ATG13
protein-codingautophagy related 13, the group of Autophagy related
Gene summary
The protein encoded by this gene is an autophagy factor and a target of the TOR kinase signaling pathway. The encoded protein is essential for autophagosome formation and mitophagy. [provided by RefSeq, Oct 2016]
- KIAA0652
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~57.3 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 ATG13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001346311.2. 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 | 2 | 2 | ||||
| missense | 68 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 70 | 0 | 2 | 72 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001333240.1 | 17 | MANE Select | |
| Ensembl | ENSP00000507809.1 | 17 | MANE Select | |
| RefSeq | NP_001136145.1 | 16 | Standard | |
| RefSeq | NP_001192048.1 | 17 | 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)
- Longevity regulating pathway - Homo sapiens (human)
- PI3K-AKT-mTOR signaling pathway and therapeutic opportunities
- Senescence and Autophagy in Cancer
Biological Process
- autophagosome assembly
- autophagy of mitochondrion
- mitophagy
- macroautophagy
- regulation of macroautophagy
Molecular Function
- protein binding
- protein kinase regulator activity
- protein kinase binding
Cellular Component
- phagophore assembly site
- mitochondrion
- endoplasmic reticulum membrane
- cytosol
- extrinsic component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000528494
- Coding exons
- 17
- Length
- 57543
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125746
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.52 | 232 | 307 | 0.756 | 0.0000155 | 3591 |
| Missense (PolyPhen) | 102 | 157.45 | 0.64784 | 1891 | ||
| Synonymous | 0.0733 | 113 | 114 | 0.991 | 0.00000601 | 1106 |
| Loss of Function | 4.20 | 4 | 27.9 | 0.143 | 0.00000119 | 360 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000072 | 0.000070 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1- RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation. {ECO:0000269|PubMed:18936157, ECO:0000269|PubMed:19211835, ECO:0000269|PubMed:19225151, ECO:0000269|PubMed:19287211, ECO:0000269|PubMed:21795849, ECO:0000269|PubMed:21855797}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- RVIS EVS
- -0.62
- RVIS percentile EVS
- 17.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |