Scholar Rock Holding 8K Entry into a Material Definitive Agreement | SRRK 24 Jun 19

Exhibit 99.1

Exhibit 99.3 F r o mN e wI n s i ghtst oN e wM e d i ci ne s June 2019

Disclaimers Various statements in this presentation concerning Scholar Rock’s future expectations, plans and prospects, including without limitation, Scholar Rock’s expectations regarding its strategy, its product candidate selection and development timing, including timing for the initiation of and reporting results from its clinical trials for its product candidates, its disease indication selection and timing for such selection, the ability of SRK-015 to affect the treatment of patients suffering from Spinal Muscular Atrophy (SMA) either as a monotherapy or in conjunction with the current standard of care, the ability of SRK-181 to affect the treatment of cancer patients in a manner consistent with preclinical data, and the projected use of cash constitute forward-looking statements for the purposes of the safe harbor provisions under The Private Securities Litigation Reform Act of 1995. The use of words such as “may,” “might,” “will,” “should,” “expect,” “plan,” “anticipate,” “believe,” “estimate,” “target,” “project,” “intend,” “future,” “potential,” or “continue,” and other similar expressions are intended to identify such forward looking statements. Actual results may differ materially from those indicated by these forward-looking statements as a result of various important factors, including, without limitation, Scholar Rock’s ability to provide the financial support and resources necessary to identify and develop multiple product candidates on the expected timeline, competition from others developing products for similar uses, Scholar Rock’s ability to obtain, maintain and protect its intellectual property, Scholar Rock’s dependence on third parties for development and manufacture of product candidates including to supply any clinical trials, and Scholar Rock’s ability to manage expenses and to obtain additional funding when needed to support its business activities and establish and maintain strategic business alliances and new business initiatives as well as those risks more fully discussed in the section entitled "Risk Factors" in the Quarterly Report on Form 10-Q for the quarter ended March 31, 2019, which is on file with the Securities and Exchange Commission, as well as discussions of potential risks, uncertainties, and other important factors in Scholar Rock’s subsequent filings with the Securities and Exchange Commission. Any forward-looking statements represent Scholar Rock’s views only as of today and should not be relied upon as representing its views as of any subsequent date. Scholar Rock explicitly disclaims any obligation to update any forward-looking statements unless required by law. A shelf registration statement on Form S-3 relating to the public offering of the shares of common stock was declared effective by the SEC on June 10, 2019. Before you invest, you should read the prospectus in the registration statement and related preliminary prospectus supplement that Scholar Rock will file with the SEC for more complete information about the company and this offering. An electronic copy of the preliminary prospectus supplement and accompanying prospectus relating to the offering will be available on the website of the SEC at www.sec.gov. Copies of the preliminary prospectus supplement, when available, and the accompanying prospectus relating to the offering may be obtained by contacting Jefferies LLC, Attention: Equity Syndicate Prospectus Department, 520 Madison Avenue 10th Floor, New York, NY 10022, or by email at prospectus_department@Jefferies.com. This presentation shall not constitute an offer to sell or the solicitation of an offer to buy nor shall there be any sale of these securities in any state or jurisdiction in which such offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such state or jurisdiction. © Scholar Rock, Inc. All rights reserved. June 2019. 2

A Novel Approach to Targeting Growth Factor Signaling Traditional approaches to targeting growth factors have been limited by: • • • Structural similarities Overlapping sets of related receptors Diverse and overlapping physiological roles Scholar Rock’s novel approach: • • • Targeting signaling proteins at a cellular level Nature’s way of regulating growth factor activity Targeting activation of growth factor precursors has the potential to offer: o o o High selectivity Potency of inhibition Localization of effect • Approach has applicability over a wide variety of growth factors 3 Traditional Target “Mature” Growth Factor Scholar Rock’s Target Growth Factor Precursor

Robust Pipeline Portfolio End of 2019 Biotech, Inc 4 *CBTs = checkpoint blockade therapies Target / Program Indication Discovery / Early Preclinical Preclinical Phase 1 Phase 2 Rights / Partner Next Anticipated Milestone INTERNAL PROPRIETARY PROGRAMS Pro/Latent Myostatin SRK-015 Spinal Muscular Atrophy (3 distinct Type 2 and Type 3 patient populations) Preliminary PK/PD Data by SRK-015 Myostatin-Related Disorders Identify Next Indication in 2020 Latent TGF SRK-181 (Context-Independent Latent TGF1) Immuno-oncology (Primary resistance to CBTs*) Initiate Phase 1 Trial Mid-2020 SRK-181 (Context-Independent Latent TGF1) Oncology Context-Dependent Latent TGF1 / Immune Cell Oncology/Immuno-oncology RGMc BMP6 Signaling Pathway (anti-RGMc) Iron-Restricted Anemias Nominate Product Candidate in 1H20 PARTNERED PROGRAMS Latent TGF Context-Independent Latent TGF1 Fibrosis Context-Dependent Latent TGF1 / LTBP1 & LTBP3 Fibrosis Undisclosed Program Fibrosis Context-Dependent Latent TGF1 / GARP Oncology/Immuno-oncology Janssen

Summary 5 Market cap $450-$500 million Cash, cash equivalents, and marketable securities ~$160 million as of March 31, 2019 Use of proceeds To fund research and development activities for planned SRK-181 Phase 1 proof of concept clinical trial in patients with solid tumors, SRK-015 Phase 3 readiness in SMA, SRK-015 second indication, RGMc and other preclinical activities, as well as working capital and other general corporate purposes. Pipeline program highlights •SRK-015 in ongoing Phase 2 clinical trial for SMA oEach of 3 cohorts represents a distinct and important patient population •SRK-015 second indication to be announced in 2020 •SRK-181 expected to enter Phase 1 clinical trial in patients with solid tumors in mid-2020 oInitial Phase 1 clinical data anticipated by end of 2021 oSignificant opportunity to expand number of patients treated by checkpoint blockade therapies •Nominate product candidate in RGMc program in 1H20 oLarge potential opportunity in iron-restricted anemias Gilead collaboration proceeds Up to an additional $1.45 billion in potential milestones, including a one-time $25 million preclinical milestone, as well as royalties on net sales

Scholar Rock Achievements Since IPO Executed strategic fibrosis collaboration with GILD -$80M upfront ($50M cash and $30M equity at $30.60/share). Up to $1.45B in potential milestones. EC granted Orphan Medicinal product designation for SRK-015 in SMA Presented additional preclinical data at AACR Transitioned to public company -Successful $86M IPO Transitioned to clinical stage -Initiated SRK-015 Phase 1 trial in healthy volunteers - SRK-181-mIgG1 rendered both TGF1-expressing and TGF1/TGF3 co-expressing mouse tumor models sensitive to anti-PD1 immunotherapy Initiated dosing of patients in SRK-015 Phase 2 trial in SMA Nov 2018 Feb 2019 Mar 2019 June 2019 Dec 2018 May 2018 April 2019 Announced positive SRK-015 interim Phase 1 healthy volunteer results Announced positive final top-line results from SRK-015 Phase 1 trial -Data to be presented at Cure SMA meeting Presented preclinical data at SITC meeting -Highlighted Role of TGF1 Inhibition in Overcoming Checkpoint Resistance Published preclinical data in SMN7 mouse models of SMA in Human Molecular Genetics - First proof-of-mechanism for unique therapeutic approach of targeting latent growth factors Nominated SRK-181 as first product candidate in TGF1 cancer immunotherapy program 6

Upcoming Key R&D Milestones Initiate Phase 2 SMA proof-of-concept trial by the end of 1Q19 Commence patient dosing in Phase 2 SMA proof-of-concept trial in 2Q19 Present final Phase 1 results at Cure SMA Annual Conference being held June 28-July 1, 2019 Announce Phase 2 trial read-outs: •Preliminary PK/PD analysis by end of 2019 SRK-015 in SMA o o • • Interim efficacy and safety analysis at 6 months in 1H20 Top-line results of 12-month treatment period 4Q20-1Q21 o Identify next indication in 2020 •Neuromuscular disorders SRK-015 • Other myostatin-related disorders o o o o Advance cancer immunotherapy product candidate, SRK-181, into a Phase 1 trial mid-2020 Announce initial data from Phase 1 trial of SRK-181 in patients with solid tumors by end of 2021 Continue to advance active discovery programs for context-dependent inhibition of TGF1 Conduct fibrosis discovery and preclinical studies in partnership with Gilead TGF1 Inhibitor o RGMc Nominate product candidate in 1H20 7

SRK-015: Inhibitor of Myostatin Activation Potential First Muscle-Directed Therapy for SMA

SRK-015: Highly Specific Inhibitor of Latent Myostatin • Myostatin is a genetically-validated, negative regulator of muscle mass expressed in skeletal muscle tissue Vertebrates lacking the myostatin gene are healthy and display increased muscle mass and strength • 9 Differentiated approach with SRK-015: Fully human monoclonal antibody (mAb) Highly selective inhibitor of the activation of myostatin precursor Half-life of 23-33 days Orphan Drug Designation for SMA granted by FDA and EC US Patent 9,758,576 covers mAbs that inhibit the activation of the myostatin precursor (expiry in 2034)

SRK-015 Opportunity in Spinal Muscular Atrophy Overall Prevalence of 30,000-35,000 in U.S. and Europe Relative Prevalence Among Patients Living With SMA Type I: • Infant-onset; often fatal Focus of Phase 2 Trial Type II and non-ambulatory type III: • • Later-onset but still early childhood Severe deficits in motor function 14% Type III 35% Ambulatory type III: • Limited mobility and substantial morbidity Type II 51% Type IV: • Population not well-characterized 10 Lally et al, Orphanet Journal of Rare Diseases, 2017 Potential to use SRK-015 in conjunction with SMN upregulators Potential to use SRK-015 as monotherapy or in conjunction with SMN upregulators

Significant Unmet Need Remains Despite Current Therapies Muscle Function in SMA (Human) Hammersmith Functional Motor Scale Expanded (HFMSE) 80 SMN Upregulator Therapies Muscle-Directed Therapies (SRK-015) Total Possible HFMSE Score of 66 60 Unmet Medical Need for Functional Improvement with Muscle-Directed Therapies 40 Address SMN deficiency to prevent further motor neuron deterioration Act directly on muscle with aim to improve functional performance n Improvement 20 nusinersen n Baseline Score 0 Mean improvement in HFMSE score experienced by patients with later-onset SMA in the Phase 3 CHERISH clinical trial of nusinersen 11 SMN = survival motor neuron HFMSE Score at Month 15 SRK-015 has the potential to drive functional performance across a range of severity observed in SMA either as a monotherapy or in conjunction with any SMN upregulator/corrector therapy Mea with Mea

SRK-015 Preclinical and Phase 1 Data Support Evaluation in SMA Preclinical and translational data support myostatin as a drug target in SMA • • • Confirmed presence of target in disease setting Achieved multi-fold increase in serum latent myostatin levels indicating target engagement Treatment of SMN7 mouse model led to improved muscle mass and strength Phase 1 data in healthy volunteers showed robust target engagement and no apparent safety signals • • • No dose-limiting toxicities identified up to highest evaluated dose of 30 mg/kg Serum half-life of 23-33 days supports planned evaluation of once every 4-week (Q4W) dosing in Phase 2 Single dose of SRK-015 led to marked increases in serum concentrations of latent myostatin; no meaningful change observed with placebo Target saturation: peak latent myostatin levels plateaued starting with a single dose at 3 mg/kg Durability of saturation: plateau was sustained up to Day 140 after multiple doses at 20 mg/kg • • 12 Phase 1 results provide first proof-of-mechanism in humans of Scholar Rock’s therapeutic approach of targeting the latent form of growth factors

SRK-015 Target Profile in SMA GOALS EVIDENCE TO DATE Translational/preclinical data support myostatin as a drug target in SMA Preclinical data demonstrate potential for substantial increases in muscle strength Phase 1 PD data demonstrate SRK-015 can successfully engage the target in a durable fashion Effectively increase motor function to drive clinically meaningful outcomes Safety profile to enable chronic dosing, including in pediatric populations Well-tolerated with no apparent safety signals based on Phase 1 data Binds myostatin precursors with high selectivity in vitro Low drug administration burden to offer broad accessibility Minimally invasive route of administration (IV) PK and PD data support an infrequent dosing regimen (e.g. once every 4 weeks) 13 Emerging evidence supports investigating the safety and efficacy of SRK-015 in SMA

SRK-015 Phase 2 Trial Design Co h o r t 2 Co h o r t 1 Co h o r t 3 • Double-blind, randomized (1:1) Design • 12-month treatment period Subjects Primary Objectives HFMSE – Hammersmith Functional Motor Scale Expanded; RHS – Revised Hammersmith Scale 14 •Safety •Mean change from baseline in HFMSE •Safety •Mean change from baseline in RHS •Safety •Mean change from baseline in HFMSE •N= 20; ages 5-21 •Open-label, single-arm •20 mg/kg SRK-015 IV Q4W •12-month treatment period •N= 15; ages 5-21 •Open-label, single-arm •20 mg/kg SRK-015 IV Q4W •12-month treatment period •N= 20; ages 2 to 2 mg/kg or 20 mg/kg SRK-015 IV Q4W •Ambulatory Type 3 SMA •Type 2 or non-ambulatory Type 3 SMA •Receiving treatment with approved SMN upregulator •Type 2 SMA •Initiated treatment with approved SMN upregulator before age 5

SRK-015: Path to Top-Line Results in SMA 1Q19 4Q20-1Q21 2Q19 End of 2019 1H 2020 Initiated trial Commenced patient dosing Preliminary PK/PD data from subset of patients Top-line results Interim efficacy and safety analysis by cohort - Start-up activities, including contracts and IRB submissions with trial sites - Full 12-month treatment period by cohort - Provided additional details of Phase 2 trial design - Further assess the pharmacologic profile of SRK-015 - Subset of patients with at least 6 months of treatment exposure SRK-015 has the potential to be the first muscle-directed therapy for patients with SMA 15

TGF1: Significant Opportunities in Oncology/Immuno-oncology and Fibrosis

TGF1 Plays Central Role in Multiple Diseases with Unmet Need Immuno-Oncology Tumor-Directed Therapy Oncology Myeloproliferative Disorders Upfront cash and equity investment: $80 million* One-time preclinical milestone: $25 million Additional milestones across 3 programs: Up to $1,425 million High single-to low double-digit tiered royalties on net sales Fibrosis 17 *Includes $30 million purchase of Scholar Rock common stock at price per share of $30.60

Inhibition of TGF1: Multipronged Approach for Immuno-Oncology Nature (on-line), Feb. 14, 2018 TGF1 is a key driver of immune system evasion by cancer cells Regulatory T cell TGF1 Tumor Associated Macrophage Cancer Associated Fibroblasts (Stromal cells) Tumor cells 18 •Pathway analysis points to TGF1 as major determinant of resistance to anti-PDL1 (atezolizumab) •TGF1 creates ‘immune excluded’ tumor microenvironment •Anti-TGF antibody enhances anti-PDL1 treatment response in syngeneic EMT6 tumor model

Renewed Industry Interest in Potential Role Inhibition in Immuno-Oncology of TGF Feb. 5, 2019 “GSK and Merck KGaA, Darmstadt, Germany announce global alliance to jointly develop and commercialise M7824, a novel immunotherapy with potential in multiple difficult-to-treat cancers” June 10, 2019 “Merck to Acquire Tilos Therapeutics: Merck Gains Portfolio of Investigational Antibodies Modulating TGF” 19 *SRK-181-mIgG1 is the murine version of SRK-181 Differentiated approach with SRK-181: Fully human monoclonal antibody (mAb) Highly selective inhibitor of the activation of TGF1 precursor (latent form) Minimal or no binding to latent TGF2 and TGF3 isoforms In preclinical models: oTGF1-specific inhibition by SRK-181-mIgG1* rendered both TGF1-and TGF1/TGF3 co-expressing tumor models sensitive to anti-PD1 oCombination of SRK-181-mIgG1 and anti-PD1 led to tumor regression and survival benefit oImproved toxicity profile; avoided cardio tox associated with less selective approaches such as pan-TGF antibody and ALK5 inhibitor

TGF1 is the Predominant Isoform in Most Human Tumors The Cancer Genome Atlas RNAseq analysis: >10,000 samples spanning 33 tumor types T G FB 1 T G FB 2 T G FB 3 k idney c lear c ell c ar c inom a s c a le ( % o f p at ie n t s a m p l e s ( + ) f o r T G F b i s o f o r m ) 100 80 c er v ic al & endoc er v ic al c anc er 60 40 20 0 20 bladder ur ot helial c ar c inom a head & nec k s quam ous c ell c ar c inom a k idney papillar y c ell c ar c inom a liv er hepat oc ellular c ar c inom a lung adenoc ar c inom a s k in c ut aneous m elanom a s t om ac h adenoc ar c inom a ac ut e m y eloid leuk em ia adr enoc or t ic al c anc er br ain low er gr ade gliom a br eas t inv as iv e c ar c inom a c holangioc ar c inom a c olon adenoc ar c inom a dif f us e lar ge B - c ell ly m phom a es ophageal c ar c inom a glioblas t om a m ult if or m e k idney c hr om ophobe lung s quam ous c ell c ar c inom a m es ot heliom a ov ar ian s er ous c y s t adenoc ar c inom a panc r eat ic adenoc ar c inom a pheoc hr om oc y t om a & par agangliom a pr os t at e adenoc ar c inom a r ec t um adenoc ar c inom a s ar c om a t es t ic ular ger m c ell t um or t hy m om a t hy r oid c ar c inom a ut er ine c ar c inos ar c om a ut er ine c or pus endom et r ioid c ar c inom a uv eal m elanom a • TGF1 prevalent in human cancers for which checkpoint therapies are approved • Expression data for most tumor types suggest that TGF signaling mainly driven by TGF1

TGF1 Blockade with SRK-181-mIgG1 Rendered Preclinical Tumor Models Susceptible to Anti-PD1 Therapy Bladder Cancer Melanoma Anti-PD1 (10 mg/kg BIW) SRK-181-mIgG1 (30 mg/kg QW) SRK-181-mIgG1* (10 mg/kg QW) Anti-PD1 (10 mg/kg BIW) Endpoint 3/12 0/12 Responders 0/12 0/13 Anti-PD1/ SRK-181-mIgG1 (30 mg/kg QW) Anti-PD1/ SRK-181-mIgG1 (10 mg/kg QW) Anti-PD1/ SRK-181-mIgG1 (10 mg/kg QW) Anti-PD1/ SRK-181-mIgG1 (3 mg/kg QW) 8/11 4/9 4/14 8/14 Days after treatment initiation Preclinical data shown above as presented at American Association of Cancer Research (AACR) Annual Meeting (April 2019) *SRK-181-mIgG1 is the murine version of SRK-181; Responder defined as tumor size <25% endpoint volume at study end 21 Tumor volume (mm3)

Inhibiting TGF1 Alone Was Sufficient to Sensitize Preclinical TGF1/3-Expressing Breast Cancer Model Control Anti-PD1 (10 mg/kg BIW) Endpoint Responders 0/9 0/9 Anti-PD1/ SRK-181-mIgG1 (10 mg/kg QW) SRK-181-mIgG1* (10 mg/kg QW) 0/10 5/10 Days after treatment initiation Preclinical data shown above as presented at American Association of Cancer Research (AACR) Annual Meeting (April 2019) *SRK-181-mIgG1 is the murine version of SRK-181 22 Tumor volume (mm3) •EMT6 model expresses both TGF1 and TGF3 •Model is poorly responsive to PD1 blockade as a monotherapy •Combination of SRK-181-mIgG1 and anti-PD1 resulted in tumor regression or tumor control

SRK-181-mIgG1† Combined with Anti-PD1 Therapy Led to Significant Survival Benefit in Preclinical Tumor Models MBT-2 Bladder Cancer Model Cloudman S91 Melanoma Model EMT6 Breast Cancer Model ** ** * *** *** Days after treatment initiation Days after treatment initiation Days after treatment initiation * P<0.05 Log-rank (Mantel-Cox test) vs. anti-PD1 **P<0.01 *** P<0.001 Preclinical data shown above as presented at American Association of Cancer Research (AACR) Annual Meeting (April 2019) †SRK-181-mIgG1 is the murine version of SRK-181 23 Survival (%) Survival (%) Survival (%)

SRK-181-mIgG1 Combination Therapy Enabled Infiltration and Expansion of CD8+ T cells in Preclinical Bladder Cancer Model Anti-PD1 Combination treatment with anti-PD1/SRK-181-mIgG1 led to: • Significant increase in effector T cells (p<0.05) o Expansion of CD8+ population to an average of 34% of the tumor's immune cells from a control average of 3.5% • Significant decrease in intratumoral immunosuppressive myeloid cells (p<0.05) o Reduction in TAM/MDSC population to 14% of the tumor's immune cells from a control average of 47% Anti-PD1/SRK-181-mIgG1 (10 mg/kg) led to increase in CD8+ cells Preclinical data shown above as presented at American Association of Cancer Research (AACR) Annual Meeting (April 2019) *SRK-181-mIgG1 is the murine version of SRK-181; Anti-PD1 dosed at 10 mg/kg twice weekly and SRK-181-mIgG1 dosed at 10 mg/kg weekly 24 IgG SRK181-mIgG1 anti-PD-1 anti-PD-1/SRK181-mIgG1

TGF1 Isoform Specificity of SRK-181 Improved Toxicity Profile Preclinical Repeat dose pilot toxicology study in adult female Sprague Dawley rats Legend Unremarkable Minimal Slight Moderate • Animals dosed with pan-TGF inhibitors, LY2109761 (inhibitor of ALK5, common TGF receptor kinase) or pan-TGF antibody, exhibited expected cardiac findings based on published data Exposure as assessed by SRK-181 serum concentration reached 2,300 µg/ml following 4 weekly doses of 100 mg/kg No SRK-181 related adverse effects were noted up to 100 mg/kg per week No cardiotoxicities (valvulopathy) were noted with SRK-181 No observed adverse effect level (NOAEL) for SRK-181 was the highest dose evaluated (100 mg/kg QW) • • • • Preclinical data shown above as presented at American Association of Cancer Research (AACR) Annual Meeting (April 2019) 25 SRK-181 10 m g/kg 30 m g/kg 100 m g/kg iv, qwk x 4 iv, qwk x 4 iv, qwk x 4 PanTGFAb 30 m g/kg iv, 1 dose LY2109761 300 m g/kg po, qd x 8 Control vehicle iv, qwk x 4 Microscopic observations in heart Valvulopathy Atrium - Mixed cell infiltrate Myocardium - Degeneration/necrosis Myocardium - Hemorrhage Myocardium - Mixed cell infiltrate, base Coronary artery - Necrosis with inflammation Cardiomyocyte - Necrosis/inflammatory cell infiltrate

SRK-181: Advancing Development for Treatment of Cancers Resistant to Checkpoint Blockade Therapies (CBTs) SRK-181 is a fully human antibody designed to bind to, and prevent the activation of, latent TGF1 with high affinity and high selectivity types for which CBTs is approved or showed clinical activity tumor regression/control and significant survival benefit, tumor models resistant to CBT 26 *SRK-181-mIgG1 is the murine version of SRK-181 TGF signalingImplicated as a culprit in primary resistance to CBTs Translational data analysesTGF1 expression is prominent in many human tumor Clinical correlation and preclinicalTGF1 excludes effector cell entry into the tumor and limits model dataimmune system access to tumor cells Preclinical studies in syngeneic mouseCombination of SRK-181-mIgG1* with anti-PD1 led to including in models that express both TGF1 and TGF3 28-day pilot toxicology study in adult rats SRK-181 showed no observed drug-related toxicity up to a weekly dose of 100 mg/kg for 4 weeks

RGMc Program: Targeting the BMP6 Signaling Pathway

Anti-RGMc Therapy: Rational Solution that Directly Addresses the Underlying Pathobiology of Iron-Restricted Anemias Genetically validated pathway of iron regulation in humans RGMa and RGMb play many different physiological roles BMP6 RGMc (HJV) Iron homeostasis BMP6 RGMc BMP Receptor Inflam-mation P SMAD 1/5/8 CNS SMAD 4 Immunity Immunity RGMa RGMb Hepcidin Inflam-mation Growth Angio-genesis CNS Adapted from Crielaard et al, Nature Reviews , 2017 28

Scholar Rock’s RGMc-Selective Antibodies Show Potent Increase in Serum Iron In Vivo Antibodies resulted in increases in serum iron and decreases in UIBC Antibodies showed up to 3 weeks prolonged increase in serum iron in SD rats after a single 20 mpk dose * * 600 500 400 300 200 300 200 100 0 29 UIBC, µg/dL Serum iron (µg/dL) **********

Building Value in All Dimensions Building on Strong Financial Foundation Advancing Clinical Development Executing Strategic Collaboration Growing Innovative Pipeline 31

Appendix

SRK-015: Aligning Therapeutic Approach with Myostatin Biology Scholar Rock’s Guiding Principles for Neuromuscular Indication Selection Key Characteristics of Spinal Muscular Atrophy (SMA) Substantial deficit in fast-twitch fibers muscle fibers 33 Younger populationGenetic disorder with onset in childhood At least partially intact innervation andPartial neural connectivity and atrophied no structural muscle abnormalitiesmuscles that largely retain structural integrity Need for increase in fast-twitch Clinical trial endpoint driven by fast-twitch fiber function Fast-twitch fiber function has a prominent role in SMA outcome measures

Traditional Approaches Can Raise Significant Safety Concerns Traditional Approaches Lack Selectivity Scholar Rock Approach • Most inhibitors of active myostatin also inhibit GDF11 and may inhibit other growth factors as well Antibodies to ActRIIb and ligand trap approaches inhibit signaling of multiple ligands Exquisite Selectivity By Targeting Precursor Form of Myostatin SRK-015 • proGDF-11 proActivin A formation Activin A GDF11 Myostatin GDF-11 Activin A Myostatin BMP9 34 Angiogenesis Kidney Reproductive function proMyostatin

Review of Preclinical Data in SMN7 Mouse Models More Severe Model Less Severe Model NA SMN upregulator + muSRK-015P SMN upregulator only muSRK-015P* Achieved multi-fold increase in serum latent myostatin levels indicating target engagement Confirms presence of target in disease setting Treatment improved muscle mass and strength Maximal torque of the plantar flexor muscle group increased: More severe model: 44%-51% Less severe model: 20%-30% Lower latent myostatin levels in the SMA group may be attributable to reduced overall muscle mass *muSRK-015P is the parental clone of SRK-015 on a mouse IgG1 framework Preclinical data published Nov 2018: Long, K., O’Shea, K., Khairallah, R., et al. Specific Inhibition of Myostatin Activation is Beneficial in Mouse Models of SMA Therapy. Human Molecular Genetics, ddy382 35

SRK-015 Phase 1 Trial Design KEY OBJEC TIVES OF P HASE 1 Evaluate the safety and tolerability, pharmacokinetics, and pharmacodynamics of SRK-015 IV S I NGL E - A S CE ND I NG D O S E ( S A D ) MU LTIP LE - A S C END I NG D O S E ( M A D ) Design Subjects Dosing 36 Q2W dosing for 3 doses at: 10, 20, or 30 mg/kg Single doses at: 1, 3, 10, 20, or 30 mg/kg 26 Adult healthy volunteers (Ages 18-55) 40 Adult healthy volunteers (Ages 18-55) Double-blind, placebo-controlled 3:1 randomization Double-blind, placebo-controlled 3:1 randomization

SRK-015 Well Tolerated in Phase 1 Healthy Volunteer Trial • • Well-tolerated with no apparent safety signals SAD cohort: AEs* were observed in 30% (9/30) SRK-015-vs. 50% (5/10) placebo-treated subjects • No dose-limiting toxicities identified up to highest evaluated dose of 30 mg/kg - Most frequently reported AE: headache • MAD cohort: AEs observed in 35% (7/20) SRK-015-vs. 67% (4/6) placebo-treated subjects - No discontinuations due to treatment-related adverse events (AEs) No treatment-related SAE No hypersensitivity reactions - - - Most frequently reported AE: postural dizziness • Single reported SAE of gallstone-induced pancreatitis • Anti-drug antibody tests were negative in all SRK-015 treated subjects - Assessed by trial investigator as unrelated to SRK-015 treatment *Term “adverse event” noted in this presentation refers to a treatment-emergent adverse event, which is defined as an AE with onset after administration of study drug through the final follow-up visit, or in the event that onset time precedes study drug administration, the AE increases in severity during the post-dosing follow-up period 37

Phase 1 Pharmacokinetic (PK) Data Support Infrequent Dosing Single-Ascending Dose Multiple-Ascending Dose 38 SRK-015 Displayed Well-Behaved, Linear PK Profile •Minimal variability observed, consistent with that commonly observed with monoclonal antibodies •Dose-proportional serum drug exposure Half-Life Supports Infrequent Dosing •Serum half-life of 23-33 days across SRK-015 dose groups •Supports planned evaluation of once every 4-week (Q4W) dosing in Phase 2

Phase 1 Pharmacodynamic (PD) Data Demonstrate Robust Sustained Target Engagement and Single-Ascending Dose Multiple-Ascending Dose 10,000 1,000 Placebo 10 mg/kg 20 mg/kg 30 mg/kg 100 10 1 0 14 28 42 56 70 84 98 112 126 140 Time (days) 39 Latent Myostatin (ng/mL) Robust Target Engagement Observed •Single dose of SRK-015 led to marked increases in serum concentrations of latent myostatin •No meaningful change observed with placebo Evidence Supports Durable Target Saturation •Peak latent myostatin levels plateaued starting with a single dose at 3 mg/kg suggesting target saturation -Single dose at 1 mg/kg only attained approx. half of peak level •Plateau was sustained demonstrating durability of effect: -Up to Day 84 after single dose at 20 mg/kg -Up to at least Day 140 after multiple doses at 20 and 30 mg/kg First proof-of-mechanism in humans of Scholar Rock’s therapeutic approach targeting the latent form of growth factors

Highlights of Strategic Fibrosis Collaboration with Gilead Collaborating to Develop Innovative Therapies for Fibrotic Diseases Responsible for antibody discovery and preclinical research thru product candidate nomination for three TGF programs Upon option exercise, responsible for preclinical and clinical development and commercialization Retains exclusive worldwide rights to develop certain TGF antibodies for oncology and cancer immunotherapy Upfront cash and equity investment: $80 million* One-time preclinical milestone: $25 million Additional development, regulatory, and commercial milestones across 3 programs: Up to $1,425 million High single-to low double-digit tiered royalties on net sales 40 *Includes $30 million purchase of Scholar Rock common stock at price per share of $30.60

Scholar Rock Holding (SRRK) 8-KEntry into a Material Definitive Agreement