ATG9A

autophagy related 9A, the group of Autophagy related

Basic information

Region (hg38): 2:219219380-219229717

Previous symbols: [ "APG9L1" ]

Links

ENSG00000198925

∙ NCBI:79065 ∙ OMIM:612204 ∙ HGNC:22408 ∙ Uniprot:Q7Z3C6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATG9A gene.

not_specified (80 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG9A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001077198.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			79 clinvar	1 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG9A	protein_coding	protein_coding	ENST00000409618	14	19946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0292	124778	0	16	124794	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	349	515	0.678	0.0000330	5431
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000821	0.0000794
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000329	0.0000327
Other	0.000165	0.000165

dbNSFP

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}.;
Pathway: 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;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.219
rvis_EVS: -0.35
rvis_percentile_EVS: 29.49

Haploinsufficiency Scores

pHI: 0.165
hipred: Y
hipred_score: 0.639
ghis: 0.542

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.559

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atg9a
Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;

Gene ontology

Biological process: autophagosome assembly;autophagy of mitochondrion;protein transport;protein localization to phagophore assembly site;late nucleophagy
Cellular component: phagophore assembly site;autophagosome membrane;endosome;late endosome;autophagosome;endoplasmic reticulum membrane;trans-Golgi network;membrane;integral component of membrane;late endosome membrane;intracellular membrane-bounded organelle;recycling endosome
Molecular function: protein binding