Common SNPs in HMGCR in Micronesians and Whites Associated With LDL-cholesterol Levels Affect Alternative Splicing of exon13

Arterioscler Thromb Vasc Biol. 2008 Nov;28(11):2078-84. doi: 10.1161/ATVBAHA.108.172288. Epub 2008 Sep 18.


Background- Variation in LDL-cholesterol (LDL-C) among individuals is a complex genetic trait involving multiple genes and gene-environment interactions.

Methods and results: In a genome-wide association study (GWAS) to identify genetic variants influencing LDL-C in an isolated population from Kosrae, we observed associations for SNPs in the gene encoding 3hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) reductase (HMGCR). Three of these SNPs (rs7703051, rs12654264, and rs3846663) met the statistical threshold of genome-wide significance when combined with data from the Diabetes Genetics Initiative GWAS. We followed up the association results and identified a functional SNP in intron13 (rs3846662), which was in linkage disequilibrium with the SNPs of genome-wide significance and affected alternative splicing of HMGCR mRNA. In vitro studies in human lymphoblastoid cells demonstrated that homozygosity for the rs3846662 minor allele was associated with up to 2.2-fold lower expression of alternatively spliced HMGCR mRNA lacking exon13, and minigene transfection assays confirmed that allele status at rs3846662 directly modulated alternative splicing of HMGCR exon13 (42.9+/-3.9 versus 63.7+/-1.0%Deltaexon13/total HMGCR mRNA, P=0.02). Further, the alternative splice variant could not restore HMGCR activity when expressed in HMGCR deficient UT-2 cells.

Conclusions: We identified variants in HMGCR that are associated with LDL-C across populations and affect alternative splicing of HMGCR exon13.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Animals
  • CHO Cells
  • Cholesterol, LDL / blood
  • Cholesterol, LDL / genetics*
  • Cricetinae
  • Cricetulus
  • European Continental Ancestry Group / genetics*
  • Exons*
  • Genotype
  • Homozygote
  • Humans
  • Hydroxymethylglutaryl CoA Reductases / genetics*
  • Hydroxymethylglutaryl CoA Reductases / metabolism
  • Linkage Disequilibrium
  • Lymphocytes / enzymology
  • Micronesia
  • Oceanic Ancestry Group / genetics*
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • RNA, Messenger / metabolism
  • Time Factors
  • Transfection


  • Cholesterol, LDL
  • RNA, Messenger
  • Hydroxymethylglutaryl CoA Reductases