Serum concentrations of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with serum lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10-8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (e.g., CYP7A1, NPC1L1, and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and impact lipid traits in three non-European populations (East Asians, South Asians, and African Americans). Our results identify several novel loci associated with serum lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B, and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.

Summary Myocardial infarction (MI), a leading cause of death around the world, displays a complex pattern of inheritance1,2. When MI occurs early in life, the role of inheritance is substantially greater1. Previously, rare mutations in low-density lipoprotein (LDL) genes have been shown to contribute to MI risk in individual families3–8 whereas common variants at more than 45 loci have been associated with MI risk in the population9–15. Here, we evaluate the contribution of rare mutations to MI risk in the population. We sequenced the protein-coding regions of 9,793 genomes from patients with MI at an early age (≤50 years in males and ≤60 years in females) along with MI-free controls. We identified two genes where rare coding-sequence mutations were more frequent in cases versus controls at exome-wide significance. At low-density lipoprotein receptor (LDLR), carriers of rare, damaging mutations (3.1% of cases versus 1.3% of controls) were at 2.4-fold increased risk for MI; carriers of null alleles at LDLR were at even higher risk (13-fold difference). This sequence-based estimate of the proportion of early MI cases due to LDLR mutations is remarkably similar to an estimate made more than 40 years ago using total cholesterol16. At apolipoprotein A-V (APOA5), carriers of rare nonsynonymous mutations (1.4% of cases versus 0.6% of controls) were at 2.2-fold increased risk for MI. When compared with non-carriers, LDLR mutation carriers had higher plasma LDL cholesterol whereas APOA5 mutation carriers had higher plasma triglycerides. Recent evidence has connected MI risk with coding sequence mutations at two genes functionally related to APOA5, namely lipoprotein lipase15,17 and apolipoprotein C318,19. When combined, these observations suggest that, beyond LDL cholesterol, disordered metabolism of triglyceride-rich lipoproteins contributes to MI risk.

Genome-wide association studies (GWAS) have replicably identified multiple loci associated with population-based plasma lipid concentrations1-5. Common genetic variants at these loci together explain <10% of the total variation of each lipid trait4,5. Rare variants of individually large effect may contribute additionally to the “missing heritability” of lipid traits6,7, however it remains to be shown to what extent rare variants will affect lipid phenotypes. Here, we demonstrate a significant accumulation of rare variants in GWAS-identified genes in patients with an extreme phenotype of abnormal plasma triglyceride (TG) metabolism. A GWAS of hypertriglyceridemia (HTG) patients revealed that common variants in APOA5, GCKR, LPL and APOB genes were associated with the HTG phenotype at genome-wide significance. We subsequently resequenced protein coding regions of these genes and found a significant burden of 154 rare missense or nonsense variants in 438 HTG patients, in contrast to 53 variants in 327 controls (P=6.2X10-8); this corresponds to a carrier frequency of 28.1% of HTG patients and 15.3% of controls (P=2.6X10-5). Many rare variants were predicted in silico to have compromised function; additionally some had previously demonstrated dysfunctionality in vitro. Rare variants in these 4 genes explained 1.1% of total variation in HTG diagnoses. Our study demonstrates a marked mutation skew that likely contributes to disease pathophysiology in patients with HTG.

Here we report that the transcription factor CREB-H is required for the maintenance of normal plasma triglyceride (TG) levels. CREB-H deficient mice displayed hypertriglyceridemia (HTG) secondary to inefficient TG clearance catalyzed by lipoprotein lipase (Lpl), partly due to defective expression of the Lpl coactivators, Apoc2, Apoa4, and Apoa5 and concurrent augmentation of the Lpl inhibitor, Apoc3. Multiple nonsynonymous mutations in CREB3L3 that produced hypomorphic or nonfunctional CREB-H protein were identified in patients with extreme HTG, implicating a critical role for CREB-H in human TG metabolism.

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