Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease

Abstract

Background: The discovery of low-frequency coding variants affecting the risk of coronary artery disease has facilitated the identification of therapeutic targets.

Methods: Through DNA genotyping, we tested 54,003 coding-sequence variants covering 13,715 human genes in up to 72,868 patients with coronary artery disease and 120,770 controls who did not have coronary artery disease. Through DNA sequencing, we studied the effects of loss-of-function mutations in selected genes.

Results: We confirmed previously observed significant associations between coronary artery disease and low-frequency missense variants in the genes LPA and PCSK9. We also found significant associations between coronary artery disease and low-frequency missense variants in the genes SVEP1 (p.D2702G; minor-allele frequency, 3.60%; odds ratio for disease, 1.14; P=4.2×10(-10)) and ANGPTL4 (p.E40K; minor-allele frequency, 2.01%; odds ratio, 0.86; P=4.0×10(-8)), which encodes angiopoietin-like 4. Through sequencing of ANGPTL4, we identified 9 carriers of loss-of-function mutations among 6924 patients with myocardial infarction, as compared with 19 carriers among 6834 controls (odds ratio, 0.47; P=0.04); carriers of ANGPTL4 loss-of-function alleles had triglyceride levels that were 35% lower than the levels among persons who did not carry a loss-of-function allele (P=0.003). ANGPTL4 inhibits lipoprotein lipase; we therefore searched for mutations in LPL and identified a loss-of-function variant that was associated with an increased risk of coronary artery disease (p.D36N; minor-allele frequency, 1.9%; odds ratio, 1.13; P=2.0×10(-4)) and a gain-of-function variant that was associated with protection from coronary artery disease (p.S447*; minor-allele frequency, 9.9%; odds ratio, 0.94; P=2.5×10(-7)).

Conclusions: We found that carriers of loss-of-function mutations in ANGPTL4 had triglyceride levels that were lower than those among noncarriers; these mutations were also associated with protection from coronary artery disease. (Funded by the National Institutes of Health and others.).

Figure 1. Loss-of-Function Alleles in ANGPTL4 and Plasma Lipid Levels

Panel A shows the loss-of-function mutations discovered by sequencing the seven exons of ANGPTL4 in 9731 persons of European ancestry. The locations of the individual mutations are depicted along the length of the ANGPTL4 gene, starting at the 5′ end (left), along with the predicted functional effect. An asterisk indicates the introduction of a premature stop codon. Panel B shows the mean plasma lipid levels according to loss-of-function allele carrier status. T bars indicate standard deviations. P values were calculated from a linear regression (with the use of a logarithm transformation in the case of triglycerides) with covariates of age, sex, and study. HDL denotes high-density lipoprotein, and LDL low-density lipoprotein.

Figure 2. Genetic Variants Affecting the Lipoprotein Lipase Pathway and the Risk of Coronary Artery Disease

Panel A shows normal physiological function of lipoprotein lipase (LPL) and regulation of LPL by gene products of ANGPTL4, APOC3, and APOA5. LPL, which is both transported across and anchored to capillary endothelial cells by the protein GPIHBP1, normally hydrolyzes the triglycerides that are present in circulating lipoproteins and reduces the plasma triglyceride level. Its activity is reduced by ANGPTL4 and APOC3 and increased by APOA5. Not shown here are other important regulators of LPL activity, including APOC2 and ANGPTL3. Green arrows indicate enhancers, and red blocked arrows indicate inhibitors. IDL denotes intermediate-density lipoprotein, and VLDL very-low-density lipoprotein. Panel B shows altered function of LPL in mutation carriers. Mutations affecting LPL and proteins interacting with LPL are shown, along with expected effect on LPL activity, plasma triglyceride levels, and risk of coronary artery disease. LPL loss of function refers to p.D36N, and gain of function refers to p.S477* (see Table S12 in the Supplementary Appendix). ANGPTL4 loss of function refers to both p.E40K and loss-of-function mutations (Tables S9, S10, and S11 in the Supplementary Appendix). APOC3^, and APOA5 loss of function refers to multiple loss-of-function mutations.