What you carry at this position in your DNA and what research says about it.
Autoimmune Disease Risk: 9/10 evidence, 19 publications.
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Sample genotype (not yours): C/C
Typical Autoimmune Risk and Slightly Higher Cholesterol
Inheriting two copies of the C allele is associated with a typical, baseline risk for several autoimmune conditions. However, this genotype is also linked to slightly higher levels of HDL and total cholesterol, as well as a minor increase in pulse pressure.
What this genotype means: Typical baseline risk for celiac disease; Slightly higher HDL cholesterol levels; Minor increase in pulse pressure.
Sample genotype (not yours): C/T
Slightly Increased Risk of Autoimmune Conditions
Carrying one copy of the T allele is linked to a slightly elevated risk for autoimmune disorders like celiac disease and Crohn's disease. This genetic change also correlates with intermediate lipid levels and slightly lower pulse pressure.
What this genotype means: Slightly increased risk for celiac disease; Slightly increased risk for Crohn's disease; Intermediate cholesterol levels.
Sample genotype (not yours): T/T
Increased Risk of Autoimmune Conditions
Inheriting two copies of the T allele is associated with an increased risk for several autoimmune disorders, including celiac disease and Crohn's disease. This genotype also correlates with lower total cholesterol and slightly lower pulse pressure.
What this genotype means: Increased susceptibility to celiac disease; Increased susceptibility to Crohn's disease; Slightly lower total and HDL cholesterol.
Gene function and biological role
Gene Function: The YDJC gene encodes a chitooligosaccharide deacetylase homolog, an enzyme whose precise physiological role in humans is still being characterized. Although its direct enzymatic functions remain under study, the genomic region containing YDJC is highly active in regulating the expression of neighboring immune-related genes [1]. Specifically, genetic variations in this locus act as strong expression quantitative trait loci (eQTLs) for the adjacent UBE2L3 gene, which is crucial for protein degradation and immune signaling [2]. Consequently, YDJC is frequently highlighted in genome-wide association studies of chronic inflammatory and autoimmune conditions [3]. Understanding this gene helps clarify how subtle changes in chromosome 22q11.21 influence systemic immune responses [4].
Variant Impact: A missense mutation in the YDJC gene, rs2298428 causes an alanine-to-threonine amino acid substitution at position 263 of the protein. Beyond altering the YDJC protein structure, this specific nucleotide change strongly influences the expression levels of the nearby UBE2L3 gene in immune cells and intestinal tissue [1]. The T allele is associated with significantly increased expression of UBE2L3, which plays a key role in ubiquitin-mediated protein degradation and immune cell activation [4]. Because of this regulatory effect, the variant is a well-established genetic marker for susceptibility to multiple autoimmune disorders [3]. Additionally, the variant shows pleiotropic associations with circulating lipid levels and cardiovascular measurements like pulse pressure [5].
Key Insight: This variant acts as a genetic bridge between metabolic traits and immune system regulation, showing that the same DNA change that influences cholesterol levels also shapes autoimmune susceptibility.
Location: YDJC. Chromosome 22 · 22q11.21 · 21.6 Mb
Estimated prevalence by population
Global 68.0%; European 66.3%; African 89.8%; East Asian 35.1%; South Asian 53.9%; Americas 48.6%; Ashkenazi 58.4%; Finnish 47.1%; Middle Eastern 60.7%; Amish 75.8%.
Estimated CC genotype frequency.
Global 27.8%; European 30.2%; African 9.9%; East Asian 48.3%; South Asian 39.0%; Americas 42.3%; Ashkenazi 36.0%; Finnish 43.1%; Middle Eastern 34.4%; Amish 22.5%.
Estimated CT genotype frequency.
Global 4.2%; European 3.4%; African 0.3%; East Asian 16.6%; South Asian 7.0%; Americas 9.2%; Ashkenazi 5.6%; Finnish 9.8%; Middle Eastern 4.9%; Amish 1.7%.
Estimated TT genotype frequency.
Showing effects for C/C genotype
Immunity & Inflammation
Autoimmune Diseases
Celiac Disease. Evidence: 7/10. Source: PMID 20190752. Typical Risk.
Lupus. Evidence: 3/10. Source: PMID 25880549. Typical Risk.
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 6/10. Source: PMID 20601676. Typical Risk.
Cardiovascular & Metabolic
Lipids & Cholesterol
HDL Cholesterol. Evidence: 9/10. Source: PMID 33462484. Slightly Higher.
Hypertension
Pulse Pressure. Evidence: 7/10. Source: PMID 33230300. Slightly Higher.
Showing effects for C/T genotype
Celiac Disease. Evidence: 7/10. Source: PMID 20190752. Slightly Increased.
Lupus. Evidence: 3/10. Source: PMID 25880549. Slightly Increased.
Crohn's Disease. Evidence: 6/10. Source: PMID 20601676. Slightly Increased.
HDL Cholesterol. Evidence: 9/10. Source: PMID 33462484. Intermediate.
Pulse Pressure. Evidence: 7/10. Source: PMID 33230300. Intermediate.
Showing effects for T/T genotype
Celiac Disease. Evidence: 7/10. Source: PMID 20190752. ~1.13x Increased Risk.
Lupus. Evidence: 3/10. Source: PMID 25880549. Increased Risk.
Crohn's Disease. Evidence: 6/10. Source: PMID 20601676. Increased Risk.
HDL Cholesterol. Evidence: 9/10. Source: PMID 33462484. Slightly Lower.
Pulse Pressure. Evidence: 7/10. Source: PMID 33230300. Slightly Lower.
What this genotype means for the people who carry it
Sample genotype: CC (Homozygous)
Maintaining the baseline C/C genotype keeps the expression of the nearby UBE2L3 gene at typical levels, avoiding the immune overactivation linked to the T allele [1]. Large-scale genetic studies show that this typical expression pattern correlates with a lower, baseline risk for celiac disease [2]. Similarly, this genotype is associated with typical susceptibility to other chronic inflammatory conditions, including Crohn's disease and rheumatoid arthritis [3]. On the metabolic side, the C allele is linked to higher levels of circulating HDL cholesterol and total cholesterol [4]. It also correlates with a very slight increase in pulse pressure, a measure of arterial stiffness [5]. While these cardiovascular and lipid shifts are statistically significant, their absolute clinical impact is generally minor compared to lifestyle factors. Overall, this genotype represents a favorable profile for autoimmune health while maintaining typical metabolic baselines.
Typical baseline risk for celiac disease; Slightly higher HDL cholesterol levels; Minor increase in pulse pressure.
Sample genotype: CT (Heterozygous)
Inheriting one copy of the T allele increases the expression of the nearby UBE2L3 gene in immune cells, which can subtly alter inflammatory responses [1]. This elevated expression is associated with a slightly higher susceptibility to celiac disease, with studies indicating a modest increase in risk [2]. The same genetic pattern is linked to a slightly elevated risk for other autoimmune conditions, such as rheumatoid arthritis and systemic lupus erythematosus [3]. In the gut, this variant has been shown to influence gene expression profiles that may affect intestinal barrier function and inflammation [4]. Conversely, this genotype correlates with slightly lower levels of total and HDL cholesterol compared to the C/C baseline [5]. It is also associated with a minor reduction in pulse pressure, suggesting a potential, though very small, cardiovascular trade-off [6]. Most individuals with this genotype do not develop autoimmune diseases, as environmental triggers and other genetic factors play major roles.
Slightly increased risk for celiac disease; Slightly increased risk for Crohn's disease; Intermediate cholesterol levels.
Sample genotype: TT (Homozygous)
Presence of two copies of the T allele leads to the highest expression levels of the nearby UBE2L3 gene, a key regulator of immune cell signaling [1]. This high-expression state is a well-documented risk factor for celiac disease, significantly increasing susceptibility compared to the typical genotype [2]. It is also strongly linked to other autoimmune and inflammatory conditions, including rheumatoid arthritis, Crohn's disease, and systemic lupus erythematosus [3]. Research indicates that this variant alters immune pathways in both the gut and systemic circulation [4]. On the metabolic side, the T/T genotype is associated with lower levels of total cholesterol, HDL cholesterol, and apolipoprotein A1 [5]. Additionally, it correlates with a slight reduction in pulse pressure, which is generally considered favorable for cardiovascular dynamics [6]. Despite these genetic associations, carrying the T/T genotype is not a direct diagnosis, and many individuals remain healthy throughout their lives.
Increased susceptibility to celiac disease; Increased susceptibility to Crohn's disease; Slightly lower total and HDL cholesterol.
Variants with shared genetic architecture
rs17849502 · NCF2 Gene · Chr 1 · Autoimmune Disease Risk
rs1893592 · UBASH3A Gene · Chr 21 · Autoimmune Disease Risk
rs1980422 · CD28 Gene · Chr 2 · Autoimmune Disease Risk
Genetics of 35 blood and urine biomarkers in the UK Biobank.
Multiple common variants for celiac disease influencing immune gene expression.
Content updated August 2026.
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