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Open AccessArticle

Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1

1
DBGen Ocular Genomics, 08028 Barcelona, Spain
2
Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avda.Diagonal 643, 08028 Barcelona, Spain
3
Barraquer—Centro de Oftalmología Barcelona, 08021 Barcelona, Spain
4
Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 08025 Barcelona, Spain
5
Institut de Biomedicina de la Universitat de Barcelona-Institut de Recerca Sant Joan de Deu (IBUB-IRSJD), 08028 Barcelona, Spain
*
Author to whom correspondence should be addressed.
These authors are equally contributors.
Genes 2019, 10(10), 732; https://doi.org/10.3390/genes10100732
Received: 4 September 2019 / Revised: 17 September 2019 / Accepted: 19 September 2019 / Published: 21 September 2019
(This article belongs to the Special Issue Alternative Splicing and Human Disease)
Aims: The aim of this study was the genetic diagnosis by next generation sequencing (NGS) of a patient diagnosed with Usher syndrome type 2 and the functional evaluation of the identified genetic variants to establish a phenotype–genotype correlation. Methods: Whole exome sequencing (WES) analysis identified two heterozygous intronic variants in CDH23, a gene responsible of Usher syndrome type 1. Evaluation of the putative splicing effects was performed in vivo, in whole blood samples, and in vitro, by transfection of midigene constructs in HEK293T cells. Results: Two intronic variants were identified in intron 45 of CDH23—one novel, c.6050-15G>A, and the other, c.6050-9G>A, already reported as a noncanonical splice site (NCSS) mutation—with partial functional characterization. In vivo and in vitro analyses showed aberrant transcripts by the addition of 13 and 7 nucleotides to exon 46, respectively. Transcript degradation by nonsense mediated decay (NMD) in blood cells could only be prevented by cycloheximide treatment. Midigene constructs showed that the two variants contributed to exon skipping and generated aberrantly spliced transcripts. Conclusions: A combination of in vivo and in vitro assays provided a comprehensive view of the physiological effects of NCSS variants, which in this case led to a clinical reassignment of the proband as affected with atypical USH1 syndrome. View Full-Text
Keywords: Usher syndrome; CDH23; splice site variants; functional analysis; phenotypic effects Usher syndrome; CDH23; splice site variants; functional analysis; phenotypic effects
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Valero, R.; de Castro-Miró, M.; Jiménez-Ochoa, S.; Rodríguez-Ezcurra, J.J.; Marfany, G.; Gonzàlez-Duarte, R. Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1. Genes 2019, 10, 732.

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