Polymorphisms in PNLIP, encoding pancreatic lipase, and associations with metabolic traits

Pancreatic lipase (EC 3.1.1.3) is an exocrine secretion that hydrolyzes die tary triglycerides in the small intestine. We developed genomic amplificati on primers to sequence the 13 exons of PNLIP, which encodes pancreatic lipa se, in order to screen for possible mutations in cell lines of four childre n with pancreatic lipase deficiency (OMIM 246600). We found no missense or nonsense mutations in these samples, but we found three silent single-nucle otide polymorphisms (SNPs), namely, 96A/C in exon 3, 486C/T in exon 6, and 1359C/T in exon 13. In 50 normolipidemic Caucasians. the PNLIP 96C and 486T alleles had frequencies of 0.083 and 0.150, respectively. The PNLIP 1359T allele was absent from Caucasian, Chinese, South Asian, and North American aboriginal samples, but had a frequency of 0.085 in an African sample, sugg esting that it is a population-specific variant. In an association analysis of 185 African neonates, the PNLIP 1359C/T SNP genotype was significantly associated with concentrations of plasma lipoproteins. These associations w ere most likely due to linkage disequilibrium with another functional varia nt at or near PNLIP. Thus, we report three new SNPs for the PNLIP, which ma y serve as markers for association analyses and for pharmacogenetic studies of pancreatic lipase inhibitors.