Abstract The lipoprotein lipase (LPL) enzyme plays a major role in lipid metabolism, primarily by regulating the catabolism of triglyceride (TG)-rich lipoprotein particles. The gene for LPL is an important candidate for affecting the risk of atherosclerosis in the general population. Pre- viously, we have shown that the HindIII polymorphism in intron 8 of the LPL gene is associated with plasma TG and HDL-cholesterol variation in Hispanics and non-His- panic whites (NHWs). However, this polymorphism is lo- cated in an intron and hence may be in linkage disequilib- rium with a functional mutation in the coding region or in- tron-exon junctions of the LPL gene. The aim of this study was to initially screen the LPL coding region and the in- tron-exon junctions by single-strand conformation poly- morphism (SSCP) analysis for mutation detection in a group of 86 individuals expressing the phenotype of high TG/low HDL, followed by association studies in a popu- lation-based sample of 1014 Hispanics and NHWs. Four sequence variations were identified by SSCP and DNA sequencing in the coding region of the gene, including two missense mutations (D9N in exon 2 and N291S in exon 6), one samesense mutation (V108V in exon 3), and one nonsense mutation (S447X in exon 9). Multiple re- gression analyses, including these four mutations and the HindIII polymorphic site, indicate that the association of the HindIII site with plasma TG (P=0.001 in NHWs and P=0.002 in Hispanics) and HDL-cholesterol (P=0.007 in NHWs and P=0.127 in Hispanics) is independent of all other LPL variable sites examined. These observations re- inforce the concept that the intronic 8 HindIII site is func- tional by itself and provide a strong rationale for future comprehensive functional studies to delineate its biologi- cal significance. Introduction Lipoprotein lipase (LPL; E.C. 3.1.1.34) plays a central role in triglyceride (TG) metabolism by regulating the catabo- lism of TG-rich lipoprotein particles. Thus, it is responsi- ble for the influx of free fatty acids into peripheral tissues for storage in the form of TG or as a source of energy. LPL performs its hydrolytic action when attached to he- parin sulfate proteoglycans as dimers at the luminal sur- face of capillary endothelial cells. Because of its physio- logical importance and its possible role in lipid-related pathologies, LPL has been extensively examined in many in vivo and in vitro studies (for recent reviews see: Jansen et al. 1998; de Graaf and Stalenhoef 1998; Olivecrona et al. 1997; Zechner 1997; Goldberg 1996; Murthy et al. 1996). The human LPL gene is located on chromosome 8p22 (Sparkes et al. 1987). The gene spans 29.6 kb and con- tains 10 exons separated by nine introns. Exons 1–9 are of average sizes (105–276 bp), whereas exon 10, which spec- ifies the entire 3’ noncoding sequence, is 1948 bp in length. About 100 different mutations have been identified so far in the human LPL gene, of which 20% occur in the non- coding regions and 80% in the coding regions (Murthy et al. 1996). The LPL mutations influence LPL function in different ways. Catalytic activity, dimerization, secretion, and heparin binding are affected differentially and in cer- tain combinations, reflecting the multifunctional nature of LPL. Different mutations are found to affect these func- tions to variable degrees depending on the contribution of affected amino acid residues to the local and the overall three-dimensional structure of LPL. In addition to the rare mutations associated with nonfunctional LPL enzyme, sev- eral sequence polymorphisms have been identified in the coding and noncoding regions of the gene, including D9N, N291S, S447X, and HindIII. The association of these poly- morphic sites with various health risk factors has been H. Razzaghi · C. E. Aston · R. F. Hamman · M. I. Kamboh Genetic screening of the lipoprotein lipase gene for mutations associated with high triglyceride/low HDL-cholesterol levels Hum Genet (2000) 107 : 257–267 Digital Object Identifier (DOI) 10.1007/s004390000367 Received: 7 April 2000 / Accepted: 17 July 2000 / Published online: 8 September 2000 ORIGINAL INVESTIGATION H. Razzaghi · C. E. Aston · M. I. Kamboh (✉) Department of Human Genetics, 624 Parran Hall, 130 DeSoto Street, University of Pittsburgh, Pittsburgh, PA 15261, USA e-mail: ikamboh@helix.hgen.pitt.edu, Tel.: +1 412 624 3066, Fax: +1 412 383 7844 R. F. Hamman Department of Preventive Medicine and Biometrics, University of Colorado School of Medicine, Denver, CO 80262, USA © Springer-Verlag 2000