In vitro analysis of the effects of intronic variants c.940+3_940+6del, c.941-3C>G, and c.2389+5G>A in the LDLR gene on pre-mRNA splicing using a minigene assay

Abstract

Familial hypercholesterolemia (FH) is an autosomal codominant disorder characterized by impaired clearance of low-density lipoproteins from the bloodstream, markedly elevated plasma total cholesterol and low density lipoprotein cholesterol levels, and early onset of atherosclerosis and cardiovascular disease. FH is one of the most common monogenic disorders in humans. The majority of FH cases are caused by pathogenic variants in three genes: LDLR (OMIM: 143890), APOB (OMIM: 107730), and PCSK9 (OMIM: 607786). More than 80 % of FH cases are associated with mutations in the LDLR gene, located on chromosome 19. In 25–75 % of patients with a clinical FH phenotype, no pathogenic variant is identified in these genes. Whole-exome sequencing and targeted gene panel sequencing of the LDLR , APOB , PCSK9 , and LDLRAP1 genes were performed in patients with an FH phenotype, followed by confirmation of the identified variants by Sanger sequencing. Three unrelated probands were found to carry intronic LDLR variants for which functional evidence was previously unavailable. The aim of this study was to functionally assess in vitro the effects of three intronic LDLR variants (NM_000527.5: c.940+3_940+6del, c.941-3C>G, and c.2389+5G>A) on pre-mRNA splicing using a minigene assay. Minigene constructs encompassing target exons with flanking intronic sequences were generated and transfected into the HEK293 and HeLa cell lines. The deleterious effect of all three variants on pre-mRNA splicing was confirmed. The fournucleotide deletion c.940+3_940+6del resulted in two aberrant transcripts: inclusion of six nucleotides from intron 6 and complete retention of the minigene intronic sequence. The c.941-3C>G variant caused loss of the canonical acceptor splice site and activation of a cryptic site, with inclusion of intronic nucleotides from intron 6. The c.2389+5G>A variant resulted in exon 16 skipping. Functional in vitro analysis is a key tool for the molecular verification of intronic variants of uncertain clinical significance and, in conjunction with clinical data, supports the establishment of a definitive molecular diagnosis.