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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	37	1	1

Variants in ATG9A

This is a list of pathogenic ClinVar variants found in the ATG9A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-219220778-G-A		not specified	Uncertain significance (Jan 18, 2023)
2-219220880-A-C		not specified	Uncertain significance (Mar 22, 2023)
2-219221098-G-A		not specified	Uncertain significance (Apr 05, 2024)
2-219221143-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-219221200-C-G		not specified	Uncertain significance (Jan 04, 2022)
2-219221208-C-T		not specified	Uncertain significance (May 05, 2023)
2-219221227-T-C		not specified	Uncertain significance (Dec 21, 2022)
2-219221254-G-A		not specified	Uncertain significance (Apr 07, 2023)
2-219222273-C-T		not specified	Uncertain significance (May 27, 2022)
2-219222311-G-A		not specified	Likely benign (Jan 10, 2023)
2-219222341-C-T		not specified	Uncertain significance (Mar 29, 2024)
2-219222390-T-C		not specified	Uncertain significance (Sep 01, 2021)
2-219222435-C-T		not specified	Uncertain significance (Oct 17, 2023)
2-219222695-G-A		not specified	Uncertain significance (Jan 17, 2023)
2-219222727-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-219222736-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-219222809-T-C		not specified	Uncertain significance (Feb 02, 2022)
2-219222875-T-C		not specified	Uncertain significance (Dec 14, 2021)
2-219223590-G-C		not specified	Uncertain significance (May 30, 2024)
2-219223605-G-A		not specified	Uncertain significance (Dec 13, 2022)
2-219223608-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-219223679-A-G		not specified	Uncertain significance (May 02, 2024)
2-219223886-G-A		not specified	Uncertain significance (Jun 16, 2024)
2-219223972-C-T		not specified	Uncertain significance (Jul 26, 2021)
2-219223994-A-C		not specified	Uncertain significance (Sep 01, 2021)

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