{{Rsnum
|rsid=2241880
|Gene=ATG16L1
|Chromosome=2
|position=233274722
|Orientation=minus
|ReferenceAllele=A
|MissenseAllele=G
|GMAF=0.3889
|Gene_s=ATG16L1,SCARNA5
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 28.6 | 56.2 | 15.2
| HCB | 14.0 | 44.1 | 41.9
| JPT | 3.5 | 37.2 | 59.3
| YRI | 7.5 | 36.7 | 55.8
| ASW | 5.3 | 42.1 | 52.6
| CHB | 14.0 | 44.1 | 41.9
| CHD | 5.6 | 36.1 | 58.3
| GIH | 23.8 | 48.5 | 27.7
| LWK | 6.4 | 31.2 | 62.4
| MEX | 12.3 | 35.1 | 52.6
| MKK | 4.5 | 46.2 | 49.4
| TSI | 23.0 | 62.0 | 15.0
| HapMapRevision=28
}}
{{ neighbor
| rsid = 2241879
| distance = 100
}}

[[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|17554300|OA=1
}}

{{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|18698678|OA=1
}} 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).

{{GWAS Summary
|SNP=rs2241880
|PubMedID=17435756
|Condition=Crohn's disease
|Gene=ATG16L1
|Risk Allele=G
|pValue=1.00E-013
|OR=1.45
|95CI=1.27-1.64
|OA=1
}}
{{PMID Auto
|PMID=19174780
|Title=Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort
}}

{{PMID Auto
|PMID=19575361
|Title=Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: A Study in the Spanish population and a meta-analysis
}}

{{omim
|id=611081
|desc=INFLAMMATORY BOWEL DISEASE 10; IBD10
|rsnum=2241880
}}

{{omim
|id=266600
|desc=INFLAMMATORY BOWEL DISEASE 1; IBD1
|rsnum=2241880
}}

{{omim
|id=610767
|desc=AUTOPHAGY 16-LIKE 1; ATG16L1
|rsnum=2241880
}}
{{PMID Auto
|PMID=19590455
|Title=Association of IL23R p.381Gln and ATG16L1 p.197Ala With Crohn Disease in the Czech Population
}}

{{PharmGKB
|RSID=rs2241880
|Name_s=
|Gene_s=ATG16L1
|Feature=
|Evidence=PubMed ID:17435756; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS Results: Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis (Initial Sample Size: 946 cases, 977 controls; Replication Sample Size: 530 trios, 353 cases, 207 controls; Risk Allele: rs2241880-G).
|Drugs=
|Drug Classes=
|Diseases=Crohn Disease
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356605
}}

{{PMID Auto
|PMID=20380008
|Title=NOD2/CARD15, ATG16L1 and IL23R gene polymorphisms and childhood-onset of Crohn's disease
|OA=1
}}
{{PMID Auto
|PMID=20485703
|Title=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
|OA=1
}}
{{PMID Auto GWAS
|PMID=20570966
|Trait=Crohn's disease
|Title=Fucosyltransferase 2(FUT2) Non-Secretor Status is associated with Crohn's Disease
|RiskAllele=
|Pval=0.000003
|OR=1.32
|ORtxt=[1.18-1.47]
|OA=1
}}
{{PMID Auto
|PMID=21206965
|Title=IL23R, NOD2/CARD15, ATG16L1 and PHOX2B polymorphisms in a group of patients with Crohn's disease and correlation with sub-phenotypes
}}

{{omim
|id=610767
|rsnum=2241880
|variant=0001
}}

{{PMID Auto
|PMID=21513755
|Title=ATG16L1 gene polymorphisms are associated with palmoplantar pustulosis
}}

{{PMID Auto
|PMID=22115380
|Title=Prediction of disease complication occurrence in Crohn's disease using phenotype and genotype parameters at diagnosis
}}

{{PMID Auto
|PMID=22457781
|Title=PTPN2 Gene Variants Are Associated with Susceptibility to Both Crohn's Disease and Ulcerative Colitis Supporting a Common Genetic Disease Background
|OA=1
}}

{{PMID Auto GWAS
|PMID=22412388
|Trait=None
|Title=A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
|RiskAllele=G
|Pval=1E-12
|OR=1.3200
|ORtxt=None
|OA=1
}}

{{ClinVar
|rsid=2241880
|Reversed=1
|FwdREF=T
|FwdALT=C
|REF=A
|ALT=G
|RSPOS=234183368
|CHROM=2
|GMAF=0.3897
|dbSNPBuildID=98
|SSR=0
|SAO=1
|VP=0x05016800000015051f130100
|GENEINFO=ATG16L1:55054; SCARNA5:677775
|GENE_NAME=ATG16L1; SCARNA5
|GENE_ID=55054; 677775
|WGT=0
|VC=SNV
|CLNALLE=1
|CLNHGVS=NC_000002.11:g.234183368A>G
|CLNORIGIN=1
|CLNSIG=255
|Tags=RV;PM;PMC;SLO;VLD;G5;HD;GNO;KGPhase1;KGPilot123;KGPROD;OTHERKG;PH3;LSD;MTP;OM
|CAF=0.6111; 0.3889
|CLNACC=RCV000001189.1
|CLNDBN=Inflammatory bowel disease 10, susceptibility to
|CLNSRC=OMIM Allelic Variant
|CLNSRCID=610767.0001
|COMMON=1
|Disease=Inflammatory bowel disease 10
}}

{{PMID|17068223}} A genome-wide association study identifies IL23R as an inflammatory bowel disease gene.

{{PMID|17447842|OA=1
}} 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|17684544|OA=1
}} 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|17924341|OA=1
}} 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|18715515|OA=1
}} Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients.

{{PMID|18853133|OA=1
}} Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.

{{PMID|19185283|OA=1
}} 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|19916168|OA=1
}} Genome-wide association studies--a summary for the clinical gastroenterologist.

{{PMID|20066736|OA=1
}} Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients.

{{PMID|20082483|OA=1
}} NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease.

{{PMID|20195480|OA=1
}} The cannabinoid 1 receptor (CNR1) 1359 G/A polymorphism modulates susceptibility to ulcerative colitis and the phenotype in Crohn's disease.

{{PMID|20222171|OA=1
}} 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|20454450|OA=1
}} 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.

{{GET Evidence
|gene=ATG16L1
|aa_change=Thr300Ala
|aa_change_short=T300A
|impact=not reviewed
|qualified_impact=Insufficiently evaluated not reviewed
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs2241880
|overall_frequency_n=4910
|overall_frequency_d=10758
|overall_frequency=0.456405
|n_genomes=31
|n_genomes_annotated=0
|n_haplomes=37
|n_articles=0
|n_articles_annotated=0
|in_omim=Y
|nblosum100=1
|autoscore=2
|webscore=N
}}

{{PMID Auto
|PMID=23535819
|Title=Lack of association of the autophagy-related gene polymorphism ATG16L1 rs2241880 in RA predisposition
}}

{{PMID Auto
|PMID=23633462
|Title=A polymorphism in an autophagy-related gene, ATG16L1, influences time to delivery in women with an unfavorable cervix who require labor induction
}}

{{PMID Auto
|PMID=23300802
|Title=PTGER4 expression-modulating polymorphisms in the 5p13.1 region predispose to Crohn's disease and affect NF-κB and XBP1 binding sites
|OA=1
}}

{{PMID Auto
|PMID=23964099
|Title=Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn's disease
}}

{{PMID Auto
|PMID=24553140
|Title=A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3
}}

{{PMID Auto
|PMID=22573572
|Title=Phenotype-genotype profiles in Crohn's disease predicted by genetic markers in autophagy-related genes (GOIA study II).
}}

{{PMID Auto
|PMID=23725363
|Title=Predicting complicated Crohn's disease and surgery: phenotypes, genetics, serology and psychological characteristics of a population-based cohort.
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}