MGTA-117 Clinical Data Update

ASH Annual Meeting

December 13, 2022

(NASDAQ: MGTA)

Agenda & Introductions

Introduction

Review of MGTA-117 Phase 1/2 Clinical Results - Cohorts 1-3

Next Steps

Q&A Session

2

Jason Gardner, D.Phil.

Lisa Olson, Ph.D.

CEO, President

Chief Scientific Officer

and Co-founder

Shawn Rose,

Steve Mahoney,

M.D., Ph.D.

J.D., M.B.A.

Senior Vice President,

Chief Financial and

Clinical Development

Operating Officer

Confidential

Forward-Looking Statements

This presentation contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995, as amended. These statements include, without limitation, implied and express statements relating to: Magenta's future business expectations, plans and prospects; the potential of, and expectations for, Magenta's product candidate pipeline; the goals, potential benefits and expected performance of Magenta's product candidates and programs; the potential of Magenta's product candidates and programs to drive expansion of patient eligibility across stem cell transplant and gene therapies; the potential of stem cell transplant as a platform for advancing cell and gene therapies; the eligibility of future patient populations with improved conditioning; MGTA-117's potential to improve upon current conditioning approaches, including the potential to reduce or eliminate the need for chemo- or radiation-based conditioning; the development of product candidates and advancement of preclinical and clinical programs, including, without limitation, patient enrollment; expectations, plans and timing for preclinical activities and clinical trials involving Magenta's product candidates; expectations, plans and timing for the generation, receipt and disclosure of preclinical and clinical data and other results involving Magenta's product candidates; timelines and expectations for patient dosing, dosing regimens and administration; regulatory engagement, interactions and alignment with regulators; the expected transition of MGTA-117 into transplant-eligible patients and gene therapy patients; that MGTA-117's evidence of depletion in the Relapsed / Refractory AML and MDS patient population provides an important readthrough for the next phase of development; that MGTA-117 is expected to more efficiently target CD117+ blast and/or stem cells in the bone marrow of transplant-eligible AML and MDS patients and gene therapy patients due to lower number or absence of blasts in those patient populations; potential study designs and partners for use of MGTA-117 in transplant eligible patients and gene therapy; and plans to develop in gene therapy and collaborations with Magenta's partners.

Words such as "anticipate," "believe," "continue," "could," "designed," "endeavor," "estimate," "expect," "goal," "intend," "may," "might," "plan," "potential," "predict," "project," "seek," "should," "target," "will," "would" and similar expressions are intended to identify forward-looking statements. The express or implied forward-looking statements included in this presentation are only predictions and are subject to a number of risks, uncertainties and assumptions, including, without limitation: uncertainties inherent in preclinical and clinical trials and in the availability and timing of data from ongoing and planned clinical and preclinical trials; the ability to initiate, enroll, conduct or complete ongoing and planned preclinical and clinical trials; vulnerability and/or fragility of, and the presence of underlying disorders in, the patient population for the clinical trials of Magenta's product candidates, including the MGTA-117 Phase 1/2 clinical trial in patients with relapsed/refractory AML and MDS; that preliminary data from Magenta's clinical trials may change materially following a more comprehensive review of the data; the delay of any current or planned preclinical or clinical trials, or the delay in development of Magenta's product candidates; whether results from preclinical or earlier clinical trials will be predictive of the results of future trials; interactions with regulatory agencies such as the U.S. Food and Drug Administration; the expected timing of submissions for regulatory approval to conduct or continue trials or to market products; Magenta's ability to successfully demonstrate the safety and efficacy of its product candidates; whether Magenta's cash resources will be sufficient to fund Magenta's foreseeable and unforeseeable operating expenses and capital expenditure requirements; and risks, uncertainties and assumptions regarding the impact of the continuing COVID-19 pandemic on Magenta's business, operations, preclinical activities, clinical trials, strategy, goals and anticipated timelines. These and other risks are described in additional detail in Magenta's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022 and its other filings made with the Securities and Exchange Commission from time to time. Any forward-looking statements contained in this presentation represent Magenta's views only as of the date of this presentation and should not be relied upon as representing its views as of any subsequent date. Magenta explicitly disclaims any obligation to update any forward-looking statements, except to the extent required by law.

3

Confidential

Improve Outcomes and Expand Use of Stem Cell Transplant & Gene Therapy

Transplant could be a path to a cure

stem cell

90,000 transplants/year globally1

Blood Cancers

~60% of

eligible

(AML, MDS)

patients

receive

transplant3

Gene Therapy

(Sickle Cell

<1% of

Disease)

eligible

patients

receive

transplant3

Autoimmune

(Multiple

Sclerosis)

Barriers to transplant

Significant Limitations

of Current Conditioning

Options:

Many patients need high intensity chemotherapy conditioning to prepare for transplant

~20%

Mortality associated with chemotherapy conditioning regimens2

Opening the door to a cure

Magenta addresses key factors

keeping patients from accessing HSCT and better outcomes

4 HSCT: Hematopoietic Stem Cell Transplant Source: 1 CIBMTR, EBMT, and APBMT Transplant Registry Data (2018), 2 Scott, BL. Biol Blood Marrow Transplant.

2020, 26 (3): S11; 3 Magenta Market Research, Data on File (2020)

Differentiated Pipeline with Potentially First-in-Class ADC Targeted Conditioning

Disease Area

Preclinical

IND-Enabling

Phase 1

Phase 2

Clinical Trial

Product

Partners

Rights

Blood Cancers

AML/MDS1

MGTA-117

Lysosomal Disorders

Gene Therapy

Targeted Conditioning:

Hemoglobinopathies

Gene Therapy

MGTA-145

Gene Therapy

Stem Cell Mobilization

Sickle Cell Disease

and Collection:

CD45-ADC

Heme Malignancies

CD$5

Targeted Conditioning:

Autoimmune Disease

Research Platform:

Novel Conditioning &

Translational Stem Cell

Sciences

5 1 AML/MDS: Acute Myeloid Leukemia or Myelodysplastic Syndromes

Confidential

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Magenta Therapeutics Inc. published this content on 13 December 2022 and is solely responsible for the information contained therein. Distributed by Public, unedited and unaltered, on 13 December 2022 14:24:05 UTC.