no revenue and a net loss of $13.6 million for the first half of 2019, driven by increased operating expenses Statement of Operations Summary (in thousands) | Metric | Six Months Ended June 30, 2019 | Six Months Ended June 30, 2018 | | :--- | :--- | :--- | | Revenue | $0 | $0 | | Research and development | $10,156 | $3,140 | | General and administrative | $4,611 | $1,782 | | Loss from operations | ($14,767) | ($4,922) | | Net loss | ($13,561) | ($4,922) | | Net loss per share | ($4.57) | ($7.14) | [Condensed Consolidated Statements of Cash Flows](index=7&type=section&id=Condensed%20Consolidated%20Statements%20of%20Cash%20Flows) Net cash used in operating activities was $12.8 million, while financing activities provided $150.6 million, primarily from the IPO Cash Flow Summary (in thousands) | Activity | Six Months Ended June 30, 2019 | Six Months Ended June 30, 2018 | | :--- | :--- | :--- | | Net cash used in operating activities | ($12,806) | ($4,408) | | Net cash used in investing activities | ($482) | ($326) | | Net cash provided by financing activities | $150,570 | $12,482 | - The primary source of financing cash flow in the first half of 2019 was **$151.9 million** in proceeds from the IPO[23](index=23&type=chunk) [Notes to Unaudited Condensed Consolidated Financial Statements](index=8&type=section&id=Notes%20to%20Unaudited%20Condensed%20Consolidated%20Financial%20Statements) Notes detail the company's early-stage biopharmaceutical focus, IPO proceeds of $149.4 million, and license agreements for TANGO technology - The company is an early-stage biopharmaceutical company pioneering a new way to treat severe genetic diseases by upregulating protein expression using its **TANGO platform**[26](index=26&type=chunk) - Completed an IPO on June 21, 2019, issuing 9,074,776 shares at $18.00 per share, resulting in net proceeds of approximately **$149.4 million**[27](index=27&type=chunk) - The company expects its cash and cash equivalents as of June 30, 2019, will be sufficient to fund operating expenses and capital expenditure requirements into **2023**[31](index=31&type=chunk) - The company has **license agreements** with CSHL and the University of Southampton, which require potential milestone payments, royalties on net sales, and a percentage of any sublicense revenue[61](index=61&type=chunk)[62](index=62&type=chunk) [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=17&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses the TANGO platform, lead candidate STK-001 for Dravet syndrome, and the financial impact of the June 2019 IPO - The company is pioneering a new way to treat severe genetic diseases by precisely upregulating protein expression using its proprietary **TANGO (Targeted Augmentation of Nuclear Gene Output) platform**[81](index=81&type=chunk)[82](index=82&type=chunk) - Lead product candidate, **STK-001**, is designed to treat Dravet syndrome, with plans to submit an IND application by early 2020 and initiate a **Phase 1/2 clinical trial** in the first half of 2020[83](index=83&type=chunk) - In August 2019, the FDA granted **orphan drug designation** to STK-001 for the treatment of Dravet Syndrome[90](index=90&type=chunk) - Existing cash, cash equivalents, and restricted cash of **$242.9 million** as of June 30, 2019, are expected to fund operating expenses and capital expenditure requirements into **2023**[89](index=89&type=chunk) [Results of Operations](index=20&type=section&id=Results%20of%20operations) Operating expenses significantly increased, with R&D rising to $10.2 million and G&A to $4.6 million for the six months ended June 30, 2019 Research and Development Expenses (in thousands) | Category | Six Months Ended June 30, 2019 | Six Months Ended June 30, 2018 | | :--- | :--- | :--- | | STK-001 | $4,337 | $392 | | Non-program specific and unallocated | $5,819 | $2,748 | | **Total R&D Expenses** | **$10,156** | **$3,140** | - The increase in R&D expenses for the six months ended June 30, 2019, was primarily due to a **$4.0 million** increase in the STK-001 program and a **$1.7 million** increase in personnel costs from higher headcount[107](index=107&type=chunk) - General and administrative expenses for the six months ended June 30, 2019, increased by **$2.8 million** year-over-year, mainly due to a **$0.8 million** increase in personnel costs and a **$1.3 million** increase in third-party services[108](index=108&type=chunk)[109](index=109&type=chunk) [Liquidity and Capital Resources](index=22&type=section&id=Liquidity%20and%20capital%20resources) Cash and equivalents totaled $242.9 million as of June 30, 2019, primarily from the IPO, expected to fund operations into 2023 - As of June 30, 2019, the company had **$242.9 million** in cash, cash equivalents and restricted cash[112](index=112&type=chunk) - The company believes its existing capital resources will fund operating expenses and capital expenditure requirements into **2023**[114](index=114&type=chunk) Cash Flow Summary (in thousands) | Activity | Six Months Ended June 30, 2019 | Six Months Ended June 30, 2018 | | :--- | :--- | :--- | | Net cash used in operating activities | ($12,806) | ($4,408) | | Net cash used in investing activities | ($482) | ($326) | | Net cash provided by financing activities | $150,570 | $12,482 | [Quantitative and Qualitative Disclosures About Market Risk](index=25&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) Primary market risk is interest rate sensitivity on $242.9 million in cash and equivalents, with a 100 basis point change impacting value by $2.4 million - The company's primary market risk exposure is interest rate sensitivity on its cash, cash equivalents, and restricted cash of **$242.9 million** as of June 30, 2019[136](index=136&type=chunk) - A hypothetical **100 basis point** change in interest rates would affect the fair market value of cash equivalents by approximately **$2.4 million**[136](index=136&type=chunk) [Controls and Procedures](index=25&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded that disclosure controls and procedures were effective as of June 30, 2019, with no material changes to internal controls - Management, including the CEO and CFO, concluded that the company's disclosure controls and procedures were **effective** as of June 30, 2019[137](index=137&type=chunk) - There were **no material changes** to the company's internal control over financial reporting during the quarter[138](index=138&type=chunk) PART II. OTHER INFORMATION [Legal Proceedings](index=26&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently a party to any legal proceedings that would materially adversely affect its business - The company is **not presently a party** to any legal proceedings that would have a material adverse effect on its business[141](index=141&type=chunk) [Risk Factors](index=26&type=section&id=Item%201A.%20Risk%20Factors) Key risks include early-stage development, reliance on STK-001, clinical trial uncertainties, commercialization challenges, financial losses, and intellectual property issues [Risks related to product development and regulatory approval](index=27&type=section&id=Risks%20related%20to%20product%20development%20and%20regulatory%20approval) Risks include STK-001 development failure, patient enrollment challenges for rare diseases, unforeseen side effects, and uncertainties in regulatory approval - The company is in early development and its business will be **materially harmed** if it is unable to develop, obtain regulatory approval for, and commercialize STK-001 and future product candidates[143](index=143&type=chunk) - Success in early preclinical studies may be **not indicative** of results in later clinical trials, and the company has not yet tested any product candidates in humans[147](index=147&type=chunk) - The low prevalence of diseases like Dravet syndrome may make it **difficult to identify patients and enroll** them in clinical trials, potentially causing significant delays[152](index=152&type=chunk) - The company's novel approach of upregulating protein expression with ASOs presents **uncertainty regarding the safety profile**, and undesirable side effects could delay or prevent regulatory approval[164](index=164&type=chunk) [Risks related to commercialization and manufacturing](index=36&type=section&id=Risks%20related%20to%20commercialization%20and%20manufacturing) Commercialization risks include market acceptance, reimbursement challenges, reliance on third-party manufacturers, and intense competition - Commercial success depends on market acceptance by providers, patients, and payors, which is **uncertain** for a novel genetic treatment[190](index=190&type=chunk) - Failure to obtain or maintain adequate insurance coverage and reimbursement for high-priced therapies for rare diseases could **severely limit marketability**[193](index=193&type=chunk) - The company relies on a **limited number of third-party manufacturers**, and any production difficulties, contaminations, or compliance failures could delay or stop supply for trials and commercialization[204](index=204&type=chunk)[205](index=205&type=chunk) - The company faces **significant competition** from large pharmaceutical companies and other biotechs with greater resources, who may develop more effective therapies or achieve regulatory approval faster[200](index=200&type=chunk)[202](index=202&type=chunk) [Risks related to our financial position](index=41&type=section&id=Risks%20related%20to%20our%20financial%20position) Financial risks include a history of operating losses, the need for substantial future funding, and potential limitations on NOL carryforwards - The company has a history of operating losses, with an accumulated deficit of **$39.3 million** as of June 30, 2019, and expects to incur losses for the foreseeable future[215](index=215&type=chunk)[216](index=216&type=chunk) - **Substantial additional funding** will be required to complete development and commercialization, and failure to obtain it could force the company to delay, reduce, or eliminate programs[217](index=217&type=chunk) - The company's ability to utilize its federal and state net operating loss (NOL) carryforwards of approximately **$24.4 million** and **$24.0 million**, respectively, may be **limited** due to 'ownership change' rules under the tax code[223](index=223&type=chunk) [Risks related to our intellectual property](index=43&type=section&id=Risks%20related%20to%20our%20intellectual%20property) Intellectual property risks include reliance on licensed patents, uncertainty of patent issuance, infringement claims, and trade secret protection challenges - The company **depends on intellectual property licensed from third parties**, and failure to comply with license obligations could lead to termination of these agreements and loss of rights to its core technology[229](index=229&type=chunk)[230](index=230&type=chunk) - There is **no guarantee** that pending patent applications will issue or that existing patents will be broad enough to prevent competitors from developing similar products[228](index=228&type=chunk)[236](index=236&type=chunk) - The company may face **costly litigation** if third parties claim its products infringe their intellectual property rights, which could block commercialization or require expensive licensing deals[249](index=249&type=chunk)[250](index=250&type=chunk) - The company relies on **trade secrets and confidentiality agreements**, which may be breached or may not provide adequate protection, potentially harming its competitive position[245](index=245&type=chunk)[246](index=246&type=chunk) [Risks related to ownership of our common stock](index=59&type=section&id=Risks%20related%20to%20ownership%20of%20our%20common%20stock) Risks include stock price volatility, significant control by principal stockholders, and reduced disclosure as an 'emerging growth' and 'smaller reporting' company - The trading price of the company's common stock may be **highly volatile** and subject to wide fluctuations[295](index=295&type=chunk) - As of June 30, 2019, executive officers, directors, and affiliates beneficially owned approximately **53.4%** of the stock, giving them **significant control** over matters subject to stockholder approval[298](index=298&type=chunk) - The company qualifies as a **'controlled company'** under Nasdaq rules due to majority ownership by an affiliate of Apple Tree Partners, exempting it from certain corporate governance requirements[299](index=299&type=chunk) - The company is an **'emerging growth company'** and a **'smaller reporting company'**, which permits reduced public reporting and disclosure obligations[306](index=306&type=chunk)[309](index=309&type=chunk) [Unregistered Sales of Equity Securities and Use of Proceeds](index=60&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) The company issued options and converted preferred stock upon IPO, generating $149.4 million in net proceeds with no material change in their planned use - Upon completion of the IPO, all outstanding convertible preferred stock automatically converted into **22,677,585 shares** of common stock[320](index=320&type=chunk) - The company received net proceeds from its IPO of approximately **$149.4 million** after deducting underwriting discounts, commissions, and offering expenses[322](index=322&type=chunk) - There has been **no material change** in the planned use of proceeds from the IPO as described in the prospectus[323](index=323&type=chunk) [Defaults Upon Senior Securities](index=61&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) No defaults upon senior securities were reported - **None**[324](index=324&type=chunk) [Mine Safety Disclosures](index=61&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) Mine safety disclosures are not applicable to the company's operations - **Not Applicable**[325](index=325&type=chunk) [Other Information](index=61&type=section&id=Item%205.%20Other%20Information) No other material information to disclose - **None**[325](index=325&type=chunk) [Exhibits](index=62&type=section&id=Item%206.%20Exhibits) Key exhibits include corporate governance documents, equity plans, and CEO/CFO certifications filed with the Form 10-Q - **Exhibits filed** include the Restated Certificate of Incorporation, Restated Bylaws, 2019 Equity Incentive Plan, 2019 Employee Stock Purchase Plan, and CEO/CFO certifications[328](index=328&type=chunk)