Expressive

rs10484433 (LINC02980): BTN3A2 expression regulator

Key takeaways

  • rs10484433 is linked to lower BTN3A2 expression in blood, muscle, heart, stomach, and esophageal tissue
  • The same variant is linked to higher LINC02980 expression in cultured fibroblasts
  • GTEx expression data covering 953 donors shows p-values as low as 1.8e-20 for these associations
  • No clinical disease associations are documented in the provided studies for this variant

Key takeaways

  • rs10484433 is linked to lower BTN3A2 expression in blood, muscle, heart, stomach, and esophageal tissue
  • The same variant is linked to higher LINC02980 expression in cultured fibroblasts
  • GTEx expression data covering 953 donors shows p-values as low as 1.8e-20 for these associations
  • Current evidence is limited to gene-expression profiling; no clinical disease associations are documented in the provided studies for this variant

What the research says GTEx v11 tissue profiling across 953 donors identifies rs10484433 as a cis-eQTL (a variant correlated with expression of a gene in its chromosomal neighborhood) for BTN3A2, with the ALT allele associated with reduced expression across seven tissues - most significantly in whole blood (slope -0.43, p=1.8e-20) and with the largest magnitude effect in esophagus muscularis (slope -0.56, p=1.0e-17) GTEx Portal. The ALT allele is additionally associated with increased LINC02980 expression in cultured fibroblasts (slope +0.60, p=1.1e-13) GTEx Portal.

Reported associations

  • BTN3A2 expression: ALT allele associated with reduced expression across seven tissues - esophagus muscularis (slope -0.56, p=1.0e-17), esophagus gastroesophageal junction (slope -0.54, p=2.9e-14), stomach (slope -0.53, p=2.3e-14), heart left ventricle (slope -0.51, p=5.3e-16), esophagus mucosa (slope -0.49, p=1.1e-15), skeletal muscle (slope -0.47, p=4.0e-16), and whole blood (slope -0.43, p=1.8e-20); all slopes in log2 units GTEx Portal
  • LINC02980 expression: ALT allele associated with increased expression in cultured fibroblasts (slope +0.60 log2 units, p=1.1e-13) GTEx Portal

Evidence quality All available evidence derives from GTEx v11 eQTL analysis (953 donors, FDR < 0.05), a large and well-powered dataset for expression QTL discovery GTEx Portal. The BTN3A2 associations are highly significant across all seven tissues, with p-values ranging from 2.9e-14 to 1.8e-20, and the LINC02980 fibroblast association also clears the significance threshold (p=1.1e-13). No replication in independent GWAS cohorts, no ClinVar clinical significance classifications, and no PharmGKB pharmacogenomic annotations appear in the provided studies. The available evidence establishes that this variant correlates with gene expression differences in specific tissues but does not address clinical consequences.

Tissue-specific expression effects

  • BTN3A2: Reduced expression with the ALT allele across seven tissues, including whole blood, skeletal muscle, stomach, heart left ventricle, and three esophageal sub-regions (muscularis, gastroesophageal junction, and mucosa) GTEx Portal
  • LINC02980: Increased expression with the ALT allele in cultured fibroblasts GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs10484433?

rs10484433 is a genetic variant in the LINC02980 genomic region. Large-scale tissue profiling from GTEx identifies it as an expression quantitative trait locus - a variant linked to differences in nearby gene activity across multiple tissue types.

What does rs10484433 do to BTN3A2 expression?

In GTEx data from 953 donors, the ALT allele of rs10484433 is associated with reduced BTN3A2 expression in seven tissue types: whole blood, skeletal muscle, stomach, heart left ventricle, and three regions of the esophagus. Effect sizes range from -0.43 to -0.56 log2 units.

Is rs10484433 linked to any diseases?

The provided studies do not document clinical disease associations for rs10484433. Current evidence is limited to tissue-specific gene expression changes observed in GTEx eQTL analysis.

What is LINC02980?

LINC02980 is the gene in whose region rs10484433 sits. In GTEx data, the ALT allele of rs10484433 is associated with increased LINC02980 expression specifically in cultured fibroblasts, with a highly significant p-value of 1.1e-13.

What does an eQTL result tell us about this variant?

An eQTL finding means the variant is statistically correlated with gene expression levels in certain tissues. For rs10484433 this means the ALT allele is linked to lower BTN3A2 activity and higher LINC02980 activity in specific cell types, but eQTL evidence alone does not indicate a clinical diagnosis or medical risk.