ATG3
autophagy related 3, the group of Autophagy related
Basic information
Region (hg38): 3:112532509-112562046
Previous symbols: [ "APG3L" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG3 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in ATG3
This is a list of pathogenic ClinVar variants found in the ATG3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-112534296-T-G | not specified | Uncertain significance (Feb 16, 2023) | ||
| 3-112534328-C-G | not specified | Uncertain significance (May 09, 2023) | ||
| 3-112536500-G-C | not specified | Uncertain significance (Apr 09, 2024) | ||
| 3-112538148-C-T | not specified | Uncertain significance (May 01, 2024) | ||
| 3-112548573-A-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 3-112548590-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 3-112548592-T-C | not specified | Uncertain significance (Feb 02, 2022) | ||
| 3-112548626-G-A | not specified | Uncertain significance (Jun 07, 2024) | ||
| 3-112550231-A-G | not specified | Uncertain significance (Jul 29, 2023) | ||
| 3-112550234-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 3-112553287-A-G | not specified | Uncertain significance (Jul 19, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATG3 | protein_coding | protein_coding | ENST00000283290 | 12 | 29538 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000713 | 0.996 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.76 | 101 | 165 | 0.614 | 0.00000788 | 2053 |
| Missense in Polyphen | 15 | 47.177 | 0.31795 | 632 | ||
| Synonymous | 0.241 | 55 | 57.3 | 0.960 | 0.00000293 | 558 |
| Loss of Function | 2.55 | 9 | 21.9 | 0.411 | 0.00000102 | 277 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000279 | 0.000276 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000981 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000331 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy, and mitochondrial homeostasis. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8-like proteins (GABARAP, GABARAPL1, GABARAPL2 or MAP1LC3A). The ATG12- ATG5 conjugate plays a role of an E3 and promotes the transfer of ATG8-like proteins from ATG3 to phosphatidylethanolamine (PE). This step is required for the membrane association of ATG8-like proteins. The formation of the ATG8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). Preferred substrate is MAP1LC3A. Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of ATG12 to itself, ATG12 conjugation to ATG3 playing a role in mitochondrial homeostasis but not in autophagy. ATG7 (E1-like enzyme) facilitates this reaction by forming an E1-E2 complex with ATG3. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway. {ECO:0000269|PubMed:11825910, ECO:0000269|PubMed:12207896, ECO:0000269|PubMed:12890687, ECO:0000269|PubMed:16704426, ECO:0000269|PubMed:20723759}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.158
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.344
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.971
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atg3
- Phenotype
- hematopoietic system 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; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;cellular protein modification process;protein targeting to membrane;macroautophagy;protein ubiquitination;mitochondrial fragmentation involved in apoptotic process;negative regulation of phagocytosis;regulation of cilium assembly
- Cellular component
- cytoplasmic ubiquitin ligase complex;cytosol
- Molecular function
- protein binding;Atg8 ligase activity;Atg12 transferase activity;ubiquitin-like protein transferase activity;enzyme binding