Expressive

rs10860794 (GNPTAB): CHPT1 Expression Variant

Key takeaways

  • The ALT allele reduces CHPT1 expression in at least 8 tissues, including arteries, thyroid, and muscle
  • The strongest effects are seen in the aorta, tibial artery, and cultured fibroblasts
  • All tissue effects point the same direction - the ALT allele consistently lowers CHPT1 levels
  • No clinical disease associations are on file from the provided studies for this variant
  • This is gene-expression data only - clinical significance has not been established from the available evidence

Key takeaways

  • The ALT allele reduces CHPT1 expression in at least 8 tissues, including arteries, thyroid, and muscle
  • The strongest effects are seen in the aorta, tibial artery, and cultured fibroblasts
  • All tissue effects point the same direction - the ALT allele consistently lowers CHPT1 levels
  • No clinical disease associations are on file from the provided studies for this variant
  • This is gene-expression data only - clinical significance has not been established from the available evidence

What the research says

Gene expression data from GTEx v11, covering 953 donors with cis-window analysis (a method that identifies variants affecting expression of genes in their immediate chromosomal neighborhood, using a false discovery rate (FDR) threshold below 0.05), shows that the ALT allele at rs10860794, a variant at the GNPTAB locus, is consistently associated with reduced expression of CHPT1 across 8 tissue types GTEx Portal. The associations are statistically robust, with p-values ranging from 5.7x10-24 in skeletal muscle to 2.3x10-41 in the tibial artery GTEx Portal. Every tissue where a signal is detected shows the same direction - lower CHPT1 expression with the ALT allele GTEx Portal.

Reported associations

  • CHPT1 expression (cis-eQTL, 8 tissues): The ALT allele is associated with reduced CHPT1 gene expression. Log2-scale expression effect sizes by tissue: cultured fibroblasts (-0.49), aorta (-0.47), tibial artery (-0.46), pancreas (-0.45), thyroid (-0.44), esophagus muscularis (-0.31), subcutaneous adipose (-0.29), skeletal muscle (-0.28) GTEx Portal

Evidence quality

All associations currently on file for rs10860794 derive from GTEx v11, a large reference dataset (953 donors) in which all 8 tissue effects listed here passed FDR below 0.05, with p-values from 5.7x10-24 to 2.3x10-41 GTEx Portal. These are gene-expression associations only - they show that the ALT allele predicts lower CHPT1 expression in those tissues, but do not by themselves establish any clinical outcome. The proteomic studies included in this entry cover large cohorts and address protein quantitative trait loci (pQTLs) methodology broadly, but none report findings specific to rs10860794 or this locus. Evidence for this variant is therefore limited to eQTL data, and clinical or disease outcome associations are absent from the available materials.

Tissue-specific expression effects

  • CHPT1: The ALT allele is linked to reduced expression in 8 tissues - most strongly in cultured fibroblasts, the aorta, and the tibial artery, with additional significant reductions in the pancreas, thyroid, esophagus muscularis, subcutaneous adipose, and skeletal muscle GTEx Portal

Lifestyle considerations

No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs10860794?

rs10860794 is a genetic variant at the GNPTAB locus. Gene expression data from GTEx shows that people carrying the ALT allele tend to have lower CHPT1 expression levels across multiple tissues.

What gene does rs10860794 affect?

Based on available tissue expression data, rs10860794 is associated with reduced expression of CHPT1 across at least 8 tissue types, including arteries, thyroid, and skeletal muscle.

Which tissues show the strongest expression effects of rs10860794?

The largest reductions in CHPT1 expression are seen in cultured fibroblasts, the aorta, and the tibial artery. Smaller but still significant effects are found in the pancreas, thyroid, esophagus, subcutaneous fat, and skeletal muscle.

Is rs10860794 linked to any disease?

The studies provided do not report any clinical disease associations for rs10860794. Its only documented effects are on CHPT1 gene expression levels in tissues, and what this means for health outcomes has not been established from the available data.

What is the difference between an eQTL and a pQTL?

An eQTL (expression quantitative trait locus) is a genetic variant linked to changes in how much a gene is expressed at the RNA level. A pQTL (protein quantitative trait locus) is a variant linked to changes in how much of a protein circulates in the blood or tissue. rs10860794 has eQTL data on file from GTEx but no pQTL data in the studies provided here.