Expressive

rs113293568 (PCDHA cluster): IK expression variant

Key takeaways

  • rs113293568 is in the PCDHA gene cluster and is linked in GTEx data to higher IK expression across at least eight tissues.
  • The expression increase is seen in brain cortex, immune cells, visceral fat, skin, artery, and esophagus, with statistical significance across all eight tissues.
  • No phenotypic or disease association is documented in the provided study sources for this variant.
  • The only provided clinical study covers metabolic genetics in 490 elite athletes but does not specifically report on this variant in the available text excerpt.

Key takeaways

  • rs113293568 is in the protocadherin alpha (PCDHA) gene cluster and is linked in GTEx eQTL data to increased IK gene expression across at least eight tissues.
  • The expression increase is seen in brain cortex, immune cells, visceral fat, skin, artery, and esophagus, with statistical significance in all eight tissues.
  • The single provided study examined metabolic genetic variants in 490 elite athletes but does not specifically report an association for this variant or its neighboring genes in the available text excerpt.
  • Evidence is limited to gene-expression-level eQTL data; no phenotypic or disease association is documented in the provided sources.

What the research says A genome-wide metabolic QTL study conducted in 490 elite athletes examined 275,016 SNPs and identified novel variant-metabolite associations at loci including FOLH1, VNN1, and SULT2A1; the available study excerpt does not report a specific association for rs113293568 or the PCDHA alpha cluster. GTEx v11 eQTL analysis (953 donors, cis-window, FDR < 0.05) identifies this variant as an expression QTL for the IK gene, with the alternate allele linked to increased IK expression across eight distinct tissue types GTEx Portal.

Reported associations

  • IK gene expression (brain cortex): Alternate allele associated with increased IK expression, slope +0.62, p=4.8e-5 GTEx Portal
  • IK gene expression (EBV-transformed lymphocytes): Increased IK expression, slope +0.61, p=1.5e-7 GTEx Portal
  • IK gene expression (adipose visceral omentum): Increased IK expression, slope +0.55, p=4.0e-9 GTEx Portal
  • IK gene expression (esophagus gastroesophageal junction): Increased IK expression, slope +0.40, p=4.8e-8 GTEx Portal
  • IK gene expression (skin, non-sun-exposed suprapubic): Increased IK expression, slope +0.38, p=1.3e-7 GTEx Portal
  • IK gene expression (artery tibial): Increased IK expression, slope +0.36, p=7.4e-10 GTEx Portal
  • IK gene expression (skin, sun-exposed lower leg): Increased IK expression, slope +0.36, p=2.8e-11 GTEx Portal
  • IK gene expression (esophagus muscularis): Increased IK expression, slope +0.35, p=6.5e-13 GTEx Portal

Evidence quality All molecular associations for rs113293568 derive from GTEx v11 eQTL data across 953 donors. All eight tissue associations reach FDR < 0.05, with p-values ranging from 4.8e-5 in brain cortex to 6.5e-13 in esophagus muscularis. The direction of effect (increased IK expression) is consistent across all eight tissues. The one clinical study provided - a metabolic GWAS in 490 elite athletes - does not specifically report results for rs113293568 in the available text; it is possible the full study contains additional information not included in the provided excerpt. No phenotypic GWAS, clinical annotation, or disease-trait association study was provided for this variant. Overall, the evidence base is narrow: statistically robust gene-expression effects have been documented, but no link to a health outcome or clinical trait is on record from the provided sources.

Tissue-specific expression effects

  • IK: Increased expression in brain cortex, EBV-transformed lymphocytes, adipose visceral omentum, esophageal gastroesophageal junction, non-sun-exposed skin, sun-exposed skin, tibial artery, and esophageal muscularis -- the alternate allele is associated with higher IK expression in all eight measured tissues GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What genes are associated with rs113293568?

rs113293568 is located in or near the protocadherin alpha (PCDHA) gene cluster, which includes PCDHA1 through PCDHA13 and PCDHAC1. In GTEx eQTL data, this variant is also linked to expression changes in the IK gene across multiple tissues.

What does rs113293568 do to gene expression?

GTEx v11 eQTL data from 953 donors shows that the alternate allele at rs113293568 is associated with increased IK gene expression in eight tissues, including brain cortex, visceral adipose tissue, lymphocytes, skin, tibial artery, and esophagus.

Is rs113293568 linked to any disease or health condition?

No disease or health trait association for rs113293568 is documented in the provided study sources. The only recorded effect is on IK gene expression levels in multiple tissues, which is a molecular finding rather than a health outcome.

What is the PCDHA gene cluster?

The PCDHA label refers to the protocadherin alpha gene family, a group of closely related genes found in proximity on the genome. The provided study data does not describe the biological function of these genes, so no further detail can be derived from the available sources.

What is an eQTL and why does it matter for rs113293568?

An eQTL, or expression quantitative trait locus, is a genetic variant associated with differences in how much a gene is expressed across individuals. For rs113293568, GTEx data identifies it as an eQTL for the IK gene, meaning people with the alternate allele tend to show higher IK expression in multiple tissues.