Detection of the benign c.2579C>T (p.A860V) variant of the LDLR gene in a pedigree-based genetic analysis of familial hypercholesterolemia

Abstract

More than 2500 variants of the low-density lipoprotein receptor (LDLR) gene have been reported in familial hypercholesterolemia (FH). However, the effects of these variants on the pathophysiology of FH have not been fully clarified. Our aim was to examine whether the c.2579C>T (p.A860V) variant of the LDLR gene affects the phenotype of FH. We present 2 index cases harboring biallelic LDLR variants, including the c.2579C>T (p.A860V) variant, which is defined as having uncertain significance in ClinVar. Genetic analysis was performed for coding regions of the LDLR and proprotein convertase subtilisin/kexin type 9 (PCSK9) genes in 2 families. Detailed clinical and biochemical data were gathered from family members. In one family, the index case involved a patient who harbored biallelic A860V and c.1528-1529insA (p.T510Nfs) LDLR variants and had 8 children; the affected children had the p.T510Nfs variant, and the unaffected children had the A860V variant. In another family, the patient involved in the index case and his sister had biallelic A860V and c.1845+2T>C LDLR variants. There was no difference in FH phenotype between these siblings and their relatives who were heterozygous for the c.1845+2T>C variant. In addition, the allele frequency of the A860V variant (0.0062/0.0095) in the Japanese population, as indicated by 2 databases, was higher than expected based on the prevalence of heterozygous FH in the Japanese population (0.002-0.005). This is the first report to show using pedigree-based genetic analysis that the A860V variant of the LDLR gene is a benign variant.