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From SNPedia

Geno Mag Summary
(C;C) 2.5 2x-3x increased risk for Crohn's disease in Caucasians
(C;T) 1.5 1.4x increased risk for Crohn's disease in Caucasians
(T;T) 0 normal
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
dbSNP (classic)rs2241880
1000 genomesrs2241880
GWAS Ctlgrs2241880
Max Magnitude2.5
? (C;C) (C;T) (T;T) 28

rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ("T300A") in a protein 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. [PMID 17200669, PMID 17435756]

In another recent (2007) report, rs2241880 is 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 (in the 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. [PMID 17484864] From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6596075 and rs17221417. [PMID 17554300OA-icon.png]

[PMID 18047540] 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.

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).[PMID 18162085]

[PMID 18366306] Review of role of rs2241880 in Crohn's disease and possibly ulcerative colitis

[PMID 18698678OA-icon.png] 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).

[PMID 18985712] 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))

[PMID 19337756] 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.

[PMID 19491842] 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).

SNP rs2241880
PubMedID [PMID 17435756OA-icon.png]
Condition Crohn's disease
Gene ATG16L1
Risk Allele G
pValue 1.00E-013
OR 1.45
95% CI 1.27-1.64

[PMID 19174780] Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort

[PMID 19575361] Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: A Study in the Spanish population and a meta-analysis


[PMID 19590455] Association of IL23R p.381Gln and ATG16L1 p.197Ala With Crohn Disease in the Czech Population

[PMID 20380008OA-icon.png] NOD2/CARD15, ATG16L1 and IL23R gene polymorphisms and childhood-onset of Crohn's disease

[PMID 20485703OA-icon.png] 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

GWAS snp
PMID [PMID 20570966OA-icon.png]
Trait Crohn's disease
Title Fucosyltransferase 2(FUT2) Non-Secretor Status is associated with Crohn's Disease
Risk Allele
P-val 0.000003
Odds Ratio 1.32 [1.18-1.47]

[PMID 21206965] IL23R, NOD2/CARD15, ATG16L1 and PHOX2B polymorphisms in a group of patients with Crohn's disease and correlation with sub-phenotypes


[PMID 21513755] ATG16L1 gene polymorphisms are associated with palmoplantar pustulosis

[PMID 22115380] Prediction of disease complication occurrence in Crohn's disease using phenotype and genotype parameters at diagnosis

[PMID 22457781OA-icon.png] PTPN2 Gene Variants Are Associated with Susceptibility to Both Crohn's Disease and Ulcerative Colitis Supporting a Common Genetic Disease Background

GWAS snp
PMID [PMID 22412388OA-icon.png]
Title A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
Risk Allele G
P-val 1E-12
Odds Ratio 1.3200 None

Risk Rs2241880(C;C)
Alt Rs2241880(C;C)
Reference Rs2241880(T;T)
Significance Other
Disease Inflammatory bowel disease 10 not specified
Variation info
CLNDBN Inflammatory bowel disease 10, susceptibility to not specified
Reversed 1
HGVS NC_000002.11:g.234183368A>G
CLNSRC OMIM Allelic Variant UniProtKB (protein)
CLNACC RCV000001189.6, RCV000180346.1,

[PMID 17068223OA-icon.png] A genome-wide association study identifies IL23R as an inflammatory bowel disease gene.

[PMID 17447842OA-icon.png] Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4.

[PMID 17455206] Confirmation of the role of ATG16L1 as a Crohn's disease susceptibility gene.

[PMID 17684544OA-icon.png] Systematic association mapping identifies NELL1 as a novel IBD disease gene.

[PMID 17894849] IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand Caucasians with inflammatory bowel disease.

[PMID 17924341OA-icon.png] Fine mapping versus replication in whole-genome association studies.

[PMID 18088053] Autophagy gene ATG16L1 influences susceptibility and disease location but not childhood-onset in Crohn's disease in Northern Europe.

[PMID 18200510] CARD15 and IL23R influences Crohn's disease susceptibility but not disease phenotype in a Brazilian population.

[PMID 18495612] [Correlation of the autophagosome gene ATG16L1 polymorphism and inflammatory bowel disease].

[PMID 18499543] ATG16L1 and IL23 receptor (IL23R) genes are associated with disease susceptibility in Hungarian CD patients.

[PMID 18715515OA-icon.png] Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients.

[PMID 18853133OA-icon.png] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.

[PMID 19185283OA-icon.png] Searching for genotype-phenotype structure: using hierarchical log-linear models in Crohn disease.

[PMID 19659808] Autophagy 16-like 1 rs2241880 G allele is associated with Crohn's disease in German children.

[PMID 19683022] Lack of association of NKX2-3, IRGM, and ATG16L1 inflammatory bowel disease susceptibility variants with celiac disease.

[PMID 19916168OA-icon.png] Genome-wide association studies--a summary for the clinical gastroenterologist.

[PMID 20066736OA-icon.png] Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients.

[PMID 20082483OA-icon.png] NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease.

[PMID 20195480OA-icon.png] The cannabinoid 1 receptor (CNR1) 1359 G/A polymorphism modulates susceptibility to ulcerative colitis and the phenotype in Crohn's disease.

[PMID 20222171OA-icon.png] T300A polymorphism of ATG16L1 and susceptibility to inflammatory bowel diseases: a meta-analysis.

[PMID 20395867] Is there a role for Crohn's disease-associated autophagy genes ATG16L1 and IRGM in formation of granulomas?

[PMID 20454450OA-icon.png] Evidence for STAT4 as a common autoimmune gene: rs7574865 is associated with colonic Crohn's disease and early disease onset.

[PMID 21673517] ATG16L1 polymorphisms are associated with NOD2-induced hyperinflammation.

[PMID 23535819] Lack of association of the autophagy-related gene polymorphism ATG16L1 rs2241880 in RA predisposition

[PMID 23633462] A polymorphism in an autophagy-related gene, ATG16L1, influences time to delivery in women with an unfavorable cervix who require labor induction

[PMID 23300802OA-icon.png] PTGER4 expression-modulating polymorphisms in the 5p13.1 region predispose to Crohn's disease and affect NF-κB and XBP1 binding sites

[PMID 23964099] Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn's disease

[PMID 24553140] A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3

[PMID 22573572] Phenotype-genotype profiles in Crohn's disease predicted by genetic markers in autophagy-related genes (GOIA study II).

[PMID 23725363] Predicting complicated Crohn's disease and surgery: phenotypes, genetics, serology and psychological characteristics of a population-based cohort.

[PMID 25899824OA-icon.png] Mesenchymal stromal cells derived from Crohn's patients deploy indoleamine 2,3-dioxygenase mediated immune suppression, independent of autophagy

[PMID 25906181OA-icon.png] ATG16L1: A multifunctional susceptibility factor in Crohn disease

[PMID 26030385OA-icon.png] Polymorphisms in Autophagy Genes Are Associated with Paget Disease of Bone

[PMID 26043189] Genetic determinants of quantitative traits associated with cardiovascular disease risk

[PMID 27128681OA-icon.png] Genetic Variation in Autophagy-Related Genes Influences the Risk and Phenotype of Buruli Ulcer.

[PMID 27748080OA-icon.png] Variants in autophagy-related genes and clinical characteristics in melanoma: a population-based study.

[PMID 28761177OA-icon.png] Analysis of autophagy gene polymorphisms in Spanish patients with head and neck squamous cell carcinoma.

[PMID 31654602] Genetic Polymorphisms of ATG16L1 and IRGM genes in Malaysian Patients with Crohn's Disease.

[PMID 31651650] Genetic polymorphisms present in IL10, IL23R, NOD2, and ATG16L1 associated with susceptibility to inflammatory bowel disease in Mexican population.

[PMID 31714311] Clinical and Genetic Factors Impact Time to Surgical Recurrence After Ileocolectomy for Crohn Disease.