Analysis of the c.757A>G p.(Ile253Val) variant of the SLC26A4 gene in GJB2-negative patients with hearing loss in Yakutia
V. G. Pshennikova,
F. M. Teryutin,
A. M. Cherdonova,
T. V. Borisova,
S. A. Fedorova,
N. A. Barashkov https://doi.org/10.25789/YMJ.2023.83.20
Abstract
In this work, we searched for the missense variant c.757A>G p.(Ile253Val) of the SLC26A4 gene in GJB2-negative patients with hearing loss (n=201) and in the control group of hearing individuals (n=103) in Yakutia. As a result, this variant was detected with a frequency of 2.02% among patients, in the control group - 1.94%. To interpretation the clinical significance, a frequency analysis of this variant and in silico evaluation were performed, the results of which are in favor of the likely benign of the c.757A>G p.(Ile253Val) variant of the SLC26A4 gene, as indicated by the high frequency of occurrence in population samples, and the fact that this missense substitution theoretically does not violate the structural stability of the pendrin protein (SLC26A4).
About the Authors
V. G. Pshennikova
Yakut Science Centre of Complex Medical Problems (YSC CMP)
Russian Federation
Russian Federation
PSHENNIKOVA Vera Gennadievna - PhD in Biology, leading researcher of the Laboratory of Molecular Genetics
F. M. Teryutin
Yakut Science Centre of Complex Medical Problems (YSC CMP)
Russian Federation
Russian Federation
TERYUTIN Fedor Mikhailovich - PhD (Medicine), researcher of the Laboratory of Molecular Genetics
A. M. Cherdonova
M.K. Ammosov North-Eastern Federal University (NEFU)
Russian Federation
Russian Federation
CHERDONOVA Aleksandra Matveevna - junior researcher of the Research Laboratory of Molecular Biology
T. V. Borisova
M.K. Ammosov North-Eastern Federal University (NEFU)
Russian Federation
Russian Federation
BORISOVA Tuyara Valerievna – junior researcher of the Research Laboratory of Molecular Biology
S. A. Fedorova
M.K. Ammosov North-Eastern Federal University (NEFU)
Russian Federation
Russian Federation
FEDOROVA Sardana Arkadievna – MD in Biology,chief researcher, head of the Laboratory of Molecular Biology
N. A. Barashkov
Yakut Science Centre of Complex Medical Problems (YSC CMP)
Russian Federation
Russian Federation
BARASHKOV Nikolay Alekseevich – PhD in Biology, leading researcher, head of the Laboratory of Molecular Genetics
References
1. Analysis of SLC26A4, FOXI1, and KCNJ10 Gene Variants in Patients with Incomplete Partition of the Cochlea and Enlarged Vestibular Aqueduct (EVA) Anomalies / L.A. Klarov, V.G. Pshennikova, G.P. Romanov [et al] // Int J Mol Sci. – 2022. – V. 23. – P.15372. DOI: 10.3390/ijms232315372.
2. Bassot C. Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain / C. Bassot, G. Minervini, E. Leonardi, S.C.E. Tosatto // Biochimie. – 2017. – V. 132. – P. 109-120. DOI: 10.1016/j.biochi.2016.10.002.
3. Common molecular etiologies are rare in nonsyndromic Tibetan Chinese patients with hearing impairment / Y. Yuan, X. Zhang, S. Huang [et al] // PLoS One. – 2012. – V. 7(2):e30720. DOI: 10.1371/journal.pone.0030720.
4. Comprehensive molecular etiology analysis of nonsyndromic hearing impairment from typical areas in China / Y. Yuan, Y. You, D. Huang [et al] // J Transl Med. – 2009. – V. 7. – P. 79. DOI: 10.1186/1479-5876-7-79.
5. Concurrent newborn hearing and genetic screening of common hearing loss variants with bloodspot-based targeted next generation sequencing in Jiangxi province / H. Luo, Y. Yang, X. Wang [et al] // Front Pediatr. – 2022. – V. 10. – P. 1020519. DOI: 10.3389/fped.2022.1020519.
6. Del Castillo F.J. DFNB1 Non-syndromic Hearing Impairment: Diversity of Mutations and Associated Phenotypes / F.J. Del Castillo, I. Del Castillo // Front Mol Neurosci. – 2017. – V. 10. – P. 428. DOI: 10.3389/fnmol.2017.00428.
7. Diagnostic Yield of Targeted Hearing Loss Gene Panel Sequencing in a Large German Cohort With a Balanced Age Distribution from a Single Diagnostic Center: An Eight-year Study / A. Tropitzsch, T. Schade-Mann, P. Gamerdinger [et al] // Ear Hear. - 2022 – V. 43(3). – P. 1049-1066. DOI: 10.1097/AUD.0000000000001159.
8. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss / A.M. Oza, M.T. DiStefano, S.E. Hemphill [et al] // Hum Mutat. – 2018. – V. 39(11). – P. 1593-1613. DOI: 10.1002/humu.23630.
9. Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population / C-C. Wu, C-Y. Tsai, Y-H. Lin [et al] // Genes. – 2019. – V. 10(10) - P. 772. DOI: 10.3390/genes10100772.
10. Genetic screening of a Chinese cohort of children with hearing loss using a next-generation sequencing panel / J. Ma, X. Ma, K. Lin [et al] // Hum Genomics. – 2023. - V. 7(1). – P. 1. DOI: 10.1186/s40246-022-00449-1.
11. Genotyping and audiological characteristics of infants with a single-allele SLC26A4 mutation / X. Zhao, L. Huang, X. Wang [et al] // Int J Pediatr Otorhinolaryngol. - 2019. – V. 116. – P. 153-158. DOI: 10.1016/j.ijporl.2018.10.046.
12. Global genetic insight contributed by consanguineous Pakistani families segregating hearing loss / Richard EM, Santos-Cortez RLP, Faridi R, [et al] // Hum Mutat. – 2019. – V. –40(1). - P. 53-72. DOI: 10.1002/humu.23666.
13. Highly accurate protein structure prediction for the human proteome / K. Tunyasuvunakool, J. Adler, Z. Wu [et al] // Nature. – 2021. – V. 596(7873). – P. 590-596. doi: 10.1038/s41586-021-03828-1.
14. Highly accurate protein structure prediction with AlphaFold / J. Jumper, R. Evans, A. Pritzel [et al] // Nature. – 2021. – V. 596. – P. 583– 589. DOI: 10.1038/s41586-021-03819-2.
15. Human SLC26A4/Pendrin STAS domain is a nucleotide-binding protein: Refolding and characterization for structural studies / A.K. Sharma, T. Krieger, A.C. Rigby [et al] // Biochem Biophys Rep. – 2016. - V. 8. – P. 184-191. DOI: 10.1016/j.bbrep.2016.08.022.
16. Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing / B. Zeng, H. Xu, Y. Yu [et al] // Front Genet. – 2022. – V. 13. – P. 1057293. DOI: 10.3389/fgene.2022.1057293.
17. Molecular architecture and the structural basis for anion interaction in prestin and SLC26 transporters / D. Gorbunov, M. Sturlese, F. Nies [et al] // Nat Commun. – 2014. – V. 5. – P. 3622. DOI: 10.1038/ncomms4622.
18. Molecular epidemiology and functional assessment of novel allelic variants of SLC26A4 in non-syndromic hearing loss patients with enlarged vestibular aqueduct in China / Y. Yuan, W. Guo, J. Tang [et al] // PLoS One. – 2012. – V. 7(11):e49984. DOI: 10.1371/journal.pone.0049984.
19. Morton C.C. Newborn hearing screening – a silent revolution / C.C. Morton, W.E. Nance // N Engl J Med. – 2006. – V. 354(20). - P. 2151-2164. DOI: 10.1056/NEJMra050700.
20. Novel mutations of SLC26A4 in Chinese patients with nonsyndromic hearing loss / Yao G, Chen D, Wang H, [et al] // Acta Otolaryngol. – 2013. – V. 133(8). – P. 833-41. DOI: 10.3109/00016489.2013.777160.
21. Pendred Syndrome Is Caused by Pathogenic variants in a Putative Sulphate Transporter Gene (PDS) / L.A. Everett, B. Glaser, J.C. Beck [et al] // Nat. Genet. – 1997. – V. 17. – P. 411–422. DOI: 10.1038/ng1297-411.
22. Pendrin, Encoded by the Pendred Syndrome Gene, Resides in the Apical Region of Renal Intercalated Cells and Mediates Bicarbonate Secretion / I.E. Royaux, S.M. Wall, L.P. Karniski, [et al] // Proc. Natl. Acad. Sci. USA. – 2001. – V. 98. – P. 4221–4226. DOI: 10.1073/pnas.071516798.
23. Scott D.A. Human Pendrin Expressed in Xenopus Laevis Oocytes Mediates Chloride/ Formate Exchange / D.A. Scott, L.P. Karniski // Am. J. Physiol. Cell Physiol. – 2000. – V. 278. – P. 207–211. DOI: 10.1152/ajpcell.2000.278.1.C207.
24. Soleimani M. Molecular physiology of the renal chloride-formate exchanger / M. Soleimani // Curr. Opin. Nephrol. Hypertens. – 2001. – V. 10. – P. 677–683. DOI: 10.1097/00041552-200109000-00020.
25. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic) / N.A. Barashkov, V.G. Pshennikova, O.L. Posukh [et al] // PLoS One. – 2016. – V. - 11(5):e0156300. DOI: 10.1371/journal.pone.0156300.
26. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology / S. Richards, N. Aziz, S. Bale [et al] // Genet Med. – 2015. – V. 17(5). - P. 405-24. DOI: 10.1038/gim.2015.30.
27. Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family / E.R. Geertsma, Y.N. Chang, F.R. Shaik [et al] // Nat Struct Mol Biol. – 2015. – V. 22. – P. 803-808. DOI: 10.1038/nsmb.3091.
28. The Pendred Syndrome Gene Encodes a Chloride-Iodide Transport Protein / D.A. Scott, R. Wang, T.M. Kreman [et al] // Nat. Genet. – 1999. – V. 21. – P. 440–443. DOI: 10.1038/7783.
29. The Pendrin Polypeptide. In: Dossena, S., Paulmichl, M. (eds) The Role of Pendrin in Health and Disease / S. Dossena, E. Bernardinelli, A.K. Sharma [et al] // Springer, Cham. – 2017. - P. 187-220. DOI: 10.1007/978-3-319-43287-8_11.
30. Thiocyanate transport in resting and IL-4-stimulated human bronchial epithelial cells: role of pendrin and anion channels / N. Pedemonte, E. Caci, E. Sondo [et al] // J Immunol. – 2007. – V. 178. P. 5144–5153. DOI: 10.4049/jimmunol.178.8.5144.
31. Whole-exome sequencing identifies genetic variants of hearing loss in 113 Chinese families / J. Pan, S. Ma, Y. Teng [et al] // Clin Chim Acta. – 2022. - V. 532. – P. 53-60. DOI: 10.1016/j.cca.2022.05.020.
Review
For citations:
Pshennikova V.G., Teryutin F.M., Cherdonova A.M., Borisova T.V., Fedorova S.A., Barashkov N.A. Analysis of the c.757A>G p.(Ile253Val) variant of the SLC26A4 gene in GJB2-negative patients with hearing loss in Yakutia. Yakut Medical Journal. 2023;(3):79-84. https://doi.org/10.25789/YMJ.2023.83.20
Views:
24
Email this article 