What you carry at this position in your DNA and what research says about it.
Crohn's Disease Risk: 7/10 evidence, 23 publications.
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Sample genotype (not yours): C/C
Typical Crohn's Disease Risk
Two copies of the C allele represent the standard, baseline susceptibility to Crohn's disease.
What this genotype means: Standard baseline risk for Crohn's disease; Typical response to imatinib and ustekinumab therapies.
Sample genotype (not yours): C/T
~2x Higher Crohn's Risk
One copy of the T allele is linked to an approximately 2.1-fold increased risk of developing Crohn's disease.
What this genotype means: Elevated risk of Crohn's disease; Potentially better clinical response to ustekinumab.
Sample genotype (not yours): T/T
Two copies of the T allele are associated with an approximately 2.1-fold increased risk of Crohn's disease.
What this genotype means: Elevated risk of Crohn's disease; Poorer response to imatinib therapy.
Gene function and biological role
Gene Function: SLC22A4 encodes the organic cation transporter 1 (OCTN1), a membrane transport protein that is highly expressed in the small intestine, colon, and immune cells [1]. This transporter plays a critical role in absorbing and distributing organic cations and specific nutrients from the diet. One of its primary physiological substrates is L-ergothioneine, a powerful antioxidant obtained solely through food sources like mushrooms. By regulating the cellular uptake of these compounds, the gene helps maintain tissue homeostasis and modulates inflammatory responses in the gut [1]. Variations in this gene are heavily studied for their role in chronic inflammatory conditions [2].
Variant Impact: A single-nucleotide change in the SLC22A4 gene, known as L503F, alters the amino acid sequence of the OCTN1 transporter [1]. This specific structural change alters the transporter's substrate affinity and transport rate, particularly for the antioxidant L-ergothioneine. Specifically, the variant protein exhibits a higher affinity for L-ergothioneine but a lower overall transport velocity. This functional alteration is thought to lead to an abnormal accumulation of organic cations in immune cells, potentially triggering or exacerbating chronic intestinal inflammation.
Key Insight: The variant alters how immune cells absorb L-ergothioneine, a dietary antioxidant found in mushrooms, which may influence gut inflammation.
Location: SLC22A4. Chromosome 5 · 5q31.1 · 132.3 Mb
Estimated prevalence by population
Global 54.4%; European 33.9%; African 85.2%; East Asian 99.5%; South Asian 79.0%; Americas 49.5%; Ashkenazi 36.6%; Finnish 47.8%; Middle Eastern 64.4%; Amish 14.2%.
Estimated CC genotype frequency.
Global 35.4%; European 48.6%; African 14.2%; East Asian 0.5%; South Asian 19.8%; Americas 41.7%; Ashkenazi 47.8%; Finnish 42.7%; Middle Eastern 31.7%; Amish 47.0%.
Estimated CT genotype frequency.
Global 10.3%; European 17.4%; African 0.6%; East Asian < 0.1%; South Asian 1.2%; Americas 8.8%; Ashkenazi 15.6%; Finnish 9.5%; Middle Eastern 3.9%; Amish 38.9%.
Estimated TT genotype frequency.
Showing effects for C/C genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 5/10. Source: PMID 15107849. Typical Risk.
Organ Systems
Respiratory Health
Nasal Polyps. Evidence: 7/10. Source: PMID 30643255. Slightly Raised Risk.
Pharmacogenomics
Chemotherapy Response
Imatinib Response. Evidence: 6/10. Source: PMID 22875622. Typical Response.
Immunosuppressant & Biologic Response
Ustekinumab Response. Evidence: 5/10. Source: PMID 27977334. Typical Response.
Showing effects for C/T genotype
Crohn's Disease. Evidence: 5/10. Source: PMID 15107849. ~2.1x Increased Risk.
Nasal Polyps. Evidence: 7/10. Source: PMID 30643255. Typical Risk.
Ustekinumab Response. Evidence: 5/10. Source: PMID 27977334. Stronger Response.
Showing effects for T/T genotype
Imatinib Response. Evidence: 6/10. Source: PMID 22875622. Poorer Response.
What this genotype means for the people who carry it
Sample genotype: CC (Homozygous)
Presence of the C/C genotype ensures that the organic cation transporter 1 (OCTN1) protein maintains its standard structure with leucine at position 503 [1]. The standard protein form regulates the uptake of dietary compounds and antioxidants like L-ergothioneine at normal physiological rates. Because this genetic profile lacks the risk-increasing T allele, it is associated with a typical, baseline risk for Crohn's disease [1] and other forms of inflammatory bowel disease [2]. Additionally, standard transport dynamics mean there is no altered response to medications like imatinib [3] or ustekinumab. Some studies suggest a slightly higher susceptibility to nasal polyps compared to those carrying the T allele [4]. Overall, this genotype represents the standard genetic baseline for gut transport and inflammatory risk. Maintaining the baseline transporter function supports typical gut health. No special dietary or therapeutic adjustments are typically indicated based on this result.
Standard baseline risk for Crohn's disease; Typical response to imatinib and ustekinumab therapies.
Sample genotype: CT (Heterozygous)
A single copy of the T allele introduces a phenylalanine residue instead of leucine at position 503 in a portion of the OCTN1 transporters [1]. This structural change increases the transporter's affinity for dietary antioxidants like L-ergothioneine, leading to altered cellular accumulation in the gut. Clinical studies have consistently linked this heterozygous genotype to an approximately 2.1-fold increased risk of Crohn's disease [1] and general inflammatory bowel disease [2]. Beyond inflammatory bowel disease, this genetic variation can also influence pharmacogenomics. For instance, some research indicates that individuals with the C/T genotype may show a better response to the biologic drug ustekinumab [3]. The altered transporter function may play a role in how the body processes such targeted therapies. Environmental factors and diet can interact with this genetic predisposition to influence overall gut health. Understanding this genetic predisposition helps clarify individual risk profiles.
Elevated risk of Crohn's disease; Potentially better clinical response to ustekinumab.
Sample genotype: TT (Homozygous)
Inheriting two copies of the T allele means all of the OCTN1 transporters carry the phenylalanine substitution at position 503 [1]. This complete alteration significantly changes the transport kinetics of organic cations and dietary compounds in the intestinal lining. Consequently, this genotype is associated with a 2.1-fold increased susceptibility to Crohn's disease [1] and general inflammatory bowel disease [2]. In addition to gut inflammation, the T/T genotype has important implications for drug transport and response. Studies have shown that patients with this genotype may experience a poorer response or shorter time to progression when treated with imatinib. The altered transporter affects how the drug is absorbed and cleared by cells [3]. These findings highlight the role of OCTN1 in both chronic inflammation and systemic drug transport. Monitoring digestive health is a common focus for individuals with this profile.
Elevated risk of Crohn's disease; Poorer response to imatinib therapy.
Variants with shared genetic architecture
rs273909 · SLC22A4 Gene · Chr 5 · Heart Disease Risk
rs10761659 · ZNF365 Gene · Chr 10 · Crohn's Disease Risk
rs7554511 · INAVA Gene · Chr 1 · Inflammatory Bowel Disease
Functional variants of OCTN cation transporter genes are associated with Crohn disease.
OCTN1 variant L503F is associated with familial and sporadic inflammatory bowel disease.
A loss-of-function variant in ALOX15 protects against nasal polyps and chronic rhinosinusitis.
Pharmacogenetics of ustekinumab in patients with moderate-to-severe plaque psoriasis.
Content updated August 2026.
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