ATG9A

protein-coding

autophagy related 9A, the group of Autophagy related

Gene summary

Enables phospholipid scramblase activity. Involved in autophagosome assembly. Located in several cellular components, including Golgi apparatus; endosome; and phagophore assembly site. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

APG9L1

MANE transcript

NM_001077198.3

Inheritance

ClinVar variants

U:104B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr2:219,219,380-219,229,717

External References & Databases

Ensembl (ENSG00000198925)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency diseaseLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0021094

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATG9A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001077198.3. 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			5 clinvar		1 clinvar	6
missense			94 clinvar	1 clinvar		95
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	104	1	1	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 86 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077198.3	RefSeq	NP_001070666.1	14	MANE Select
ENST00000361242.9	Ensembl	ENSP00000355173.4	14	MANE Select
NM_024085.5	RefSeq	NP_076990.4	14	Standard
ENST00000396761.6	Ensembl	ENSP00000379983.2	14	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)
Mitophagy - animal - Homo sapiens (human)
miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase

Biological Process

autophagosome assembly
autophagy of mitochondrion
protein transport
protein localization to phagophore assembly site
late nucleophagy

Molecular Function

protein binding

Cellular Component

phagophore assembly site
autophagosome membrane
endosome
late endosome
autophagosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409618
Coding exons: 14
Length: 19946
Individuals with no LoFs: 124778
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 124794
p: 0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.60	349	515	0.678	0.0000330	5431
Missense (PolyPhen)		98	199.66	0.49083		2186
Synonymous	-0.417	217	209	1.04	0.0000132	1721
Loss of Function	4.76	6	37.4	0.161	0.00000176	411

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in autophagy and cytoplasm to vacuole transport (Cvt) vesicle formation. Plays a key role in the organization of the preautophagosomal structure/phagophore assembly site (PAS), the nucleating site for formation of the sequestering vesicle. Cycles between a juxta-nuclear trans-Golgi network compartment and late endosomes. Nutrient starvation induces accumulation on autophagosomes. Starvation-dependent trafficking requires ULK1, ATG13 and SUPT20H. {ECO:0000269|PubMed:16940348}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.219
RVIS EVS: -0.35
RVIS percentile EVS: 29.49

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.559

Gene Damage Prediction

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