What you carry at this position in your DNA and what research says about it.
Crohn's Disease Risk: 6/10 evidence, 49 publications.
You're viewing every possible genotype for this variant.
None of these is your result. Use the genotype toggle to compare them, then sign up and upload your DNA to see which one is yours.
Sample genotype (not yours): A/A
Typical Crohn's Disease Risk
Two copies of the reference allele are associated with typical risk for Crohn's disease. This genotype maintains normal cellular autophagy and standard defense against intestinal pathogens.
What this genotype means: Normal intestinal autophagy; Typical baseline risk of Crohn's disease; Standard bacterial clearance in the gut.
Sample genotype (not yours): A/G
Slightly Increased Crohn's Disease Risk
Carrying one copy of the variant allele is associated with a slightly increased risk of developing Crohn's disease. However, this heterozygous state may offer unique protection against certain bacterial infections.
What this genotype means: Mildly reduced intestinal autophagy; Slightly increased risk of Crohn's disease; Potential evolutionary resistance to certain gut infections.
Sample genotype (not yours): G/G
Moderately Increased Crohn's Disease Risk
Two copies of the variant allele are associated with a moderately increased risk of Crohn's disease. This genotype leads to accelerated degradation of the ATG16L1 protein, reducing cellular autophagy.
What this genotype means: Significantly reduced intestinal autophagy; Two- to three-fold increased risk of Crohn's disease; Compromised Paneth cell function in the gut.
Gene function and biological role
Gene Function: The ATG16L1 gene encodes a protein crucial for autophagy, the cellular process of degrading and recycling damaged components and clearing intracellular pathogens [1]. This gene is highly expressed in the intestinal tract, where autophagy helps maintain epithelial barrier integrity and regulate immune responses [2]. Proper ATG16L1 function is essential for the specialized secretory cells of the gut, known as Paneth cells, which release antimicrobial peptides [3]. Impairment of this pathway can lead to chronic inflammation and susceptibility to inflammatory bowel diseases [4].
Variant Impact: The rs2241880 variant is a missense mutation that changes the amino acid at position 300 from threonine to alanine (p.Thr300Ala) [4]. This specific change makes the ATG16L1 protein highly sensitive to cleavage and degradation by the enzyme caspase-3 [5]. Consequently, cells carrying the variant allele exhibit reduced autophagy efficiency and impaired clearance of intracellular bacteria [1]. This molecular defect is a major genetic driver of susceptibility to Crohn's disease, particularly in populations of European ancestry [6].
Key Insight: The variant allele causes the ATG16L1 protein to be rapidly chopped up by cellular enzymes, which cripples the gut's natural self-cleaning process. While this increases Crohn's risk, carrying just one copy of the variant may actually help the immune system fight off Salmonella infections.
Location: ATG16L1. Chromosome 2 · 2q37.1 · 233.3 Mb
Estimated prevalence by population
Global 32.5%; European 23.1%; African 45.6%; East Asian 47.0%; South Asian 23.9%; Americas 41.7%; Ashkenazi 15.9%; Finnish 31.6%; Middle Eastern 23.7%; Amish 22.3%.
Estimated AA genotype frequency.
Global 47.5%; European 49.9%; African 43.8%; East Asian 43.1%; South Asian 50.0%; Americas 45.8%; Ashkenazi 48.0%; Finnish 49.2%; Middle Eastern 50.0%; Amish 49.8%.
Estimated AG genotype frequency.
Global 20.0%; European 27.0%; African 10.5%; East Asian 9.9%; South Asian 26.1%; Americas 12.6%; Ashkenazi 36.1%; Finnish 19.2%; Middle Eastern 26.4%; Amish 27.8%.
Estimated GG genotype frequency.
Showing effects for A/A genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 6/10. Source: PMID 17200669. Typical Risk.
Intestinal Autophagy. Evidence: 3/10. Source: PMID 24553140. Normal Autophagy.
Crohn's Disease Location. Evidence: 6/10. Source: PMID 17484864. Typical Location.
Showing effects for A/G genotype
Crohn's Disease. Evidence: 6/10. Source: PMID 17200669. ~1.4x Increased Risk.
Intestinal Autophagy. Evidence: 3/10. Source: PMID 24553140. Slightly Reduced.
Crohn's Disease Location. Evidence: 6/10. Source: PMID 17484864. Predisposed to Ileal.
Showing effects for G/G genotype
Crohn's Disease. Evidence: 6/10. Source: PMID 17200669. ~2x-3x Increased Risk.
Intestinal Autophagy. Evidence: 3/10. Source: PMID 24553140. Significantly Reduced.
Crohn's Disease Location. Evidence: 6/10. Source: PMID 17484864. Strongly Predisposed.
What this genotype means for the people who carry it
Sample genotype: AA (Homozygous)
Maintaining two copies of the standard threonine-encoding allele ensures optimal stability of the ATG16L1 protein. This stability allows the cellular autophagy machinery to function at peak efficiency, successfully clearing cellular waste and targeting invading pathogens for destruction [1]. Research indicates that this genotype is associated with the lowest risk of developing Crohn's disease, particularly of the ileum [2]. The protective nature of this genotype is especially pronounced in populations of European descent [3]. Normal autophagy also supports the healthy function of specialized secretory cells in the gut, which help maintain a balanced microbiome [4].
Normal intestinal autophagy; Typical baseline risk of Crohn's disease; Standard bacterial clearance in the gut.
Sample genotype: AG (Heterozygous)
Possessing one copy of the alanine variant introduces a moderate level of protein instability, as the altered ATG16L1 protein is more susceptible to cleavage by caspase-3 [1]. This leads to a mild reduction in autophagy efficiency and a slightly elevated risk of developing Crohn's disease, particularly in the ileal region of the bowel [2]. Interestingly, having one variant allele alters how cells handle intracellular pathogens [3]. This genotype is highly prevalent across diverse global populations, appearing in over forty percent of people globally [4].
Mildly reduced intestinal autophagy; Slightly increased risk of Crohn's disease; Potential evolutionary resistance to certain gut infections.
Sample genotype: GG (Homozygous)
Carrying two copies of the alanine variant results in a highly unstable ATG16L1 protein that is rapidly degraded by caspase-3 [1]. This rapid degradation severely compromises the cell's ability to perform autophagy, leading to impaired clearance of intracellular bacteria and increased cellular stress [2]. Consequently, this genotype is associated with a two- to three-fold increased risk of developing Crohn's disease, particularly in the ileum [3]. The lack of functional autophagy also causes abnormalities in Paneth cells, which are critical for secreting antimicrobial peptides in the gut [4]. This defect can trigger chronic intestinal inflammation and alter the gut microbiome [4].
Significantly reduced intestinal autophagy; Two- to three-fold increased risk of Crohn's disease; Compromised Paneth cell function in the gut.
Variants with shared genetic architecture
rs10210302 · ATG16L1 Gene · Chr 2 · Crohn's Disease Risk
rs1000113 · IRGM Gene · Chr 5 · Crohn's Disease Risk
rs10761659 · ZNF365 Gene · Chr 10 · Crohn's Disease Risk
Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn's disease.
A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3.
Content updated August 2026.
ReadYourDNA provides educational interpretation of DNA data you already have. It is not diagnostic, not a substitute for professional medical advice, diagnosis, or treatment, and is not intended to diagnose, treat, cure, or prevent any disease. Talk to a clinician before acting on any result.
Raw DNA Data Reports for 23andMe & AncestryDNA · About ReadYourDNA · FAQ · Methodology & Science · Pricing · Support and complaints · Legal & Contact · Health Traits · Pharmacogenomics · Carrier Status · Variant Explorer · The Human Karyotype · Privacy Policy · Terms of Service · Accessibility · Consumer Health Data Privacy · Your Privacy Choices · Editorial Standards · Your Data, Checkable · Sample Report · ReadYourDNA and Promethease compared · What is inside a 23andMe raw data file · What is inside an AncestryDNA raw data file · What a chatbot can and cannot do with your raw DNA file · Where a raw DNA file can still be uploaded in 2026
Written, maintained and operated by Martin Pechhacker, sole proprietor, Vienna, Austria. Trade register GISA 40064420. support@readyourdna.com