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A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease

Objective: Variants of the polycystic kidney and hepatic disease 1 (PKHD1) gene are associated with autosomal recessive polycystic kidney disease (ARPKD). This study aimed to identify the genetic causes in a Chinese pedigree with ARPKD and design a minigene construct of the PKHD1 gene to investigate...

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Autores principales: Miao, Mingzhu, Feng, Liqun, Wang, Jue, Xu, Cheng, Su, Xiaotian, Zhang, Guoying, Lu, Shoulian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10339289/
https://www.ncbi.nlm.nih.gov/pubmed/37456659
http://dx.doi.org/10.3389/fgene.2023.1207772
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author Miao, Mingzhu
Feng, Liqun
Wang, Jue
Xu, Cheng
Su, Xiaotian
Zhang, Guoying
Lu, Shoulian
author_facet Miao, Mingzhu
Feng, Liqun
Wang, Jue
Xu, Cheng
Su, Xiaotian
Zhang, Guoying
Lu, Shoulian
author_sort Miao, Mingzhu
collection PubMed
description Objective: Variants of the polycystic kidney and hepatic disease 1 (PKHD1) gene are associated with autosomal recessive polycystic kidney disease (ARPKD). This study aimed to identify the genetic causes in a Chinese pedigree with ARPKD and design a minigene construct of the PKHD1 gene to investigate the impact of its variants on splicing. Methods: Umbilical cord samples from the proband and peripheral blood samples from his parents were collected, and genomic DNA was extracted for whole-exome sequencing (WES). Bioinformatic analysis was used to identify potential genetic causes, and Sanger sequencing confirmed the existence of variants within the pedigree. A minigene assay was performed to validate the effects of an intronic variant on mRNA splicing. Results: Two variants, c.9455del (p.N3152Tfs*10) and c.2408-13C>G, were identified in the PKHD1 gene (NM_138694.4) by WES; the latter has not been previously reported. In silico analysis predicted that this intronic variant is potentially pathogenic. Bioinformatic splice prediction tools revealed that the variant is likely to strongly impact splice site function. An in vitro minigene assay revealed that c.2408-13C>G can cause aberrant splicing, resulting in the retention of 12 bp of intron 23. Conclusion: A novel pathogenic variant of PKHD1, c.2408-13C>G, was found in a fetus with ARPKD, which enriches the variant spectrum of the PKHD1 gene and provides a basis for genetic counseling and the diagnosis of ARPKD. Minigenes are optimal to determine whether intron variants can cause aberrant splicing.
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spelling pubmed-103392892023-07-14 A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease Miao, Mingzhu Feng, Liqun Wang, Jue Xu, Cheng Su, Xiaotian Zhang, Guoying Lu, Shoulian Front Genet Genetics Objective: Variants of the polycystic kidney and hepatic disease 1 (PKHD1) gene are associated with autosomal recessive polycystic kidney disease (ARPKD). This study aimed to identify the genetic causes in a Chinese pedigree with ARPKD and design a minigene construct of the PKHD1 gene to investigate the impact of its variants on splicing. Methods: Umbilical cord samples from the proband and peripheral blood samples from his parents were collected, and genomic DNA was extracted for whole-exome sequencing (WES). Bioinformatic analysis was used to identify potential genetic causes, and Sanger sequencing confirmed the existence of variants within the pedigree. A minigene assay was performed to validate the effects of an intronic variant on mRNA splicing. Results: Two variants, c.9455del (p.N3152Tfs*10) and c.2408-13C>G, were identified in the PKHD1 gene (NM_138694.4) by WES; the latter has not been previously reported. In silico analysis predicted that this intronic variant is potentially pathogenic. Bioinformatic splice prediction tools revealed that the variant is likely to strongly impact splice site function. An in vitro minigene assay revealed that c.2408-13C>G can cause aberrant splicing, resulting in the retention of 12 bp of intron 23. Conclusion: A novel pathogenic variant of PKHD1, c.2408-13C>G, was found in a fetus with ARPKD, which enriches the variant spectrum of the PKHD1 gene and provides a basis for genetic counseling and the diagnosis of ARPKD. Minigenes are optimal to determine whether intron variants can cause aberrant splicing. Frontiers Media S.A. 2023-06-29 /pmc/articles/PMC10339289/ /pubmed/37456659 http://dx.doi.org/10.3389/fgene.2023.1207772 Text en Copyright © 2023 Miao, Feng, Wang, Xu, Su, Zhang and Lu. 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
Miao, Mingzhu
Feng, Liqun
Wang, Jue
Xu, Cheng
Su, Xiaotian
Zhang, Guoying
Lu, Shoulian
A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title_full A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title_fullStr A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title_full_unstemmed A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title_short A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
title_sort novel pkhd1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10339289/
https://www.ncbi.nlm.nih.gov/pubmed/37456659
http://dx.doi.org/10.3389/fgene.2023.1207772
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