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Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness

Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candi...

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Autores principales: Chen, Penghui, Wang, Longhao, Chai, Yongchuan, Wu, Hao, Yang, Tao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8693380/
https://www.ncbi.nlm.nih.gov/pubmed/34956325
http://dx.doi.org/10.3389/fgene.2021.773922
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author Chen, Penghui
Wang, Longhao
Chai, Yongchuan
Wu, Hao
Yang, Tao
author_facet Chen, Penghui
Wang, Longhao
Chai, Yongchuan
Wu, Hao
Yang, Tao
author_sort Chen, Penghui
collection PubMed
description Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A > T and c.580G > A in EYA4, c.322-57_322-8del in PAX3, c.991-15_991-13del in DFNA5, c.6087-3T > G in PTPRQ and c.164+5G > A in USH1G. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A > T and c.580G > A in EYA4, c.991-15_991-13del in DFNA5), intron retention (c.322-57_322-8del in PAX3), exon skipping and intron retention (c.6087-3T > G in PTPRQ) and shortening of exon (c.164+5G > A in USH1G). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis.
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spelling pubmed-86933802021-12-23 Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness Chen, Penghui Wang, Longhao Chai, Yongchuan Wu, Hao Yang, Tao Front Genet Genetics Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A > T and c.580G > A in EYA4, c.322-57_322-8del in PAX3, c.991-15_991-13del in DFNA5, c.6087-3T > G in PTPRQ and c.164+5G > A in USH1G. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A > T and c.580G > A in EYA4, c.991-15_991-13del in DFNA5), intron retention (c.322-57_322-8del in PAX3), exon skipping and intron retention (c.6087-3T > G in PTPRQ) and shortening of exon (c.164+5G > A in USH1G). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis. Frontiers Media S.A. 2021-12-08 /pmc/articles/PMC8693380/ /pubmed/34956325 http://dx.doi.org/10.3389/fgene.2021.773922 Text en Copyright © 2021 Chen, Wang, Chai, Wu and Yang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Chen, Penghui
Wang, Longhao
Chai, Yongchuan
Wu, Hao
Yang, Tao
Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title_full Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title_fullStr Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title_full_unstemmed Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title_short Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
title_sort detection and functional verification of noncanonical splice site mutations in hereditary deafness
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8693380/
https://www.ncbi.nlm.nih.gov/pubmed/34956325
http://dx.doi.org/10.3389/fgene.2021.773922
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