Splicing defects caused by exonic mutations in<i>PKD1</i>as a new mechanism of pathogenesis in autosomal dominant polycystic kidney disease

Claverie-Martı́n, Félix; González-Paredes, Francisco Javier; Ramos-Trujillo, Elena

doi:10.1080/15476286.2015.1014291

Cited by 23 publications

(20 citation statements)

References 55 publications

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“…Splicing defects caused by exonic mutations have been implicated in the pathogenesis in ADPKD. 28 No trans-heterozygous mutations of PKD1/2 genes were identified, possibly reflecting the small cohort.…”

Section: Discussionmentioning

confidence: 99%

Somatic Mutations in Renal Cyst Epithelium in Autosomal Dominant Polycystic Kidney Disease

Tan¹,

Zhang

Michaeel³

et al. 2018

JASN

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Section: Discussionmentioning

confidence: 99%

Somatic Mutations in Renal Cyst Epithelium in Autosomal Dominant Polycystic Kidney Disease

Tan¹,

Zhang

Michaeel³

et al. 2018

JASN

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“…Also, the last three positions and the first two in the exons are an integral part of the 5′ and 3′ splice sites consensus sequences, respectively. Therefore, exonic mutations may affect splicing by altering regulatory elements, by abolishing or reducing the strength of the splice sites, or by creating new splice sites [ 1 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease

Suarez-Artiles

Perdomo‐Ramirez

Ramos-Trujillo

et al. 2018

Genes

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Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing. Using predictive bioinformatics tools, we selected thirteen missense mutations and one synonymous mutation based on their potential effects on splicing regulatory elements or splice sites. These mutations were analyzed in a minigene splicing assay. Results of the RNA analysis showed that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation c.741G>T; p.(Trp247Cys) generated splicing silencer sequences and disrupted splicing enhancer motifs that resulted in skipping of exon 9, while mutations c.2581G>A; p.(Ala861Thr) and c.2581G>C; p.(Ala861Pro) abolished a 5′ splice site leading to skipping of exon 23. Mutation c.741G>T represents the first OCRL exonic variant outside the conserved splice site dinucleotides that results in alteration of pre-mRNA splicing. Our results highlight the importance of evaluating the effects of OCRL exonic mutations at the mRNA level.

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“…This study underlines the importance of assessing the potential splicing effects of synonymous changes in known disease causing genes. The signi cance of synonymous variants in PKD1 and NPHP3, underlying ADPKD and nephronophthisis, respectively, has recently been described (21,48). Interpretation of variants of unknown signi cance in WES and WGS datasets is a major challenge in the NGS era and often requires functional studies to assess their signi cance.…”

Section: Discussionmentioning

confidence: 99%

Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles

Molinari

Srivast

Dewhurst

et al. 2020

Preprint

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Background PKHD1 is the main genetic cause of autosomal recessive polycystic kidney disease (ARPKD), a hereditary hepato-renal fibrocystic disorder which is the most important cause of end-stage renal disease during early childhood. ARPKD can also present in adulthood with milder phenotypes. In this study, we describe a 24-year-old woman with atypical polycystic kidney, no family history of renal disease and no obvious extra-renal manifestations who was referred for genetic investigation. Methods We used a combination of next generation sequencing, Sanger sequencing and RNA and microscopy studies performed on urine-derived renal epithelial cells (URECs) to provide a genetic diagnosis of ARPKD. Results A next generation sequencing panel of cystic ciliopathy genes allowed the identification of two heterozygous sequence changes in PKHD1 (c.6900C>T; p.(Asn2300=) and c.7964A>C; p.(His2655Pro)). The pathogenicity of the synonymous PKHD1 variant is not clear and requires RNA studies, which cannot be carried out efficiently on RNA extracted from proband blood, due to the low expression levels of PKHD1 in lymphocytes. Using URECs as a source of kidney-specific RNA, we show that PKHD1 is alternatively spliced around exon 43, both in control and proband URECs. The variant p.(Asn2300=) shifts the expression ratio in favour of a shorter, out-of-frame transcript. To further study the phenotypic consequence of these variants, we investigated the ciliary phenotype of patient URECs, which were abnormally elongated and presented multiple blebs along the axoneme. Conclusions We confirm the power of URECs as a tool for functional studies on candidate variants in inherited renal disease, especially when the expression of the gene of interest is restricted to the kidney and we describe, for the first time, ciliary abnormalities in ARPKD patient cells.

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Splicing defects caused by exonic mutations inPKD1as a new mechanism of pathogenesis in autosomal dominant polycystic kidney disease

Cited by 23 publications

References 55 publications

Somatic Mutations in Renal Cyst Epithelium in Autosomal Dominant Polycystic Kidney Disease

Somatic Mutations in Renal Cyst Epithelium in Autosomal Dominant Polycystic Kidney Disease

Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease

Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles

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