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Primary hypercholesterolemia is characterized by elevated LDL-cholesterol (LDL-C) levels isolated in autosomal dominant hypercholesterolemia (ADH) or associated with elevated triglyceride levels in familial combined hyperlipidemia (FCHL). Rare <i>APOE</i> variants are known in ADH and FCHL. We explored the <i>APOE</i> molecular spectrum in a French ADH/FCHL cohort of 5743 unrelated probands. The sequencing of <i>LDLR</i>, <i>PCSK9</i>, <i>APOB</i>, and <i>APOE</i> revealed 76 carriers of a rare <i>APOE</i> variant, with no mutation in <i>LDLR</i>, <i>PCSK9,</i> or <i>APOB</i>. Among the 31 <i>APOE</i> variants identified here, 15 are described in ADH, 10 in FCHL, and 6 in both probands. Five were previously reported with dyslipidemia and 26 are novel, including 12 missense, 5 synonymous, 2 intronic, and 7 variants in regulatory regions. Sixteen variants were predicted as pathogenic or likely pathogenic, and their carriers had significantly lower polygenic risk scores (wPRS) than carriers of predicted benign variants. We observed no correlation between LDL-C levels and wPRS, suggesting a major effect of <i>APOE</i> variants. Carriers of p.Leu167del were associated with a severe phenotype. The analysis of 11 probands suggests that carriers of an <i>APOE</i> variant respond better to statins than carriers of a <i>LDLR</i> mutation. Altogether, we show that the <i>APOE</i> variants account for a significant contribution to ADH and FCHL.