ATG9B
Basic information
Region (hg38): 7:151012209-151024499
Previous symbols: [ "NOS3AS" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (101 variants)
- not_provided (3 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. These statistics are base on transcript: NM_001317056.2. 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 | 4 | |||||
missense | 97 | 100 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 97 | 7 | 0 |
Highest pathogenic variant AF is 8.48951e-7
GnomAD
Source:
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:
- 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
- ghis
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- gene_indispensability_score
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
- Phenotype
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
- Molecular function