GeneBe

ATG16L1

protein-coding

autophagy related 16 like 1, the group of WD repeat domain containing|Autophagy related

Gene summary

The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]

Previous symbols:
  • APG16L
  • ATG16L

MANE transcript

NM_030803.7

Inheritance

—

ClinVar variants

U:58B:12

Top phenotype

ATG16L1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr2:233,210,051-233,295,674

External References & Databases

Ensembl (ENSG00000085978)NCBI Gene (55054)OMIM (610767)HGNC:21498GenCCUniProt (Q676U5)AlphaFoldClinVar (ATG16L1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~85.6 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 ATG16L1 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 53
ATG16L1-related disorderTotal: 7
not providedTotal: 3
Inflammatory bowel disease 10Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030803.7. 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
7
clinvar
1
clinvar
 10
missense
54
clinvar
4
clinvar
 58
nonsense
1
clinvar
 1
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total005811170
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_030803.7RefSeqNP_110430.518MANE Select
ENST00000392017.9EnsemblENSP00000375872.418MANE Select
NM_001190266.2RefSeqNP_001177195.116Standard
NM_001190267.2RefSeqNP_001177196.115Standard

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)
  • NOD-like receptor signaling pathway - Homo sapiens (human)
  • Nanoparticle triggered autophagic cell death
  • Senescence and Autophagy in Cancer

Biological Process

  • autophagosome assembly
  • protein transport
  • macroautophagy
  • protein localization to phagophore assembly site
  • negative stranded viral RNA replication

Molecular Function

  • protein binding
  • ubiquitin-like protein transferase activity
  • identical protein binding
  • GTPase binding

Cellular Component

  • autophagosome membrane
  • autophagosome
  • cytosol
  • axoneme
  • phagophore assembly site membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000392017
Coding exons
18
Length
85624
Individuals with no LoFs
125737
Homozygous LoFs
0
Heterozygous LoFs
9
Defined
125746
p
0.0000358
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.632073450.6010.00001923957
Missense (PolyPhen)63133.950.470311629
Synonymous0.3221281330.9640.000007451173
Loss of Function4.94741.20.1700.00000249419

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000540.000054rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000260.000026rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Plays an essential role in autophagy: interacts with ATG12-ATG5 to mediate the conjugation of phosphatidylethanolamine (PE) to LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C), to produce a membrane-bound activated form of LC3 named LC3-II. Thereby, controls the elongation of the nascent autophagosomal membrane (PubMed:24553140, PubMed:23376921, PubMed:24954904, PubMed:27273576, PubMed:23392225). Regulates mitochondrial antiviral signaling (MAVS)-dependent type I interferon (IFN-I) production (PubMed:25645662). Negatively regulates NOD1- and NOD2- driven inflammatory cytokine response (PubMed:24238340). Instead, promotes with NOD2 an autophagy-dependent antibacterial pathway (PubMed:20637199). Plays a role in regulating morphology and function of Paneth cell (PubMed:18849966). {ECO:0000269|PubMed:18849966, ECO:0000269|PubMed:22749352, ECO:0000269|PubMed:23376921, ECO:0000269|PubMed:23392225, ECO:0000269|PubMed:24238340, ECO:0000269|PubMed:24553140, ECO:0000269|PubMed:24954904, ECO:0000269|PubMed:25645662, ECO:0000269|PubMed:27273576}.;
Disease
DISEASE: Inflammatory bowel disease 10 (IBD10) [MIM:611081]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269|PubMed:17200669, ECO:0000269|PubMed:17435756, ECO:0000269|PubMed:17484864, ECO:0000269|PubMed:18047540, ECO:0000269|PubMed:18499543, ECO:0000269|PubMed:18985712, ECO:0000269|PubMed:19659808, ECO:0000269|PubMed:24553140, ECO:0000269|PubMed:24656308, ECO:0000269|PubMed:25645662, ECO:0000269|PubMed:27273576}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.106

Intolerance Scores

LoFtool
0.296
RVIS EVS
0.15
RVIS percentile EVS
64.51

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.933

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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