ATG9B
protein-codingautophagy related 9B, the group of Autophagy related
Gene summary
This gene functions in the regulation of autophagy, a lysosomal degradation pathway. This gene also functions as an antisense transcript in the posttranscriptional regulation of the endothelial nitric oxide synthase 3 gene, which has 3' overlap with this gene on the opposite strand. Mutations in this gene and disruption of the autophagy process have been associated with multiple cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]
- NOS3AS
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.3 kbGenCC 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 ATG9B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001317056.2. 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 | 1 | 4 | 5 | |||
| missense | 102 | 3 | 105 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 1 | 105 | 7 | 0 | 113 |
Highest pathogenic variant AF is 8.4895123e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001303985.1 | 13 | MANE Select | |
| Ensembl | ENSP00000491504.1 | 13 | MANE Select | |
| Ensembl | ENSP00000479879.1 | 13 | Standard | |
| Ensembl | ENSP00000475737.2 | 13 | 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)
- Nanoparticle triggered autophagic cell death
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
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377974
- Coding exons
- 14
- Length
- 12290
- Individuals with no LoFs
- 4402
- Homozygous LoFs
- 120393
- Heterozygous LoFs
- 6
- Defined
- 124801
- p
- 0.812
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.516 | 499 | 468 | 1.07 | 0.0000256 | 5709 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 1.0 | 0.88 | notable |
| Latino/Admixed American | 1.0 | 0.83 | notable |
| Ashkenazi Jewish | 1.0 | 0.73 | notable |
| East Asian | 1.0 | 0.88 | notable |
| Finnish | 1.0 | 0.77 | notable |
| European (Non-Finnish) | 1.0 | 0.81 | notable |
| South Asian | 1.0 | 0.81 | notable |
| Other | 1.0 | 0.79 | notable |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.148
Essentials
- Essential (CRISPR2)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |