ATG14
autophagy related 14, the group of PIK3C3 complex subunits|Autophagy related
Basic information
Region (hg38): 14:55366391-55411830
Previous symbols: [ "KIAA0831" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (65 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014924.5. 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 | 2 | |||||
| missense | 63 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATG14 | protein_coding | protein_coding | ENST00000247178 | 10 | 45467 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.174 | 0.826 | 125734 | 0 | 13 | 125747 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.546 | 253 | 279 | 0.908 | 0.0000151 | 3221 |
| Missense in Polyphen | 46 | 68.465 | 0.67188 | 844 | ||
| Synonymous | -0.735 | 116 | 106 | 1.09 | 0.00000595 | 934 |
| Loss of Function | 3.71 | 7 | 28.3 | 0.248 | 0.00000178 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000719 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000982 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for both basal and inducible autophagy. Determines the localization of the autophagy-specific PI3-kinase complex PI3KC3-C1 (PubMed:18843052, PubMed:19050071). Plays a role in autophagosome formation and MAP1LC3/LC3 conjugation to phosphatidylethanolamine (PubMed:19270696, PubMed:20713597). Promotes BECN1 translocation from the trans-Golgi network to autophagosomes (PubMed:20713597). Enhances PIK3C3 activity in a BECN1-dependent manner. Essential for the autophagy-dependent phosphorylation of BECN1 (PubMed:23878393). Stimulates the phosphorylation of BECN1, but suppresses the phosphorylation PIK3C3 by AMPK (PubMed:23878393). Binds to STX17-SNAP29 binary t- SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion (PubMed:25686604). Modulates the hepatic lipid metabolism (By similarity). {ECO:0000250|UniProtKB:Q8CDJ3, ECO:0000269|PubMed:18843052, ECO:0000269|PubMed:19050071, ECO:0000269|PubMed:19270696, ECO:0000269|PubMed:20713597, ECO:0000269|PubMed:23878393, ECO:0000269|PubMed:25686604}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.31
- rvis_percentile_EVS
- 31.93
Haploinsufficiency Scores
- pHI
- 0.298
- hipred
- Y
- hipred_score
- 0.611
- ghis
- 0.570
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atg14
- Phenotype
- digestive/alimentary phenotype;
Gene ontology
- Biological process
- autophagosome assembly;mitophagy;regulation of protein phosphorylation;negative regulation of protein phosphorylation;positive regulation of protein phosphorylation;endosome to lysosome transport;cellular response to starvation;posttranscriptional regulation of gene expression;macroautophagy;autophagosome membrane docking;cellular response to glucose starvation;positive regulation of phosphatidylinositol 3-kinase activity;regulation of protein complex stability;regulation of triglyceride metabolic process;response to mitochondrial depolarisation
- Cellular component
- autophagosome membrane;autophagosome;endoplasmic reticulum membrane;cytosol;axoneme;phagophore assembly site membrane;phosphatidylinositol 3-kinase complex, class III;mitochondria-associated endoplasmic reticulum membrane;phagocytic vesicle;extrinsic component of omegasome membrane;extrinsic component of phagophore assembly site membrane
- Molecular function
- protein binding;GTPase binding