Applied Genetic Technologies : AGTC 2021 R&D Presentation

Corporate Overview

July 22, 2021 Research Day

Forward-Looking Statements	2

This presentation contains forward-looking statements that reflect Applied Genetic Technologies Corporation's ("AGTC" or the "Company") plans, estimates, assumptions and beliefs. Forward-looking statements include statements regarding AGTC's Phase 2/3 trial design for XLRP and the Phase 1/2 expansion trial for XLRP, including the effectiveness of AGTC's pre-selection methodology for pre-specifying loci, its anticipated timeline and potential to receive FDA approval to begin the XLRP pivotal trial, AGTC's proposed clinical development of ACHM B3, the potential results of both of its ACHM trials, the timing for completing and reporting data in its XLRP and ACHM clinical programs, its ability to enroll patients for its clinical trials, the expected costs of its clinical programs and its planned manufacturing activities, business strategies and operations, regulatory progress, potential growth and market opportunities, and the effects of competition. Forward-looking statements include all statements that are not historical facts and can be identified by terms such as "anticipates," "believes," "could," "seeks," "estimates," "expects," "intends," "may," "plans," "potential," "predicts," "projects," "should," "will," "would" or similar expressions and the negatives of those terms. Actual results could differ materially from those discussed in the forward-looking statements, due to a number of important factors. Risks and uncertainties that may cause actual results to differ materially include, among others: AGTC cannot predict when or if it will obtain regulatory approval to continue to progress its clinical trials, commercialize a product candidate or receive reasonable reimbursement; uncertainty inherent in clinical trials and the regulatory review process; risks and uncertainties associated with drug development and commercialization; risks related to the COVID-19 pandemic that may delay clinical trial enrollment; gene therapy is still novel with only a few approved treatments so far; factors that could cause actual results to differ materially from those described in the forward-looking statements are set forth under the heading "Risk Factors" in the Company's most recent Annual Report on Form

10-K and subsequent periodic reports filed with the SEC. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Also, forward-looking statements represent management's plans, estimates, assumptions and beliefs only as of the date of this presentation. Except as required by law, AGTC assumes no obligation to update or revise these forward-looking statements publicly, whether as a result of new information, new events or otherwise.

Advanced Technology Achieves Potential Best-in-Class Clinical Data 3

Leveraging technology expertise to build a compelling pipeline

XLRP

Potential Best-in-Class

Late-Stage Asset

Improvements in visual function sustained for at least twelve months

No product-related SAEs

across 100-fold dose

range

Diversified

Pipeline

High-Value

Programs

2Q 21 ACHM data

show visual sensitivity improvements support continued clinical development

Diversified programs across ophthalmology, neurodegenerative and otology indications

Science

Differentiated with

Demonstrated

Capabilities

Broad pre-clinical data

Robust use of disease- specific animal modeling

Manufacturing

Unmatched

Productivity,

Scalability & Quality

10-fold reduction in process residuals and 10-fold increase in productivity

At commercial scale: 40

L produces ≥ 2000 ophthalmic doses

	A Pipeline with Significant Clinical and Commercial Potential	4
			IND ENABLING	PHASE 1/2	PHASE 2/3	NEXT MILESTONE*	Patient Population (approx.)
	OCULAR
	XLRP				12-month data from P1/2 trial at AAO in Nov.	20,000
	RPGR (ORPHAN DRUG)			3-month data Skyline 4Q 21
			(US and EU)
						6-month data Vista 4Q 22
	ACHM		CNGB3 (ORPHAN DRUG)
					3-month Pediatric data both trials 4Q 21	27,000 (US and EU)
		CNGA3 (ORPHAN DRUG)
	Retinitis Pigmentosa	UNIQUE CHR & NEUROPROSTHETIC		Partnership with Bionic Sight; complete dosing	20,000 (US and EU)
	Dry AMD	COMPLEMENT FACTOR H		IND filing	1,000,000 GA (US)
	Stargardts	ABCA4			IND filing	65,000 (US and EU)

NEURODEGENERATIVE

FTD

ALS

PROGRANULIN	IND filing; partnering effort	50,000 (US)
		Development candidate; partnering effort	30,000 (US)
C9ORF72

OTOLOGY

Non-Syndromic	GJB2	Partnership with Otonomy; IND filing	200,000 (US and EU)
Hearing Loss

*Anticipated milestones based on calendar year, not AGTC's fiscal year

5

AGTC Research Day July 2021

Pre-Clinical Pipeline