Expressive

rs117149202 (LINC01584/AGBL1): AKAP13 eQTL variant

Key takeaways

  • rs117149202 consistently increases expression of the AKAP13 gene across five tissue types, including brain, nerve, muscle, and gut
  • The strongest statistical signal for this expression effect is in tibial nerve tissue (p=7.2e-7)
  • The variant sits near LINC01584 and AGBL1, but its measured expression effect falls on the neighboring AKAP13 gene
  • No disease or trait association for this specific variant was reported in the reviewed childhood glioma genome-wide association study

Key takeaways

  • rs117149202 consistently increases expression of the AKAP13 gene across five tissue types, including brain, nerve, muscle, and gut
  • The strongest statistical signal for this expression effect is in tibial nerve tissue (p=7.2e-7)
  • The variant sits near LINC01584 (a long intergenic non-coding RNA) and AGBL1 (a protein-coding gene), but its measured expression-regulatory effect falls on the neighboring AKAP13 gene
  • No disease or trait association for this specific variant was reported in the reviewed childhood glioma genome-wide association study

What the research says GTEx v11 reference data (953 donors, cis-window analysis, FDR<0.05) identifies rs117149202 as a cis-eQTL (a variant that influences the expression level of a nearby gene) for AKAP13 (A-kinase anchoring protein 13) across five tissues, with the alternate allele consistently associated with increased AKAP13 expression in all five GTEx Portal. A multi-ancestry genome-wide association study meta-analysis of 4069 children with glioma and 8778 controls across three population-based cohorts tested common variants genome-wide; the primary genome-wide significant finding was at 9p21.3 (CDKN2B-AS1, OR 1.273, p=6.974e-10 for childhood astrocytoma), a separate region, with no genome-wide significant result reported for rs117149202 or its neighboring genes.

Reported associations

  • AKAP13 expression in colon sigmoid: The alternate allele is associated with increased AKAP13 expression (effect slope +0.30, p=4.8e-5) GTEx Portal
  • AKAP13 expression in brain caudate basal ganglia: The alternate allele is associated with increased AKAP13 expression (effect slope +0.30, p=1.3e-4) GTEx Portal
  • AKAP13 expression in skeletal muscle: The alternate allele is associated with increased AKAP13 expression (effect slope +0.28, p=1.6e-5) GTEx Portal
  • AKAP13 expression in esophagus muscularis: The alternate allele is associated with increased AKAP13 expression (effect slope +0.22, p=4.0e-5) GTEx Portal
  • AKAP13 expression in tibial nerve: The alternate allele is associated with increased AKAP13 expression, the strongest statistical signal among the five affected tissues (effect slope +0.21, p=7.2e-7) GTEx Portal

Evidence quality Direct evidence for rs117149202 comes solely from GTEx v11 eQTL reference data (953 donors, cis-window, FDR<0.05), which meets the standard significance threshold across all five reported tissue-gene associations GTEx Portal. No genome-wide significant disease association for this specific variant was reported in the provided studies. The accompanying childhood glioma GWAS meta-analysis (4069 cases, 8778 controls, three population-based cohorts, six genetic ancestries) identified 9p21.3 as the sole genome-wide significant locus; no genome-wide significant finding was reported for rs117149202. eQTL evidence identifies a potential regulatory mechanism but does not establish disease causality or clinical consequence on its own.

Tissue-specific expression effects

  • AKAP13: The alternate allele is associated with increased expression in tibial nerve (slope +0.21, p=7.2e-7), skeletal muscle (slope +0.28, p=1.6e-5), esophagus muscularis (slope +0.22, p=4.0e-5), colon sigmoid (slope +0.30, p=4.8e-5), and brain caudate basal ganglia (slope +0.30, p=1.3e-4); the direction is consistently positive across all five tissues, meaning the variant allele is linked to higher AKAP13 expression in each GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What does rs117149202 do?

According to GTEx reference data, rs117149202 is linked to increased expression of the AKAP13 gene in five tissues: tibial nerve, skeletal muscle, esophagus, colon, and brain caudate basal ganglia. This type of variant is called a cis-eQTL, meaning it regulates a nearby gene's activity levels.

Which genes are near rs117149202?

The variant is located near LINC01584, a long intergenic non-coding RNA, and AGBL1, a protein-coding gene. GTEx data shows its expression-regulatory effect reaches the neighboring AKAP13 gene across multiple tissues.

Is rs117149202 associated with any disease?

No genome-wide significant disease association for rs117149202 has been reported in the provided studies. A childhood glioma genome-wide association study was part of the reviewed research, but that study's significant finding was at a different chromosomal region (9p21.3, CDKN2B-AS1), not at this variant's location.

What is AKAP13 and why does its expression matter?

AKAP13 (A-kinase anchoring protein 13) is a scaffold protein that organizes signaling molecules inside cells. Changes in how much AKAP13 a tissue produces could influence cellular communication pathways, though the functional health consequences of this specific eQTL effect have not been established.

What is an eQTL?

An eQTL (expression quantitative trait locus) is a DNA variant associated with differences in how much a particular gene is expressed in a given tissue. Finding that rs117149202 is an eQTL for AKAP13 means people carrying the alternate allele tend to show higher AKAP13 RNA levels in those tissues, though this does not directly predict any health outcome.