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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | Stoke Therapeutics Second Quarter 2026 Business Update Webcast for Investors & Analysts August 3, 2026 1
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Forward-Looking Statements and Other Legal Notices 2 This presentation has been prepared by Stoke Therapeutics, Inc. (“Stoke” or “us”) for informational purposes only and not for any other purpose. Nothing contained in this presentation is, or should be construed as, a recommendation, promise or representation by the presenter(s) or Stoke or any officer, director, employee, ag ent or advisor of Stoke. This presentation does not purport to be all-inclusive or contain all of the information you may desire. Information provided in this presentation speaks only as of the date hereof. Stoke assumes no obligation to publicly update any information or forward-looking statement, whether written or oral, that may be made from time to time, whether as a result of new information, future developments, subsequent events, or circumstances after the date hereof, or to reflect the occurrence of unanticipated events. This presentation contains forward-looking statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to, statements regarding: the ability of zorevunersen to treat the underlying causes of Dravet syndrome and reduce seizures or show improvements in behavior or cognition at the in dicated dosing levels or at all; the potential benefits, safety and efficacy of zorevunersen; the clinical development of zorevunersen, STK-002 and our other product candidates, including the initiation, timing and expected progress of clinical trials (including our EMPEROR Phase 3 study and our OSPREY Phase 1 study); the timing of regulatory interactions or the outco mes thereof; our ability to achieve an NDA submission or approval on the expedited timeframe disclosed or at all; the ability of STK-002 to treat the underlying causes of Autosomal Dominant Optic Atrophy (ADOA) and maintain or improve vision; the potential for us to advance and develop our research and development programs, including our ability to enhance our platform expansion under our new CSO ; ou r expectations, plans, aspirations and goals, including those related to the potential of zorevunersen and our collaborations with Biogen and Acadia; the anticipated market, access, reimbursement and label, if any, for zorevunersen; our future operating results, financial position and cash runway and ability to fund operations through to a potential U.S. launch of zorevunersen in early 2028. Statements including words such as “anticipate,” “believe,” "expect," “hope,” “plan,” “will,” “continue,” “ongoing,” or “potential,” and statements in the future tense are forward -looking statements. These forward-looking statements involve risks and uncertainties, as well as assumptions, which, if they prove incorrect or do not fully materialize, could cause our results to differ materially from those expressed or implie d by such forward-looking statements, including, but not limited to, risks and uncertainties related to: our ability to advance, obtain regulatory approval of, and ultimately commercialize our product can didates, including zorevunersen and STK-002; the timing of data readouts and interim and final results of nonclinical and clinical studies; nonclinical and clinical data being voluminous and detailed, and regulatory authorities may interpret or weigh the importance of data differently and reach different conclusions than us or others, request additional information, have additional recommendations, or change the ir guidance or requirements before or after approval; receiving Breakthrough Therapy Designation may not lead to a faster development or regulatory review or approval and does not mean zorevunersen will receive marketing approval; our ability to fund development activities and achieve development goals; our ability to protect our intellectual property; and other risks and uncertainties described under the heading “Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2025, our quarterly reports on Form 10-Q and the other documentation we file form time to time with the Securities and Exchange Commission. These forward-looking statements speak only as of the date of this presentation, and we undertake no obligation to revise or update any forward -looking statements to reflect events or circumstances after the date hereof. By attending or receiving this presentation you acknowledge that you are cautioned not to place undue reliance on the forward -looking statements, which speak only as of the date such statements are made, you will be solely responsible for your own assessment of the market and our market position, and that you will conduct your own analysis and be solely responsible for forming your own view of the potential future performance of Stoke. Certain information contained in or that may accompany this presentation relate to or are based on studies, research, publica tions, surveys and other data obtained from third-party sources and our own internal estimates and research. While we believe these third-party studies, research, publications, and surveys and other data to be reliable as of the date of this presentation, we have not independently verified, and we make no representation as to the adequacy, fairness, accuracy or completeness of any information obtained fr om third-party sources. This presentation discusses product candidates, including zorevunersen and STK-002, that have not yet been approved for marketing by the U.S. Food and Drug Administration or any other regulatory age ncy
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | Opening Remarks Ian F. Smith Chief Executive Officer & Director 3
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Advancing Through a Period of Execution and Expansion 4 Zorevunersen Phase 3 Progress • Enrollment of 162 patients completed in June 2026 • No treatment discontinuations to date • Data readout expected Q3 2027 Pipeline Beyond Zorevunersen • Dose escalation continuing following completion of sentinel cohort in the Phase 1 study of STK-002 in patients with ADOA • Lead optimization underway to identify a clinical candidate for SYNGAP1-related disorders • Appointment of CSO Thomas McCauley, PhD U.S. NDA Preparation Underway • Pre-NDA meeting with FDA scheduled for H2 2026 • Rolling submission planned to initiate in Q1 2027 and complete in 2H 2027 • Long-term 4-year OLE data support ongoing educational efforts $420M pro-forma cash position supports investment in the business, provides runway through to a potential U.S. launch of zorevunersen in early 2028
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | 5 Phase 3 Progress and 4-Year OLE Data Barry Ticho, M.D., Ph.D. Chief Medical Officer
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Phase 3 Enrollment of 162 Patients Completed in June 2026 Supports a Data Readout in Q3 2027 6 • 162 patients enrolled (U.S., UK, Japan) in 10 months • Final patient randomized in June 2026 • 52 Week treatment period after which all data will be analyzed • Data readout anticipated in Q3 2027 Patient Progression Through Key Study Milestones Rolling U.S. NDA submission planned to initiate in Q1 2027 and complete in H2 2027 ~145 through Week 8 completion of 2x70mg loading doses or sham ~80 through Week 24 completion of 3 doses or sham ~60 through Week 28 primary endpoint First patients approaching Week 52 No treatment discontinuations ~ Additional patients in Europe 30 • Completion of enrollment expected in August • Data not planned for inclusion in U.S. NDA submission n=162
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Substantial, Durable Reductions in Seizure on Top of SOC Observed Through Four Years of Treatment with Zorevunersen 7 Data for all patients who continued treatment in the OLEs separated by dose received in the Ph1/2a studies Data cut date: 19 Feb 2026; 1 Month = 4 Weeks; One patient who received an incorrect dose of zorevunersen in Phase 1/2a, 3 patients who experienced less than the minimum number of convulsive seizures during Phase 1/2a baseline, and 1 patient who transferred into OLE with a delay of approximately 10 months were excluded. Patients were not included in 6M after last Ph1/2a dose time point if they didn’t enter OLE. No exclusions were made for ASM modification. Intervals with <50% diary data were excluded for individual patients.
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Development in Patients with Dravet Syndrome Differs Markedly from That of Neurotypical Children 8 Comparison of developmental trajectory between neurotypical children and patients with Dravet syndrome Graph provided for illustrative purposes only; progress not drawn to scale. 1 Sullivan J, Wirrell E, Knupp K. et al. Natural history of children and adolescents with Dravet syndrome: a 24-month follow- up. Neurology. 2025;105:e214388 Neurodevelopmental progress Age Neurodevelopment plateaus at ~2 years of age for most children living with Dravet syndrome1
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN MARGIN MARGIN 4-Year Phase 1/2 OLE Data Showed Continuing Improvements in Cognition and Behavior Datacut date: 19 Feb 2026; no patient exclusion; Data included through Week 192. 1 year = 48 weeks. “n” represents the number of completed patient visits at each timepoint shown; these values may not correspond exactly to the number of patients contributing to the model-based estimates for each subdomain. Mixed-effects model for repeated measures constructed using available data from enrolled patients in OLE studies. Statistical analyses are post-hoc and exploratory. 9 <0.01 statistical significance achieved in 5 key subdomains for each year compared to OLE baseline Year 1 (n=68) Year 2 (n=60) Year 3 (n=42) Year 4 (n=14) Phase 3 EMPEROR Subdomains
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN MARGIN MARGIN Zorevunersen Generally Well-Tolerated with Long-Term Dosing Phase 1/2a data cut: December 12, 2023 (after End of Study); OLE data cut: Feb 19, 2026. *≥1 CSF protein value >50 mg/dL. 72 /75 patients in the OLEs had at least one assessment after baseline. 68/72 (94%) had elevated values and 40/68 (59%) were classified as a TEAE. CSF, cerebrospinal fluid; SUSAR, suspected unexpected serious adverse reaction; TEAE, treatment-emergent adverse event; TESAE, treatment-emergent serious adverse event. 10 >930 doses administered to date in the Phase 1/2 and OLE studies Patients have received treatment for more than 5 years • CSF protein elevation* occurred in 94% of patients and was classified as a TEAE in 59% o No serious or severe clinical manifestations associated with CSF protein elevation were observed o One patient discontinued treatment due to elevated CSF protein • 1 patient died due to SUDEP and 1 due to malnutrition; both deaths were unrelated to zorevunersen • 30% of patients experienced a study drug–related TEAE • Most common: CSF protein elevations (14%) and procedural vomiting (5%) • 22% of patients experienced a TESAE • All were unrelated to the study drug except for one patient with SUSARs • 1 patient died due to SUDEP, unrelated to zorevunersen Phase 1/2a studies (n=81) OLE studies (n=75)
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN MARGIN MARGIN Confidence in the Value of zorevunersen as a Potential Disease-Modifying Treatment for Dravet Syndrome 11Source 1Stoke blinded HCP market research, Feb 2026, n=30; Stoke blinded payer research, Jan/Feb 2026, n=8. 2 Engl J Med 2026;394:969-982 Phase 3 Progress • Dosing regimen, endpoint selection and powering assumptions informed by robust Phase 1/2 and 2-year OLE dataset • <1 year enrollment driven by high awareness and need • Data readout anticipated in Q3 2027 to complete planned U.S. rolling NDA submission in H2 2027 Longitudinal Data • 5 years of clinical data from the Phase 1/2 and OLEs provide confidence in the disease-modifying potential of zorevunersen • By our Phase 3 readout, an additional year of OLE data are expected • HCPs and payers indicate these OLE data may be the most compelling data at the time of a potential approval1 Visibility & Credibility • Publication of zorevunersen data in NEJM2, the world’s leading medical journal is enhancing awareness and understanding • Publication supports education and access efforts • Educational efforts to continue through 2026 and into 2027 with existing and new analyses of data from the Ph1/2 OLEs
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | Expanding the Pipeline Barry Ticho, M.D., Ph.D. Chief Medical Officer 12
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN MARGIN MARGIN Autosomal Dominant Optic Atrophy (ADOA): A Progressive Vision Disorder Caused by OPA1 Haploinsufficiency Sources: Kjer. Acta Ophthalmologica Scandinavica. 1996; Yu-Wai-Man P et al. Ophthalmology, 2010; Yu-Wai-Man P, Chinnery PF. Ophthalmology, 2013; Physician and Payer Interviews; P. Amati-Bonneau P et al. The International Journal of Biochemistry & Cell Biology, 2009; Lenaers G, Hamel C, Delettre C, et al. Orphanet J Rare Dis, 2012; Chun BY and Rizzo JF III. Curr Opin Ophthalmol, 2016; Le Roux B, Lenaers G, Zanlonghi X et al. Orphanet J Rare Dis, 2019; “What is ADOA?” Autosomal Dominant Optic Atrophy Association. Accessed August 11, 2025, from https://www.adoaa.org/what-is-adoa NaV1.1 protein expression people are affected globally with a higher incidence of ~1 out of 10,000 in Denmark due to a founder effect ~13,000 people affected in the U.S., UK, EU-4, and Denmark 1 out of 30,000 >400 Different OPA1 mutations reported in ADOA patients of patients are registered legally blind of patients are symptomatic by age 10 46% 80% 65-90% of cases caused by mutations in one allele of the OPA1 gene, most of which lead to a HAPLOINSUFFICIENCY 50% OPA1 protein expression and disease manifestation Up to RESULTING in 13
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN Phase 1 OSPREY Study of STK-002 in Patients with ADOA 14 Phase 1 Study Design (UK and Europe) 1 2 3 4 Intravitreal injection in one eye 48-week duration Patients ages ≥18 to <55y (n=21) Single ascending doses (0.1, 0.3, 0.5, & 0.7 mg/eye) Primary Endpoint: Safety, tolerability, and exposure of single ascending doses of STK-002 Secondary Endpoints: Changes in visual function (LCVA), ocular structures, quality of life, and electroretinographic measures (e.g., ERG, PhNR) after single doses of STK-002 Exploratory Endpoints: Mitochondrial function as measured by OcuMet Beacon FPF Dosing complete in sentinel cohort Dose escalation continuing and initial data anticipated in H1 2027 Notes: LCVA = low contrast visual acuity, ERG= Electroretinogram, PhNR = ¥Photopic negative response, FPF=Flavoprotein fluorescence
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | 15 Preparing for a Potential U.S. Launch Jason Hoitt Chief Patient Officer
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Significant Market Opportunity *Numbers may not add up due to rounding. EU4: Germany, France, Italy and Spain; ASMs: anti-seizure medications. 1 Based on preliminary management estimates, which scaled annual incidence to prevalence using country-specific live birth rates over the past 85 years and adjusted for Dravet-specific mortality. The estimate is based on incidence rates published by Wu et al., Pediatrics, 2015. Lagae et al., Developmental Medicine & Child Neurology, 2017; 2018 Health Advances Report; Dravet Syndrome Foundation Voice of the Patient Report.; 2Sullivan J, Wirrell E, Knupp K. et al. Natural history of children and adolescents with Dravet syndrome: a 24-month follow-up. Neurology. 2025;105:e214388 16 There are currently no disease-modifying medicines approved for the treatment of Dravet syndrome 2-year natural history study2 demonstrated frequent seizures and significant cognitive and behavioral impairments despite treatment with standard ASMs, including: • A plateauing in neurodevelopment at ~2 years of age leading to a widening gap between children with Dravet syndrome and their neurotypical peers • On average, 14.3 seizures/28 days at baseline and a 10.6 percent increase in major motor seizure frequency over two years ~38K patients with Dravet syndrome across 7 major geographic markets 16K US 16K EU4 + UK 7K Japan PREVALENCE OF DRAVET SYNDROME* ~38K 1 PATIENTS SIGNIFICANT NEED DESPITE AVAILABILITY OF ANTI-SEIZURE MEDICINES (ASMs)
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | MARGIN MARGIN Concentrated U.S. Market and Established Infrastructure Provide Foundation for Early Adoption 17 of identified U.S. patients are cared for by the top 50 sites Treating Sites Existing Infrastructure Zorevunersen Experience Sources: Stoke primary research, July 2026; Komodo claims-based site model, Dec 2025; Field Medical insights. Quote from qualitative HCP interviews ~50% of top 50 sites have established intrathecal administration infrastructure100% of top 50 sites have participated in zorevunersen clinical studies~50% “We’ve used Spinraza for years and we’ve already established the infrastructure of recurrent intrathecal injections for these patients. I can’t imagine that I’m going to need a completely different infrastructure."
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | Path to Potential U.S. Approval and Launch 18 Q3 2026 Q4 2026 Q1 2027 Q2 2027 Q3 2027 Q4 2027 Q1 2028 H2 2026 Pre-NDA Meeting with FDA Planned Start of Rolling U.S. NDA Submission Anticipated Phase 3 Readout from EMPEROR H2 2027 Completion of Rolling U.S. NDA Submission Potential U.S. Approval & Launch March: Phase 1/2 and 3-Year OLE Data Published in The New England Journal of Medicine May: 4-Year Phase 1/2 OLE Data Announced June: Completion of enrollment of 162 patients into EMPEROR (U.S., UK, JP) 1H 2026 Note: Timeline is not comprehensive and reflects the estimated timing of activities which are subject to change.
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | Financial Summary Thomas Leggett Chief Financial Officer 19
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | $420 Million Pro-Forma Cash, Cash Equivalents, & Marketable Securities Current financial position anticipated to fund operations through to potential U.S. commercialization of zorevunersen in early 2028 Second Quarter 2026 Financial Summary based on $354.3M as of June 30, 2026 and $65.7M from a subsequent ATM sale 20
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© COPYRIGHT 2026 | STOKE THERAPEUTICS | © COPYRIGHT 2026 | STOKE THERAPEUTICS | Q&A 21