TY - JOUR

T1 - Assessing the Functional Significance of Novel and Rare Variants of the SLC26A4 Gene Found in Patients with Hearing Loss by Minigene Assay

AU - Danilchenko, Valeriia Yu

AU - Panina, Ekaterina A

AU - Zytzar, Marina V

AU - Orishchenko, Konstantin E

AU - Posukh, Olga L

N1 - This research was funded by the Russian Science Foundation (grant No. 24-75-00029, https://rscf.ru/en/project/24-75-00029/) (to V.Y.D. and E.A.P.); by the Budget Projects of Institute of Cytology and Genetics SB RAS No. FWNR-2022-0021 (to O.L.P. and M.V.Z.) and No. FWNR-2022-0015 (to K.E.O.); by the Ministry of Science and Higher Education of the Russian Federation (grant No. FSUS-2024-0018) (to K.E.O.).

PY - 2025/11/4

Y1 - 2025/11/4

N2 - The SLC26A4 gene is one of the key genes involved in the etiology of hearing loss. It encodes pendrin, a transmembrane transporter protein functioning as a multifunctional anion exchanger. About 600 pathogenic SLC26A4 variants are known to cause either nonsyndromic recessive hearing loss (DFNB4) or Pendred syndrome (hearing loss and thyroid dysfunction). While most pathogenic variants occur in coding regions and disrupt pendrin structure or function, about 25% are thought to impair splicing. For many, pathogenicity has been assessed only in silico, with limited experimental confirmation. We identified several novel and rare SLC26A4 variants in patients with hearing loss from the Tyva and Altai Republics (Southern Siberia, Russia). Based on splicing predictions, six variants-intronic c.2034+1G>A, c.1545-168A>G, c.1708-125T>C, c.1708-18T>A, c.1804-31C>T, and exonic c.942A>G-were selected for analysis using a minigene assay. The results of in vitro analysis only partially matched in silico predictions: c.2034+1G>A caused aberrant splicing; c.1708-18T>A led to exon 16 skipping only in a small proportion of transcripts; the remaining variants showed no detectable splicing effect. These findings underscore the need for integrating in silico predictions with in vitro validation to accurately assess the functional impact of genetic variants, enabling their correct interpretation and reliable molecular diagnosis.

AB - The SLC26A4 gene is one of the key genes involved in the etiology of hearing loss. It encodes pendrin, a transmembrane transporter protein functioning as a multifunctional anion exchanger. About 600 pathogenic SLC26A4 variants are known to cause either nonsyndromic recessive hearing loss (DFNB4) or Pendred syndrome (hearing loss and thyroid dysfunction). While most pathogenic variants occur in coding regions and disrupt pendrin structure or function, about 25% are thought to impair splicing. For many, pathogenicity has been assessed only in silico, with limited experimental confirmation. We identified several novel and rare SLC26A4 variants in patients with hearing loss from the Tyva and Altai Republics (Southern Siberia, Russia). Based on splicing predictions, six variants-intronic c.2034+1G>A, c.1545-168A>G, c.1708-125T>C, c.1708-18T>A, c.1804-31C>T, and exonic c.942A>G-were selected for analysis using a minigene assay. The results of in vitro analysis only partially matched in silico predictions: c.2034+1G>A caused aberrant splicing; c.1708-18T>A led to exon 16 skipping only in a small proportion of transcripts; the remaining variants showed no detectable splicing effect. These findings underscore the need for integrating in silico predictions with in vitro validation to accurately assess the functional impact of genetic variants, enabling their correct interpretation and reliable molecular diagnosis.

KW - Humans

KW - Sulfate Transporters/genetics

KW - Male

KW - Female

KW - Mutation

KW - Hearing Loss, Sensorineural/genetics

KW - Hearing Loss/genetics

KW - RNA Splicing

KW - Exons

KW - Siberia

KW - Goiter, Nodular

U2 - 10.3390/ijms262110732

DO - 10.3390/ijms262110732

M3 - Article

C2 - 41226768

VL - 26

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 21

M1 - 10732

ER -