rs11479 (SCO2/TYMP): Gene expression in blood and brain

Key takeaways

• rs11479 reduces SCO2 expression in whole blood; SCO2 helps build the cellular machinery cells use for energy production.
• The same variant also reduces CPT1B expression, an enzyme that shuttles fats into mitochondria, across nerve, brain, skin, and blood tissue.
• Expression effects span at least five nearby genes, suggesting broad local regulatory influence at this locus.
• Available evidence is mechanistic, describing gene regulation rather than direct disease or trait associations.
• Large GWAS studies of blood traits in Asian ancestry populations provide broader genomic context for this region.

What the research says GTEx v11 eQTL data from 953 donors (FDR < 0.05) shows the alternate allele at rs11479 reduces SCO2 (which encodes a copper chaperone essential for assembling cytochrome c oxidase, the mitochondrial complex central to cellular energy production) expression in whole blood and reduces CPT1B (carnitine palmitoyltransferase 1B, an enzyme that transports long-chain fatty acids into mitochondria) expression in tibial nerve, cerebellum, lower leg skin, and whole blood GTEx Portal. The alternate allele is also associated with reduced CIMAP1B expression in whole blood, increased LMF2 (lipase maturation factor 2, involved in lipoprotein lipase processing) expression in brain cerebellum, and increased expression of a nearby unannotated transcript (ENSG00000273272) in EBV-transformed lymphocytes GTEx Portal.

Reported associations

• SCO2 expression (whole blood): The alternate allele is associated with reduced expression of SCO2 in whole blood GTEx Portal
• CPT1B expression (multiple tissues): Reduced expression of this fatty-acid-transport enzyme in tibial nerve, brain cerebellum, lower leg skin, and whole blood GTEx Portal
• CIMAP1B expression (whole blood): Reduced expression of CIMAP1B (a gene encoding a microtubule-associated protein) in whole blood GTEx Portal
• LMF2 expression (cerebellum): Increased expression of LMF2 in brain cerebellum GTEx Portal
• ENSG00000273272 expression (lymphocytes): Increased expression of this unannotated nearby transcript in EBV-transformed lymphocytes GTEx Portal

Evidence quality All gene-expression associations reported here derive from GTEx v11 eQTL data (953 donors, FDR < 0.05). eQTL evidence documents effects on gene expression levels in specific tissues; it is mechanistic evidence, not a direct disease or phenotype association. Two GWAS studies of hematological traits in Asian ancestry populations are provided as broader context: one covering 42 blood test phenotypes in approximately 50,000 British South Asian adults, testing roughly 4.8 million common imputed variants at a study-wide significance threshold of P < 1.2 x 10^-9; and one examining exome-wide coding variants across 12 hematological traits including platelet count in a discovery cohort of 5,257 Han Chinese adults with independent replication in 3,827 additional subjects. Neither provided study text reports a specific association at rs11479, limiting phenotypic interpretation from those sources. No conflicting findings are present across the provided materials.

Tissue-specific expression effects

• CPT1B: Reduced expression in tibial nerve, brain cerebellum, lower leg skin, and whole blood GTEx Portal
• SCO2: Reduced expression in whole blood GTEx Portal
• CIMAP1B: Reduced expression in whole blood GTEx Portal
• LMF2: Increased expression in brain cerebellum GTEx Portal
• ENSG00000273272: Increased expression in EBV-transformed lymphocytes GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.