ATG14

autophagy related 14, the group of PIK3C3 complex subunits|Autophagy related

Basic information

Region (hg38): 14:55366391-55411830

Previous symbols: [ "KIAA0831" ]

Links

ENSG00000126775 ∙ NCBI:22863 ∙ OMIM:613515 ∙ HGNC:19962 ∙ Uniprot:Q6ZNE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATG14 gene.

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.

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				1		1
missense			44	1		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	0

Variants in ATG14

This is a list of pathogenic ClinVar variants found in the ATG14 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-55369623-C-T		not specified	Uncertain significance (Nov 25, 2024)
14-55369633-T-C		not specified	Uncertain significance (Jun 18, 2024)
14-55369663-C-G		not specified	Uncertain significance (Nov 09, 2022)
14-55369702-C-T		not specified	Uncertain significance (Jun 09, 2022)
14-55369762-T-C		not specified	Uncertain significance (Oct 29, 2024)
14-55369827-A-C		not specified	Uncertain significance (Apr 09, 2024)
14-55369830-C-T		not specified	Likely benign (Dec 15, 2023)
14-55369831-G-A		not specified	Uncertain significance (Aug 04, 2024)
14-55369852-A-G		not specified	Uncertain significance (Feb 21, 2024)
14-55369878-A-G		not specified	Uncertain significance (Feb 06, 2023)
14-55369891-C-G		not specified	Uncertain significance (Apr 10, 2023)
14-55369925-C-A		not specified	Uncertain significance (Dec 21, 2023)
14-55377856-T-G		not specified	Uncertain significance (Oct 30, 2023)
14-55378009-T-A		not specified	Uncertain significance (May 08, 2023)
14-55380619-G-A			Likely benign (May 01, 2022)
14-55380651-G-A		not specified	Uncertain significance (Mar 01, 2024)
14-55380658-T-C		not specified	Uncertain significance (Jan 27, 2022)
14-55380673-G-A		not specified	Uncertain significance (Nov 03, 2023)
14-55380686-C-T		not specified	Uncertain significance (Mar 01, 2024)
14-55380688-T-C		not specified	Uncertain significance (Feb 05, 2024)
14-55381997-C-A		not specified	Uncertain significance (Nov 13, 2023)
14-55382003-T-C		not specified	Uncertain significance (Dec 20, 2023)
14-55382156-G-C		not specified	Uncertain significance (Jun 29, 2023)
14-55382186-G-A		not specified	Uncertain significance (Jan 21, 2025)
14-55385881-C-T		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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