Expressive

rs11943692 (CSN2/STATH): Color Vision and Heart eQTL

Key takeaways

  • rs11943692 sits between the CSN2 (casein beta) and STATH (statherin) genes and was identified in a color vision defects GWAS of Silk Road isolated communities.
  • The study tested two color vision traits, Deutan-Protan (red-green spectrum) and Tritan (blue-yellow spectrum), in 520 individuals using False Discovery Rate correction.
  • GTEx v11 data from 953 donors shows this variant reduces UGT2B4 expression in heart left ventricle tissue.
  • Evidence is preliminary: one small study in a specialized isolated population with no reported replication in other groups.

Key takeaways

  • rs11943692 sits between the CSN2 (casein beta, a milk protein gene) and STATH (statherin, a salivary protein gene) genes and was identified in a genome-wide association study of color vision defects in Silk Road isolated communities.
  • The study examined two color vision defect traits in 520 individuals, using a False Discovery Rate correction method.
  • GTEx v11 data from 953 donors shows this variant is linked to reduced expression of UGT2B4 (an enzyme involved in metabolizing hormones and drugs) in heart left ventricle tissue.
  • Evidence is preliminary, coming from a single small study in a genetically specialized population with no reported replication.

What the research says A GWAS of 520 individuals from Silk Road isolated communities analyzed two color vision defect (CVD) traits: Deutan-Protan (DP, involving defective perception of the red-yellow-green spectrum) and Tritan (TR, involving altered perception of blue, yellow, and orange hues), with results corrected using a False Discovery Rate linkage-based approach. Per GTEx v11 eQTL data from 953 donors, the alternate allele at rs11943692 is associated with reduced expression of UGT2B4 and the uncharacterized gene ENSG00000294378, both in heart left ventricle tissue GTEx Portal.

Reported associations

  • Color vision defects (Deutan-Protan and Tritan traits): Identified in a GWAS of color vision defect phenotypes in 520 individuals from Silk Road isolated communities, with statistical correction via a False Discovery Rate linkage-based approach.
  • UGT2B4 expression (heart left ventricle): The alternate allele is associated with reduced UGT2B4 expression in heart left ventricle tissue (log2-normalized slope approximately -1.11, p=5.9e-5) GTEx Portal.
  • ENSG00000294378 expression (heart left ventricle): The alternate allele is associated with reduced expression of this gene in heart left ventricle tissue (log2-normalized slope approximately -0.91, p=9.9e-5) GTEx Portal.

Evidence quality The primary genetic study was conducted in 520 individuals from Silk Road isolated communities, populations with reduced genetic variation and environmental homogeneity that can enhance statistical power for detecting associations with complex traits. However, the small sample size and specialized ancestral background limit how broadly these findings apply. The published abstract highlights other candidate genes (PIWIL4, MBD2, NTN1, VPS54, IQGAP1, NMB, and MC5R) without specifically naming rs11943692, and no independent replication in other populations is described. The GTEx eQTL associations are derived from 953 donors with FDR < 0.05, with individual p-values of 5.9e-5 and 9.9e-5 for UGT2B4 and ENSG00000294378 respectively GTEx Portal. Overall, the evidence for this variant's associations should be treated as preliminary.

Tissue-specific expression effects

  • UGT2B4: The alternate allele is associated with reduced expression in heart left ventricle tissue. UGT2B4 encodes UDP-glucuronosyltransferase 2B4, an enzyme involved in metabolizing hormones, certain drugs, and other compounds GTEx Portal.
  • ENSG00000294378: The alternate allele is associated with reduced expression in heart left ventricle tissue. The biological function of this gene in heart tissue is not characterized in the provided data GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What genes are near rs11943692?

rs11943692 sits between CSN2 (casein beta, a milk protein gene) and STATH (statherin, a salivary protein gene). GTEx eQTL data also shows it affects expression of UGT2B4, an enzyme gene involved in metabolizing hormones and drugs, specifically in heart left ventricle tissue.

Is rs11943692 linked to color blindness?

This variant was identified in a genome-wide association study of color vision defects in 520 people from Silk Road isolated communities. The study analyzed two traits: Deutan-Protan (affecting red-green spectrum perception) and Tritan (affecting blue-yellow spectrum perception). These findings are preliminary with no reported replication in other populations.

What does the UGT2B4 gene do, and why is it relevant here?

UGT2B4 encodes the enzyme UDP-glucuronosyltransferase 2B4, which helps the body break down hormones, certain drugs, and other compounds. GTEx data shows rs11943692 is associated with reduced UGT2B4 expression specifically in heart left ventricle tissue, though the clinical significance of this expression change is not established.

How strong is the evidence for rs11943692?

Evidence is limited. The primary study included only 520 people from genetically isolated Silk Road communities, a small and specialized sample with no reported replication elsewhere. The GTEx eQTL data is from 953 donors with FDR correction, providing more robust support for the expression effects, but the color vision association remains preliminary.

What is a GWAS and why was one done for color vision?

A genome-wide association study (GWAS) scans hundreds of thousands of genetic variants across the genome to find ones statistically linked to a trait. Color vision defects can have complex, multifactorial causes beyond the well-known Mendelian forms, and this study used genetically isolated Silk Road communities to boost the power to detect such subtle associations.