Pathogenic variants in the SLC26A4 gene (OMIM #605646, 21 exons), encoding the transmembrane protein pendrin, are one of the most significant genetic causes of hearing loss. It is known that about 25% of all pathogenic SLC26A4 variants, which are localized in both intronic and exonic gene regions (near the exon–intron boundaries), lead to aberrant splicing. A detailed analysis of the SLC26A4 gene in Tuvinian patients with hearing loss (the Tyva Republic, Southern Siberia) revealed a specific spectrum of variations, including both already known pathogenic variants and novel variants with unclear clinical significance. One of the novel variants, c.1545TG, is localized at a position that is potentially «sensitive» to splicing (the 1st nucleotide in exon 14). The segregation of this variant with hearing loss observed in the pedigrees of patients and the significant increase in the frequency of c.1545TG in the sample of patients compared to the control sample indicate its pathogenic significance. The aim of this work is to analyze the effect of novel variant c.1545TG of the SLC26A4 gene on the splicing process using minigene assay. A system of minigenes was created, including the analyzed variant c.1545TG, and the wild-type variant. The study was carried out on HEK293T cell line and repeated on HeLa and SW480 cells. Comparative analysis of splicing patterns in minigenes with variant c.1545TG and with wild type did not reveal any differences. Thus, variant c.1545TG of the SLC26A4 gene does not lead to splicing disruption, and its pathogenic effect may be due to the substitution of phenylalanine (Phe) for leucine (Leu) at amino acid position 515 (p.Phe515Leu) of the pendrin protein.
E. A. Panina (Wed,) studied this question.