What you carry at this position in your DNA and what research says about it.
Autoimmune Disease Risk: 8/10 evidence, 19 publications.
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Sample genotype (not yours): A/A
Typical Autoimmune and Gut Inflammatory Risk
Two copies of the common A allele represent the baseline genetic profile. This genotype is associated with standard immune regulation and typical susceptibility to inflammatory conditions.
What this genotype means: Typical immune regulation; Baseline risk for inflammatory bowel disease.
Sample genotype (not yours): A/G
Slightly Increased Risk for Autoimmune and Gut Inflammation
Carrying one copy of the G allele is linked to a mild increase in susceptibility to autoimmune and inflammatory bowel diseases. This genetic variation slightly reduces the activity of a key immune-regulating enzyme.
What this genotype means: Slightly reduced PTPN2 enzyme activity; Increased susceptibility to Crohn's disease and type 1 diabetes.
Sample genotype (not yours): G/G
Moderately Increased Risk for Autoimmune and Gut Inflammation
Carrying two copies of the G allele is associated with a more pronounced increase in susceptibility to autoimmune and inflammatory bowel diseases. This genotype significantly reduces the activity of a key immune-regulating enzyme.
What this genotype means: Significantly reduced PTPN2 enzyme activity; Moderately increased risk for Crohn's disease and type 1 diabetes.
Gene function and biological role
Gene Function: The PTPN2 gene encodes a protein tyrosine phosphatase enzyme that acts as a vital brake on the immune system [1]. It is highly expressed in immune cells, particularly T cells, where it regulates cytokine signaling pathways [2]. By dampening inflammatory signals, the enzyme helps maintain the delicate balance of the immune system and prevents it from attacking the body's own tissues [1]. It also plays a crucial role in maintaining the integrity of the intestinal barrier and regulating autophagy, the process cells use to clear out debris and bacteria [3]. When this gene or its protein product is impaired, the body becomes significantly more susceptible to chronic inflammatory and autoimmune conditions [1].
Variant Impact: The rs1893217 variant is an intronic change in the PTPN2 gene that alters how the gene is expressed and how the resulting protein functions [1]. Carrying the risk allele leads to a reduction in PTPN2 expression and a loss of its phosphatase activity, which impairs the immune system's ability to regulate itself [1]. Specifically, this change reduces signaling through the interleukin-2 receptor in key immune cells, which can lead to aberrant T cell activation [1]. It also disrupts autophagy, making it harder for intestinal cells to handle and clear out bacteria [3]. These combined cellular defects create a state of hyper-responsiveness to inflammatory signals, predisposing carriers to autoimmune and gut disorders [1] [3].
Key Insight: The PTPN2 gene acts as an essential brake on the immune system, and carrying the G allele of this variant reduces the enzyme's activity, making it harder for the body to turn off inflammatory responses. This variant also impairs autophagy in the gut, which reduces the intestinal barrier's ability to clear out bacteria and prevent inflammation.
Location: PTPN2. Chromosome 18 · 18p11.21 · 12.8 Mb
Estimated prevalence by population
Global 76.9%; European 70.2%; African 88.8%; East Asian 68.6%; South Asian 65.8%; Americas 81.6%; Ashkenazi 81.6%; Finnish 72.2%; Middle Eastern 78.8%; Amish 91.0%.
Estimated AA genotype frequency.
Global 21.4%; European 27.1%; African 10.9%; East Asian 28.5%; South Asian 30.7%; Americas 17.4%; Ashkenazi 17.5%; Finnish 25.6%; Middle Eastern 19.9%; Amish 8.8%.
Estimated AG genotype frequency.
Global 1.8%; European 2.6%; African 0.3%; East Asian 3.0%; South Asian 3.6%; Americas 0.9%; Ashkenazi 0.9%; Finnish 2.3%; Middle Eastern 1.3%; Amish 0.2%.
Estimated GG genotype frequency.
Showing effects for A/A genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 6/10. Source: PMID 21102463. Typical.
Ulcerative Colitis. Evidence: 6/10. Source: PMID 26192919. Typical.
Autoimmune Diseases
Celiac Disease. Evidence: 6/10. Source: PMID 20190752. Typical.
Cardiovascular & Metabolic
Diabetes & Glycemic Traits
Type 1 Diabetes. Evidence: 8/10. Source: PMID 19430480. Typical.
Showing effects for A/G genotype
Crohn's Disease. Evidence: 6/10. Source: PMID 21102463. ~1.4x Risk.
Ulcerative Colitis. Evidence: 6/10. Source: PMID 26192919. Slightly Increased.
Celiac Disease. Evidence: 6/10. Source: PMID 20190752. Slightly Increased.
Type 1 Diabetes. Evidence: 8/10. Source: PMID 19430480. Slightly Increased.
Showing effects for G/G genotype
Crohn's Disease. Evidence: 6/10. Source: PMID 21102463. ~2x Risk.
Ulcerative Colitis. Evidence: 6/10. Source: PMID 26192919. ~1.13x Risk.
Celiac Disease. Evidence: 6/10. Source: PMID 20190752. ~1.17x Risk.
Type 1 Diabetes. Evidence: 8/10. Source: PMID 19430480. ~1.35x Risk.
What this genotype means for the people who carry it
Sample genotype: AA (Homozygous)
Having two copies of the common A allele means the PTPN2 gene is expressed at normal levels and the resulting enzyme functions effectively to regulate immune responses [1]. This typical enzyme activity helps maintain a stable intestinal barrier and supports normal autophagy, allowing the gut to handle bacterial antigens without triggering excessive inflammation [2]. Because the immune system's regulatory pathways function as expected, there is no elevated risk for autoimmune conditions like type 1 diabetes or celiac disease [3] [4]. The baseline risk for inflammatory bowel diseases, including Crohn's disease and ulcerative colitis, remains at the standard population level [5] [6]. Maintaining a balanced diet and supporting gut health through standard lifestyle choices is generally sufficient for individuals with this genetic profile.
Typical immune regulation; Baseline risk for inflammatory bowel disease.
Sample genotype: AG (Heterozygous)
Carrying one copy of the G allele is associated with a slight reduction in PTPN2 enzyme activity, which can mildly compromise the body's ability to control inflammatory signals [1]. This reduction in enzyme function can impair autophagy, making it slightly more difficult for intestinal cells to clear out bacteria and maintain a strong gut barrier [2]. As a result, there is a modest increase in susceptibility to inflammatory bowel diseases, with Crohn's disease risk rising by approximately 1.4 times [3]. The risk for other autoimmune conditions, such as type 1 diabetes and celiac disease, is also slightly elevated compared to the baseline population [4] [5]. While this genetic profile increases susceptibility, it is only one of many factors, and lifestyle choices that support gut health can play a protective role.
Slightly reduced PTPN2 enzyme activity; Increased susceptibility to Crohn's disease and type 1 diabetes.
Sample genotype: GG (Homozygous)
Carrying two copies of the G allele leads to a significant reduction in PTPN2 enzyme activity, which compromises the body's ability to regulate inflammatory signals [1]. This loss of enzyme function impairs autophagy, making it difficult for intestinal cells to clear out bacteria and maintain a strong gut barrier [2]. Consequently, this genotype is linked to a roughly twofold increase in the risk of developing Crohn's disease [3]. The risk for other autoimmune conditions, such as type 1 diabetes, celiac disease, and ulcerative colitis, is also moderately elevated [4] [5] [6]. Proactive measures, such as maintaining a gut-friendly diet and managing stress, can be particularly beneficial for individuals with this genetic profile to help mitigate the risk of chronic inflammation.
Significantly reduced PTPN2 enzyme activity; Moderately increased risk for Crohn's disease and type 1 diabetes.
Variants with shared genetic architecture
rs2542151 · PTPN2 Gene · Chr 18 · Autoimmune Disease Risk
rs7234029 · PTPN2 Gene · Chr 18 · Crohn's Disease Risk
rs10761659 · ZNF365 Gene · Chr 10 · Crohn's Disease Risk
Multiple common variants for celiac disease influencing immune gene expression.
Content updated August 2026.
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