Protein structural insights into a rare PCSK9 gain-of-function variant (R496W) causing familial hypercholesterolemia in a Saudi family: whole exome sequencing and computational analysis

Abstract

Familial hypercholesterolemia (FH) is a globally underdiagnosed genetic condition associated with premature cardiovascular death. The genetic etiology data on Arab FH patients is scarce. Therefore, this study aimed to identify the genetic basis of FH in a Saudi family using whole exome sequencing (WES) and multidimensional bioinformatic analysis. Our WES findings revealed a rare heterozygous gain-of-function variant (R496W) in the exon 9 of the PCSK9 gene as a causal factor for FH in this family. This variant was absent in healthy relatives of the proband and 200 healthy normolipidemic controls from Saudi Arabia. Furthermore, this variant has not been previously reported in various regional and global population genomic variant databases. Interestingly, this variant is classified as "likely pathogenic" (PP5) based on the variant interpretation guidelines of the American College of Medical Genetics (ACMG). Computational functional characterization suggested that this variant could destabilize the native PCSK9 protein and alter its secondary and tertiary structural features. In addition, this variant was predicted to negatively influence its ligand-binding ability with LDLR and Alirocumab antibody molecules. This rare PCSK9 (R496W) variant is likely to expand our understanding of the genetic basis of FH in Saudi Arabia. This study also provides computational structural insights into the genotype-protein phenotype relationship of PCSK9 pathogenic variants and contributes to the development of personalized medicine for FH patients in the future.

Keywords: cardiovascular diseases; familial hypercholesterolemia; pcsk9; sanger sequence; whole exome sequence.

FIGURE 1

Pedigree of a four-generation Saudi family with a clinically diagnosed FH patient. The arrow indicates the index case, which was screened by both whole exome sequencing and sanger sequencing, while II.1, III.2, and III.4 were screened by the sanger sequencing method.

FIGURE 2

The sequence analysis of PCSK9, c.1486C>T variant. (A). The genotypes and the chromatograms of the screened family members using sanger sequencing method, (B). Pathogenicity prediction scores for PCSK9 variant in Franklin server by ACMG Classification (https://franklin.genoox.com/clinical-db/home) showing the likely pathogenic prediction under PP5 classification.

FIGURE 3

Analysis of PCSK9 tertiary structure models. (A). The 3D protein model of the wildtype PCSK9 where R496 built by Swiss-Model, (B). The 3D protein model of the mutant PCSK9 (496W), showing the drastic conformational changes, (C). Molecular docking of wildtype PCSK9 with LDLR, (D). Molecular docking of mutant PCSK9 with LDLR.

FIGURE 4

3D Visualization of the interaction between PCSK9 proteins and Alirocumab. Alirocumab with the wildtype PCSK9 protein (A), and with the mutant PCSK9 protein (B) provided by the DockThor-VS web server, where the ball-and-stick indicating interactions of the Alirocumab with different amino acid residues in the wildtype and mutant PCSK9 proteins.