Analysis of the effect on splicing of the SLC26A4 gene variants identified in patients with hearing loss from the Republics of Tyva and Altai (Southern Siberia)

The SLC26A4 gene is one of the most significant in the etiology of hereditary forms of hearing loss in many populations of the world. Currently, about 600 pathogenic SLC26A4 variants are known and, apparently, at least 25% of them lead to aberrant splicing. This study presents the results of an experimental in vitro analysis of the effect on splicing of several rare variants of the SLC26A4 gene identified in patients with hearing loss from the Republics of Tyva and Altai (Southern Siberia), using a minigene assay. The choice of these variants is due to the ambiguity of assessments obtained using bioinformatic prognostic programs. The pathogenic effect of the intronic variant c.2034+1G>A, leading to aberrant splicing, was experimentally confirmed. Functional analysis of the intronic variant c.1708- 18T>A showed that the acceptor site disruption and exon 16 skipping were observed only in a small proportion of transcripts with this variant, and three intronic variants c.1545-168A>G, c.1708-125T>C, c.1804-31C>T and the exon variant c.1545T>G did not affect the splicing process in the in vitro system. The obtained data emphasize the importance of an integrated approach to assessing the effects of genetic variants, combining in silico predictions with in vitro functional analysis, which is necessary for the correct interpretation of the identified genetic variations and accurate molecular genetic diagnosis.

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