SEMA3A rs10235789: What Your Genotype Means
The rs10235789 variant is a single nucleotide polymorphism located within the SEMA3A gene. It has been statistically associated with variations in the formation and depth of Fuchs' crypts, which are small structural openings in the iris.
What each genotype means
Typical iris crypt pattern
This genotype represents the most common genetic configuration at this location. Research suggests this variant is associated with variations in the structural features of the iris, specifically the formation and depth of iris crypts. This is a trait-based association and does not indicate any medical condition or health risk.
Carried by approximately 45-50% of individuals of European ancestry, based on a minor allele frequency of roughly 0.30.
Varied iris crypt pattern
Carrying one copy of the T allele may contribute to differences in the appearance of iris crypts compared to those without the variant. These associations are based on genome-wide studies of iris morphology and represent normal human biological variation. This finding is not a diagnostic indicator and has no known clinical health implications.
This heterozygous genotype is common, appearing in roughly 40-45% of European populations.
Distinct iris crypt pattern
Individuals with this genotype possess two copies of the variant allele associated with iris crypt depth and structure. While this marker is linked to specific physical patterns in the iris, it is considered a normal variation in human ocular development. There is no evidence suggesting this genotype impacts eye health or function.
This genotype is less common, found in approximately 5-10% of individuals of European ancestry.
Understanding the Variant
The rs10235789 variant is a specific change in the DNA sequence located in intron 6 of the SEMA3A gene on chromosome 7. In genetics, a single nucleotide polymorphism (SNP) like this represents a variation at a single position in the genome. Because this variant sits within an intron—a non-coding region of the gene—it does not directly alter the protein sequence of the SEMA3A protein. Instead, researchers study such variants to understand how they might influence gene expression or regulatory processes. This particular SNP has been identified through genome-wide association studies (GWAS) as a marker that correlates with specific physical traits, specifically the structural appearance of the iris in the human eye.
The Role of SEMA3A
The SEMA3A gene encodes a protein belonging to the semaphorin family, which is well-known for its role in axonal guidance—the process by which neurons send out axons to reach their correct targets in the nervous system. Beyond its function in the brain, SEMA3A is involved in pathways that control neurogenesis and cell migration. Because the development of the iris involves complex tissue patterning, researchers have hypothesized that the same biological pathways governing neuronal development may also influence the formation of iris structures. The association between SEMA3A and iris crypts suggests that the genetic factors shaping our nervous system may have broader roles in determining the physical characteristics of other tissues, such as the iris, during human development.
Research and Evidence
Scientific evidence linking rs10235789 to iris crypts is based on quantitative trait loci studies. Research has consistently observed a statistical association between this variant and the grade or depth of Fuchs' crypts across diverse populations, including European, East Asian, and South Asian groups. While these findings are statistically significant, the evidence strength is considered limited in terms of clinical utility. The variant explains only a small percentage of the total variance in iris crypt patterns, suggesting that many other genetic and environmental factors contribute to these physical traits. It is important to note that while this gene has been studied in the context of other conditions like schizophrenia in separate literature, the primary association for this specific SNP in the context of physical appearance is limited to iris morphology.
Interpreting Your Results
If you have received information about your rs10235789 genotype, it is important to understand that this is a marker for a normal physical variation rather than a medical condition. Iris patterns are complex, polygenic traits, meaning they are influenced by many different genes working in combination with environmental factors. Having a specific genotype at this location does not provide a diagnostic or predictive tool for health outcomes. This information is purely educational and relates to the study of human physical diversity. You cannot use this information to make medical decisions or assess health risks. If you have concerns about your eye health or vision, you should always consult with an ophthalmologist or a qualified healthcare professional, as genetic markers for iris patterns are not clinical indicators of eye disease.
How common is this variant?
The minor allele frequency for rs10235789 is approximately 0.30 in European populations and 0.45 in East Asian populations, indicating that the variant is relatively common across these groups.
Frequently asked questions
Is rs10235789 associated with eye disease?
No, rs10235789 is associated with normal variations in iris structure, such as the depth of Fuchs' crypts. It is not considered a marker for eye disease or vision impairment.
Can I use this SNP to predict my eye color?
No, this SNP is associated with iris texture and pattern, not iris color. Eye color is determined by a different set of genes, such as those involved in melanin production.
Why is SEMA3A linked to the eye?
SEMA3A is involved in neuronal development and tissue patterning. Researchers believe the same biological pathways that guide nerve cell growth may also influence how iris tissue forms during development.
Is this genetic association the same for everyone?
The association between rs10235789 and iris crypts has been observed across European, East Asian, and South Asian populations. However, the expression of these traits can vary significantly between individuals due to other genetic and environmental factors.
Sources & further reading
Educational information only, last refreshed 10/26/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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