rs10102717 (INTS10-LPL): Metabolic Syndrome Variant
Key takeaways
- The INTS10-LPL region has been linked to metabolic syndrome in a genome-wide association study (GWAS) of over 107,000 Taiwanese adults.
- LPL (lipoprotein lipase), a gene central to fat breakdown in the blood, was one of 22 genes flagged through gene-set analysis in this study.
- The alternate allele at this position increases expression of the INTS10 gene in spleen and non-sun-exposed skin tissue.
- All current disease-level evidence is from a single large study in an Asian (Taiwanese) population; independent replication is not documented in the provided sources.
Key takeaways
- The INTS10-LPL region has been linked to metabolic syndrome in a genome-wide association study (GWAS) of over 107,000 Taiwanese adults.
- LPL (lipoprotein lipase), a gene central to fat breakdown in the blood, was one of 22 genes flagged through gene-set analysis in this study.
- The alternate allele at this position increases expression of the INTS10 gene in spleen and non-sun-exposed skin tissue.
- All current disease-level evidence is from a single large study in an Asian (Taiwanese) population; independent replication is not documented in the provided sources.
What the research says A GWAS of 107,230 individuals from the Taiwan Biobank -- among whom 23% had metabolic syndrome (MetS), a cluster of conditions including central obesity, hypertension, insulin resistance, and dyslipidemia -- analyzed over 9 million SNPs and identified 549 SNPs significantly associated with MetS across 10 genomic risk loci; gene-set analysis from the same study implicated LPL as one of 22 associated genes, and the nearby variant rs326 was listed as one of the 10 notable lead loci. Separately, GTEx v11 eQTL (expression quantitative trait locus) analysis links the alternate allele at rs10102717 to increased INTS10 expression in spleen (slope +0.22, p=5.0e-5) and non-sun-exposed suprapubic skin (slope +0.08, p=8.5e-5) GTEx Portal.
Reported associations
- Metabolic syndrome (LPL gene region): LPL was identified among 22 genes associated with MetS through gene-set analysis in a GWAS of 107,230 Taiwanese adults; the nearby variant rs326 was listed as one of the 10 notable genomic risk loci in the same study. The specific variant rs10102717 is not named by name in the provided study text.
- INTS10 expression in spleen: The alternate allele at rs10102717 is associated with increased INTS10 gene expression in spleen tissue (slope +0.22, p=5.0e-5) GTEx Portal.
- INTS10 expression in non-sun-exposed skin: The alternate allele is also associated with increased INTS10 expression in suprapubic skin (slope +0.08, p=8.5e-5) GTEx Portal.
Evidence quality The disease-level evidence for this locus comes from one large-scale GWAS (n=107,230 Taiwanese adults from the Taiwan Biobank, genotyped with TWB1.0 and TWB2.0 chips covering over 650,000 SNPs, with imputation expanding coverage to over 9 million SNPs). The sample size is substantial and the study employed genome-wide significance thresholds, but the LPL association derives from gene-set analysis and the named lead variant at this locus is rs326 -- rs10102717 is not referenced by name in the provided study text, so no specific effect size for this variant can be drawn from the provided sources. The cohort is limited to a Taiwanese population, which constrains generalizability to other ancestries. Independent replication in other populations or cohorts is not described in the provided sources, and the evidence for rs10102717 specifically should be considered preliminary. The GTEx eQTL data (GTEx v11, 953 donors, cis-window, FDR<0.05) offer independent mechanistic context but represent expression-level associations, not disease outcomes.
Tissue-specific expression effects
- INTS10: The alternate allele is associated with increased expression in spleen (larger effect, slope +0.22) and non-sun-exposed suprapubic skin (smaller effect, slope +0.08). These findings suggest the variant may act as a regulatory element for INTS10 in immune and skin tissue, though clinical significance has not been established in the provided sources. GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs10102717?
rs10102717 is a single nucleotide polymorphism (SNP) -- a single-letter variation in the DNA sequence -- located in the intergenic region between the INTS10 and LPL genes. It has been studied in the context of metabolic syndrome risk and gene expression regulation in immune and skin tissue.
What is the LPL gene and why is it linked to metabolic syndrome?
LPL (lipoprotein lipase) encodes an enzyme that breaks down fat molecules carried in the bloodstream. Variants in or near LPL have been associated with blood lipid levels and metabolic syndrome, a condition defined by central obesity, high blood pressure, insulin resistance, and abnormal blood fats.
What is INTS10 and what does it do?
INTS10 encodes a subunit of the Integrator complex, a protein group involved in processing small nuclear RNAs and regulating gene activity. Its specific role in metabolic disease is not well characterized in the provided research, though GTEx data show that this variant influences its expression level in spleen and skin.
Is rs10102717 associated with metabolic syndrome?
A GWAS of 107,230 Taiwanese adults found that the broader LPL gene region is associated with metabolic syndrome. The specific variant rs10102717 is not named as a lead finding in the study text, and current evidence for this particular SNP should be considered preliminary pending replication in additional populations.
What does GTEx data show for rs10102717?
GTEx v11 data, drawn from 953 tissue donors, show that the alternate allele at rs10102717 is associated with higher INTS10 expression in spleen and non-sun-exposed skin. These are expression-level associations and do not directly indicate a disease outcome.