ATG2A

protein-coding

autophagy related 2A, the group of bridge-like lipid transfer protein family|Autophagy related|MicroRNA protein coding host genes

Gene summary

Enables lipid transfer activity. Involved in autophagosome assembly and positive regulation of autophagosome assembly. Is active in organelle membrane contact site. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015104.3

Inheritance

—

ClinVar variants

U:322B:29

Top phenotype

Premature ovarian failure

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr11:64,894,546-64,917,209

External References & Databases

Ensembl (ENSG00000110046)

Transcript & Mutation Effects

hg38 • Region Span ~22.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATG2A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 318

not providedTotal: 10

Premature ovarian failureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015104.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar	2 clinvar	9
missense			309 clinvar	21 clinvar	3 clinvar	333
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	322	24	5	351

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015104.3	RefSeq	NP_055919.2	41	MANE Select
ENST00000377264.8	Ensembl	ENSP00000366475.3	41	MANE Select
NM_001367971.1	RefSeq	NP_001354900.1	41	Standard
NM_001367972.1	RefSeq	NP_001354901.1	41	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Autophagy - animal - Homo sapiens (human)
Autophagy - other - Homo sapiens (human)

Biological Process

autophagosome assembly
autophagy of mitochondrion

Molecular Function

protein binding

Cellular Component

phagophore assembly site
nucleus
lipid droplet
cytosol
extrinsic component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377264
Coding exons: 41
Length: 22716
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.81	1027	1.20e+3	0.853	0.0000808	12254
Missense (PolyPhen)		223	346.41	0.64374		3616
Synonymous	0.407	522	534	0.978	0.0000371	4165
Loss of Function	6.70	22	90.9	0.242	0.00000473	995

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00012	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion. {ECO:0000269|PubMed:22219374}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.327
RVIS EVS: -1.06
RVIS percentile EVS: 7.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.896

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium