ATG9B

autophagy related 9B, the group of Autophagy related

Basic information

Region (hg38): 7:151012208-151024499

Previous symbols: [ "NOS3AS" ]

Links

ENSG00000181652 ∙ NCBI:285973 ∙ OMIM:612205 ∙ HGNC:21899 ∙ Uniprot:Q674R7 ∙ 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 ATG9B gene.

• Inborn genetic diseases (53 variants)
• not provided (19 variants)
• not specified (2 variants)
• Premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG9B 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				3		3
missense			45			45
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding			8	5	10	23
Total	0	1	53	9	10

Variants in ATG9B

This is a list of pathogenic ClinVar variants found in the ATG9B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-151012373-C-T		not specified	Uncertain significance (Jan 26, 2022)
7-151012375-C-T			Likely benign (Dec 31, 2019)
7-151012483-G-T		not specified	Benign (May 13, 2021)
7-151013266-T-C		not specified	Uncertain significance (Oct 25, 2023)
7-151013280-A-G			Likely benign (Dec 31, 2018)
7-151013281-C-G		not specified	Uncertain significance (Jun 13, 2023)
7-151013289-T-C			Likely benign (Jul 25, 2018)
7-151013304-G-A			Benign (Dec 31, 2019)
7-151013368-G-A		not specified	Uncertain significance (Jan 19, 2024)
7-151013540-A-C			Benign (May 15, 2021)
7-151013712-G-A			Benign (May 05, 2021)
7-151013729-C-T			Likely benign (Jul 01, 2022)
7-151013763-G-A		not specified	Uncertain significance (Dec 14, 2023)
7-151013792-G-C			Benign/Likely benign (Jan 01, 2024)
7-151013819-T-C		not specified	Benign (May 04, 2021)
7-151013871-G-A			Likely benign (Apr 24, 2018)
7-151013882-G-A			Benign (Dec 31, 2019)
7-151013925-A-G		NOS3-related disorder	Likely benign (Nov 12, 2020)
7-151014017-C-G		not specified	Uncertain significance (Feb 23, 2023)
7-151014025-C-T			Likely benign (Jul 31, 2018)
7-151014031-C-T			Benign (Dec 31, 2019)
7-151014055-C-A			Benign (Dec 31, 2019)
7-151014101-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-151014116-G-A		not specified	Uncertain significance (Apr 13, 2023)
7-151014131-G-A		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG9B	protein_coding	protein_coding	ENST00000377974	14	12290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.25e-17	0.0733	4402	120393	6	124801	0.812

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.516	499	468	1.07	0.0000256	5709
Missense in Polyphen		195	184.1	1.0592		2295
Synonymous	-0.648	223	211	1.06	0.0000118	2046
Loss of Function	1.03	30	36.8	0.816	0.00000195	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.88
Ashkenazi Jewish	1.00	0.726
East Asian	1.01	0.877
Finnish	1.00	0.768
European (Non-Finnish)	1.00	0.811
Middle Eastern	1.01	0.877
South Asian	1.00	0.813
Other	1.00	0.787

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 (By similarity). {ECO:0000250}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death (Consensus)

Recessive Scores

• pRec: 0.148

Haploinsufficiency Scores

• pHI: 0.0815
• hipred: N
• hipred_score: 0.199

Essentials

• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg9b

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;protein localization to phagophore assembly site;late nucleophagy
• Cellular component: phagophore assembly site;autophagosome membrane;autophagosome;integral component of membrane;cytoplasmic vesicle