Atherosclerosis 152 (2000) 193 – 201 DNA sequence variation in human apolipoprotein C4 gene and its effect on plasma lipid profile  M. Ilyas Kamboh a, *, Christopher E. Aston a , Richard F. Hamman b a Department of Human Genetics, Graduate School of Public Health, Uniersity of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA 15261, USA b Department of Preentie Medicine and Biometrics, Uniersity of Colorado Health Science Center, Dener, CO, USA Received 18 March 1999; received in revised form 13 September 1999; accepted 3 November 1999 Abstract Human apolipoprotein C-IV (apoC-IV, protein; APOC 4, gene) is a new member of the APO E /C 1/C 2 gene cluster. In transgenic mice, human apoC-IV is predominantly associated with very low-density lipoprotein (VLDL) and thus may play an important role in lipid metabolism. To our knowledge, the extent and nature of APOC 4 genetic variation and its role in lipid metabolism are unknown. In this study we have assessed the presence of genetic variation in all three exons of APOC 4 and their flanking intronic sequence by SSCP and DNA sequencing. A total of five point mutations were observed, including two in the non-coding part of exon 1 (A609G and G620A), two in exon 2 (codons 36 and 52) and one in exon 3 (codon 96). The three mutations in exons 2 and 3 predict amino acid substitutions, Leu36Pro, Gly52Asp, and Leu96Arg. The frequencies of the variant alleles were: 0.010 for 609G, 0.039 for 620A, 0.502 for Pro36, 0.003 for Asp52 and 0.357 for Arg96. Significant pairwise linkage disequilibrium was observed between five of the ten APOC 4 pairs, including nt. 620/codon 36, nt. 620/codon 96, codon 36/codon 52, codon 36/codon 96 and codon 52/codon 96. A general linear model analysis reveled a significant association of the Leu36Pro and the Leu96Arg polymorphisms with triglyceride levels in women. This is consistent with the proposed role of apoC-IV in triglyceride metabolism. The characterization of APOC 4 genetic variation may lead to the identification of a specific role of apoC-IV in lipid metabolism or in other physiologic pathways. © 2000 Elsevier Science Ireland Ltd. All rights reserved. Keywords: ApoC-IV; Genetic variation; Association; Lipid; Linkage disequilibrium www.elsevier.com/locate/atherosclerosis 1. Introduction Recently, a new member of the apolipoprotein (apo, protein; APO, gene) gene family, designated APOC 4, has been identified in the APO E /C 1/C 2 gene cluster on human chromosome 19q 13.2 [1]. The APOC 4 gene is linked to the APOC 2 gene, with its 3 terminus lying only 555 bp upstream of the APOC 2 gene (see Fig. 1). The APOC 4 gene consists of three exons and two introns and the total gene sequence encompasses about 4.2 kb region [1] (Fig. 1). The APOC 4 cDNA sequence predicts a protein of 127 amino acids with 25 residues in the signal peptide. Human apoC-IV is expressed only in liver [1,2], but it is not detected in normal plasma [3]. Although the function of apoC-IV is not clear at this stage, there is evidence that it may play a role in lipid metabolism because (1) like other apolipoproteins, it has two amphiphatic -helical domains, which can in- teract with lipid, and (2) the human apoC-IV in trans- genic mice is associated with very low density lipoprotein (VLDL) with expression of apoC-IV in transgenic mice causing hypertriglyceridemia [3]. To our knowledge, no genetic variation has been reported in the APOC 4 gene. As common genetic variations in genes coding for apolipoproteins have been shown to affect plasma lipoprotein-lipid levels (reviewed in [4,5]), identification and examination of genetic variation in the APOC 4 gene in relation to plasma lipid profile may help to understand its role in lipid metabolism. The aims of this study were: (1) to  The findings of this paper were presented at the 72nd Scientific Sessions of the American Heart Association in Atlanta, GA, USA, on November 7, 1999. * Corresponding author. Tel.: +1-412-624-3066; fax: +1-412-383- 7844. E-mail address: ikamboh@helix.hgen.pitt.edu (M.I. Kamboh). 0021-9150/00/$ - see front matter © 2000 Elsevier Science Ireland Ltd. All rights reserved. PII:S0021-9150(99)00459-1