Expressive

rs117409786 (CPVL): Tissue Gene Expression Variant

Key takeaways

  • rs117409786 reduces CPVL gene activity in testis and tibial nerve tissue.
  • The same variant also raises activity of CPVL-AS1, a neighboring antisense RNA gene, in testis tissue.
  • These are gene expression effects from GTEx v11 data (953 donors), not confirmed disease associations.
  • No clinical trait or disease association for this variant is confirmed in the available sources.
  • A color vision defects GWAS in Silk Road populations studied this genomic region but found other gene candidates, not CPVL.

Key takeaways

  • rs117409786 reduces CPVL gene activity in testis and tibial nerve tissue.
  • The same variant also raises activity of CPVL-AS1, a neighboring antisense RNA gene, in testis tissue.
  • These are gene expression effects from GTEx v11 data (953 donors), not confirmed disease associations.
  • No clinical trait or disease association for this variant is confirmed in the available sources.
  • A color vision defects GWAS in Silk Road populations studied this genomic region but found other gene candidates, not CPVL.

What the research says GTEx v11 data from 953 donors identifies rs117409786 as a cis-eQTL (a variant that influences the activity of genes within its immediate chromosomal neighborhood) for two genes: CPVL (carboxypeptidase vitellogenic-like) and its antisense neighbor CPVL-AS1, an RNA that runs in the opposite direction on the same DNA region and may regulate CPVL activity GTEx Portal. Carriers of the ALT allele show reduced CPVL expression in testis and tibial nerve, and increased CPVL-AS1 expression in testis, with all three associations reaching FDR<0.05 significance GTEx Portal. A GWAS investigating multifactorial color vision defects in 520 individuals from Silk Road genetic isolates identified other gene candidates (PIWIL4, MBD2, NTN1 for Deutan-Protan defects; VPS54, IQGAP1, NMB, MC5R for Tritan defects) but did not report CPVL or this locus among its primary findings.

Reported associations

  • CPVL expression (testis): ALT allele linked to reduced CPVL expression (effect slope -0.61, p=2.5e-6) across 953 GTEx donors GTEx Portal
  • CPVL expression (tibial nerve): ALT allele linked to reduced CPVL expression (slope -0.48, p=2.1e-6) in tibial nerve tissue GTEx Portal
  • CPVL-AS1 expression (testis): ALT allele linked to increased expression of the neighboring CPVL antisense RNA 1 gene (slope +0.96, p=3.6e-8) in testis tissue GTEx Portal

Evidence quality All reported associations for rs117409786 derive from the GTEx v11 eQTL dataset (953 donors, cis-window analysis, FDR<0.05), a reasonably powered reference resource for tissue-specific gene expression GTEx Portal. These findings describe changes in RNA levels rather than protein function or disease outcomes. A GWAS of color vision defects in Silk Road genetic isolates (n=520) was conducted in a context that might have been expected to involve this genomic region, but CPVL was not among its reported candidates, providing no phenotypic replication for this locus. The overall evidence for rs117409786 is therefore preliminary and confined to expression-level effects in two tissue types.

Tissue-specific expression effects

  • CPVL: Reduced expression in testis and tibial nerve in carriers of the ALT allele GTEx Portal
  • CPVL-AS1: Increased expression in testis in carriers of the ALT allele GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is the CPVL gene?

CPVL (carboxypeptidase vitellogenic-like) encodes an enzyme belonging to the carboxypeptidase family. GTEx v11 data shows its expression in testis and tibial nerve is influenced by nearby genetic variants, including rs117409786.

What does rs117409786 do to CPVL expression?

Per GTEx v11 data from 953 donors, the ALT allele of rs117409786 is associated with reduced CPVL expression in both testis (p=2.5e-6) and tibial nerve (p=2.1e-6). The same allele also increases expression of the neighboring CPVL-AS1 antisense RNA gene in testis (p=3.6e-8).

Is rs117409786 linked to color vision defects?

A GWAS in Silk Road isolated communities investigated multifactorial color vision defects but did not report CPVL or rs117409786 among its primary gene associations. No confirmed link between this variant and color vision defects is established in the available research.

What tissues are affected by the rs117409786 eQTL?

GTEx data identifies testis and tibial nerve as the two tissues where rs117409786 significantly reduces CPVL expression. The CPVL-AS1 antisense gene shows increased expression in testis only.

How strong is the evidence for rs117409786?

Current evidence is limited to tissue-level gene expression data from GTEx v11 (953 donors, FDR<0.05). No GWAS or clinical study provides a confirmed association between this variant and a specific disease or health trait in the available sources, so the evidence is preliminary.