GeneBe

ATG14

protein-coding

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

Gene summary

Enables GTPase binding activity; phosphatidylinositol 3-kinase inhibitor activity; and protein-membrane adaptor activity. Involved in several processes, including early endosome to late endosome transport; macroautophagy; and phosphatidylinositol 3-kinase/protein kinase B signal transduction. Acts upstream of or within endosome to lysosome transport. Located in autophagosome and phagophore assembly site membrane. Is extrinsic component of omegasome membrane and extrinsic component of phagophore assembly site membrane. Is active in phagophore assembly site. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:
  • KIAA0831

MANE transcript

NM_014924.5

Inheritance

—

ClinVar variants

U:74B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr14:55,366,391-55,411,830

External References & Databases

Ensembl (ENSG00000126775)NCBI Gene (22863)OMIM (613515)HGNC:19962GenCCUniProt (Q6ZNE5)AlphaFoldClinVar (ATG14)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~45.4 kb
Loading mutation effect viewer...

GenCC 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 ATG14 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 72
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014924.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
clinvar
 4
missense
70
clinvar
2
clinvar
 72
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00744078
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_014924.5RefSeqNP_055739.210MANE Select
ENST00000247178.6EnsemblENSP00000247178.510MANE Select
ENST00001042478.1EnsemblENSP00000712295.14Standard
XM_011536563.3RefSeqXP_011534865.17Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

Biological Process

  • autophagosome assembly
  • mitophagy
  • regulation of protein phosphorylation
  • negative regulation of protein phosphorylation
  • positive regulation of protein phosphorylation

Molecular Function

  • protein binding
  • GTPase binding

Cellular Component

  • autophagosome membrane
  • autophagosome
  • endoplasmic reticulum membrane
  • cytosol
  • axoneme

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000247178
Coding exons
10
Length
45467
Individuals with no LoFs
125734
Homozygous LoFs
0
Heterozygous LoFs
13
Defined
125747
p
0.0000517
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5462532790.9080.00001513221
Missense (PolyPhen)4668.4650.67188844
Synonymous-0.7351161061.090.00000595934
Loss of Function3.71728.30.2480.00000178291

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000720.000070rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS
-0.31
RVIS percentile EVS
31.93

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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