ATG16L1 - Autophagy Related 16 Like 1

The ATG16L1 gene provides instructions for making a protein called autophagy related 16-like 1. This protein is part of a larger family of proteins that are required for a process called autophagy. Cells use this process to recycle worn-out cell parts and break down certain proteins when they are no longer needed. Autophagy also plays an important role in controlled cell death (apoptosis). Additionally, autophagy is involved in the body's inflammatory response and helps the immune system destroy some types of harmful bacteria and viruses. R


Studies with SNPs


Assoicated with Crohn's disease. R

  • The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.19 (CI 1.01-1.41), and for homozygotes, 1.85 (CI 1.56-2.21) R
  • Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. R
  • Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. R
  • Worldwide population differentiation at disease-associated SNPs. R
  • Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study. R


Known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. R R

Confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others - IBD5 and NOD2 genes. Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. R 

From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6596075 and rs17221417. R

  • Associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1.66, P= 0.0017). The population-attributable risk of carrying allele G is 0.24 and is 0.19 for homozygosity for allele G in CD. R
  • In another study, rs2241880 has been associated with Crohn's disease; the minor allele is somewhat protective in that it lessens the odds of acquiring the disease (odds ratio 0.74, CI: 0.65-0.84, p=3.7x10e-6). R
  • Review of role of rs2241880 in Crohn's disease and possibly ulcerative colitis. R
  • Replicated increased risk for Crohn's disease with rs2241880(C) allele in a study of Italian patients, but saw no association to ulcerative colitis (UC). R
  • Strongly associated with ileal Crohn's disease (allelic P = 1.24 x 10(-6)). Children with GG genotype had a more than 3-fold elevated risk for disease as compared to the wildtype AA homozygotes (odds ratio [OR], 3.1; 95% confidence interval [CI], 1.93-4.94; P = 1.8 x 10(-6)) R
  • Meta-analysis of 24 studies performed, including 13,022 Crohn's disease cases and 17,532 controls. Confirmed increased risk for disease for carriers of (C) allele (1.9x or 1.4x, for homozygous and heterozgous genotypes), but only in Caucasians and not in Asians. R
  • Study of 557 CD and 425 UC patients and 672 ethnically matched Spanish controls and a meta-analysis confirmed an association between rs2241880(C) and CD (p=6.5 x 10(-9), odds ratio =1.62). R
  • Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. R
  • Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: A Study in the Spanish population and a meta-analysis. R
  • Association of IL23R p.381Gln and ATG16L1 p.197Ala With Crohn Disease in the Czech Population. R
  • NOD2/CARD15, ATG16L1 and IL23R gene polymorphisms and childhood-onset of Crohn's disease. R
  • Replication and meta-analysis of 13,000 cases defines the risk for interleukin-23 receptor and autophagy-related 16-like 1 variants in Crohn's disease. R
  • IL23R, NOD2/CARD15, ATG16L1 and PHOX2B polymorphisms in a group of patients with Crohn's disease and correlation with sub-phenotypes. R
  • ATG16L1 gene polymorphisms are associated with palmoplantar pustulosis. R
  • Prediction of disease complication occurrence in Crohn's disease using phenotype and genotype parameters at diagnosis. R
  • PTPN2 Gene Variants Are Associated with Susceptibility to Both Crohn's Disease and Ulcerative Colitis Supporting a Common Genetic Disease Background. R
  • A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. R
  • Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 & modulates expression of PTGER4. R
  • Confirmation of the role of ATG16L1 as a Crohn's disease susceptibility gene. R
  • Systematic association mapping identifies NELL1 as a novel IBD disease gene. R
  • IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand Caucasians with inflammatory bowel disease. R
  • Fine mapping versus replication in whole-genome association studies. R
  • Autophagy gene ATG16L1 influences susceptibility and disease location but not childhood-onset in Crohn's disease in Northern Europe. R
  • CARD15 and IL23R influences Crohn's disease susceptibility but not disease phenotype in a Brazilian population. R
  • Correlation of the autophagosome gene ATG16L1 polymorphism and inflammatory bowel disease. R
  • ATG16L1 and IL23 receptor (IL23R) genes are associated with disease susceptibility in Hungarian CD patients. R
  • Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients. R
  • Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. R
  • Searching for genotype-phenotype structure: using hierarchical log-linear models in Crohn disease. R
  • Autophagy 16-like 1 rs2241880 G allele is associated with Crohn's disease in German children. R
  • Lack of association of NKX2-3, IRGM, and ATG16L1 inflammatory bowel disease susceptibility variants with celiac disease. R
  • Genome-wide association studies--a summary for the clinical gastroenterologist. R
  • Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients. R
  • NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease. R
  • The cannabinoid 1 receptor (CNR1) 1359 G/A polymorphism modulates susceptibility to ulcerative colitis and the phenotype in Crohn's disease. R
  • T300A polymorphism of ATG16L1 and susceptibility to inflammatory bowel diseases: a meta-analysis. R
  • Is there a role for Crohn's disease-associated autophagy genes ATG16L1 and IRGM in formation of granulomas? R
  • Evidence for STAT4 as a common autoimmune gene: rs7574865 is associated with colonic Crohn's disease and early disease onset. R
  • ATG16L1 polymorphisms are associated with NOD2-induced hyperinflammation. R
  • Lack of association of the autophagy-related gene polymorphism ATG16L1 rs2241880 in RA predisposition. R
  • A polymorphism in an autophagy-related gene, ATG16L1, influences time to delivery in women with an unfavorable cervix who require labor induction. R
  • PTGER4 expression-modulating polymorphisms in the 5p13.1 region predispose to Crohn's disease and affect NF-κB and XBP1 binding sites. R
  • Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn's disease. R
  • A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3. R
  • Phenotype-genotype profiles in Crohn's disease predicted by genetic markers in autophagy-related genes (GOIA study II). R
  • Predicting complicated Crohn's disease and surgery: phenotypes, genetics, serology and psychological characteristics of a population-based cohort. R
  • Mesenchymal stromal cells derived from Crohn's patients deploy indoleamine 2,3-dioxygenase mediated immune suppression, independent of autophagy. R
  • ATG16L1: A multifunctional susceptibility factor in Crohn disease. R
  • Polymorphisms in Autophagy Genes Are Associated with Paget Disease of Bone. R
  • Genetic determinants of quantitative traits associated with cardiovascular disease risk. R


  • Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. R
  • A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. R
  • Identification of two maternal transmission ratio distortion loci in pedigrees of the Framingham heart study. R


  • Crohn's disease (P=7.00*10-41). R
  • Crohn's disease (P=5.00*10-9). R


  • Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. R
  • An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. R
  • Predicting complicated Crohn's disease and surgery: phenotypes, genetics, serology and psychological characteristics of a population-based cohort. R

Chromosomal Location

Cytogenetic Location: 2q37.1, which is the long (q) arm of chromosome 2 at position 37.1

Molecular Location: base pairs 233,251,571 to 233,295,674 on chromosome 2 (Homo sapiens Annotation Release 108, GRCh38.p7). R