ATG16L1

Chr 2

autophagy related 16 like 1

Also known as: APG16L, ATG16A, ATG16L, IBD10, WDR30

NCBI Gene: 55054ENSG00000085978UniProt: Q676U5

ATG16L1 encodes a protein that is essential for autophagy, mediating the conjugation of phosphatidylethanolamine to ATG8 family proteins to control autophagosomal membrane elongation and also participating in non-canonical autophagy pathways. Mutations cause susceptibility to inflammatory bowel disease, particularly Crohn disease, with the gene being highly constrained against loss-of-function variants (pLI 0.96, LOEUF 0.32). The protein also regulates innate immune responses and Paneth cell function in the intestinal epithelium.

Summary from RefSeq, OMIM, UniProt
Research Assistant →

Primary Disease Associations & Inheritance

{Inflammatory bowel disease (Crohn disease) 10}MIM #611081
1
Active trials
99
Pubs (1 yr)
34
P/LP submissions
0%
P/LP missense
0.32
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical Summary— ATG16L1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.96). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
34 unique Pathogenic / Likely Pathogenic· 61 VUS of 133 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.32LOEUF
pLI 0.965
Z-score 4.94
OE 0.17 (0.10–0.32)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.63Z-score
OE missense 0.60 (0.54–0.67)
207 obs / 344.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.17 (0.10–0.32)
0≤0.351.4
Missense OE0.60 (0.54–0.67)
0≤0.61.4
Synonymous OE0.96
0≤1.21.6
LoF obs/exp: 7 / 41.2Missense obs/exp: 207 / 344.6Syn Z: 0.32
DN
0.4784th %ile
GOF
0.4382th %ile
LOF
0.68top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.32

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

133 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic33
Likely Pathogenic1
VUS61
Likely Benign10
Benign2
33
Pathogenic
1
Likely Pathogenic
61
VUS
10
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
33
0
33
Likely Pathogenic
0
0
1
0
1
VUS
1
51
9
0
61
Likely Benign
0
4
0
6
10
Benign
0
1
0
1
2
Total156437107

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ATG16L1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
ATG16L1 promotes virus trafficking to early endosomes and conducts its degradation by 2BC to benefit foot-and-mouth disease virus replication.
Gong X et al.·Int J Biol Macromol
2026
Tributyltin induces conjugation of ATG8s to single membranes via the V-ATPase-ATG16L1 axis, leading to transcription factor EB activation in human cell lines.
Hatamiya S et al.·Arch Toxicol
2026
Insufficient Expression of the Autophagic Protein ATG16L1 Results in Accelerated Carcinogenesis Related to an Aberrant B Cell Response.
Mendiola D et al.·Cancer Rep (Hoboken)
2026Open Access
C3-CD18-VATPase-ATG16L1 and C3-ATG16L1 axes restrict the escape of microbes through the autophagy-lysosome pathway.
Yang W et al.·J Immunol
2026
Chronic enteritis triggered by diet westernization is driven by epithelial ATG16L1-mediated autophagy.
Mayr L et al.·Autophagy
2026Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients