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

Suarez-Artiles, Lorena; Perdomo‐Ramirez, Ana; Ramos-Trujillo, Elena; Claverie-Martı́n, Félix

doi:10.3390/genes9010015

Cited by 23 publications

(12 citation statements)

References 63 publications

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“…The pathogenicity was finally highlighted thanks to mRNA analysis on testis tissue which found aberrant splicing with exon 5 skipping. The exact mechanism of exon skipping remains unknown, even though we suspect modification of Exonic Sequence Enhancer (ESE) which could disturb splicing as it has already been reported for other exonic mutations ( 28 ). This exon skipping should lead to a frameshift and create a premature stop codon downstream (r.830_990del, p.Ala277Aspfs * 11), activating NMD responsible for degrading this allele.…”

Section: Discussionmentioning

confidence: 82%

Aberrant Splicing Is the Pathogenicity Mechanism of the p.Glu314Lys Variant in CYP11A1 Gene

et al. 2018

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Context: The cholesterol side chain cleavage enzyme (CYP11A1) catalyzes the conversion of cholesterol to pregnenolone, the first rate-limiting step of steroidogenesis. CYP11A1 mutations are associated with primary adrenal insufficiency (PAI) as well as disorders of sex development (DSD) in 46,XY patients.Objective: To define the pathogenicity mechanism for the p.Glu314Lys variant, previously reported, and found in four additional patients with CYP11A1 deficiency.Subjects and Methods: DNA of four patients presenting with delayed PAI and/or 46,XY DSD were studied by Sanger or Massively Parallel sequencing. Three CYP11A1 mutations were characterized in vitro and in silico, and one by mRNA analysis on testicular tissue.Results: All patients were compound heterozygous for the previously described p.Glu314Lys variant. In silico studies predicted this mutation as benign with no effect on splicing but mRNA analysis found that it led to incomplete exon 5 skipping. This mechanism was confirmed by minigene experiment. The protein carrying this mutation without exon skipping should conserve almost normal activity, according to in vitro studies. Two other mutations found in trans, the p.Arg120Gln and p.Arg465Trp, had similar activity compared to negative control, consistent with the in silico studies.Conclusions: We provide biological proof that the p. Glu314Lys variant is pathogenic due to its impact on splicing and seems responsible for the moderate phenotype of the four patients reported herein. The present study highlights the importance of considering the potential effect of a missense variant on splicing when it is not predicted to be disease causing.

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Section: Discussionmentioning

confidence: 82%

Aberrant Splicing Is the Pathogenicity Mechanism of the p.Glu314Lys Variant in CYP11A1 Gene

et al. 2018

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“…Therefore, it is necessary to study the effects of exonic variants in the SLC12A3 gene of GS on potential splicing, with the discovery of novel variants. In the absence of RNA samples to study alternative splicing, minigene analysis, the effectiveness of which has been confirmed by different studies (Fraile-Bethencourt et al, 2019;Suarez-Artiles, Perdomo-Ramirez, Ramos-Trujillo, & Claverie-Martin, 2018;Takeuchi et al, 2015;Tournier et al, 2008), is still the most direct and credible experimental approach to assess whether a variant influences recognition of an exon and potentially causes phenotypic changes (Bao, Moakley, & Zhang, 2019). In previous studies, we have used this approach to assess the consequences on pre-mRNA splicing of presumed mutations associated with different diseases (Han et al, 2019;Wang et al, 2020;Zhang et al, 2021).…”

Section: Discussionmentioning

confidence: 84%

Minigene splicing assays reveal new insights into exonic variants of the SLC12A3 gene in Gitelman Syndrome.

Shi

Liu

Zhang

et al. 2021

Preprint

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Gitelman syndrome (GS) is a kind of salt-losing tubular disease, most of which is caused by SLC12A3 gene variants, and missense variants account for the majority. Recently, the phenomenon of exon skipping, in which exonic variants disrupt normal pre-mRNA splicing, has been related to a variety of diseases. The purpose of this study was to identify the effect of previously presumed missense SLC12A3 variants on pre-mRNA splicing using bioinformatics tools and minigenes. The results revealed that, among ten candidate variants, six variants (c.602G>A, c.602G>T, c.1667C>T, c.1925G>A, c.2548G>C and c.2549G>C) led to complete or incomplete exon skipping by affecting exonic splicing regulatory elements and/or disturbing canonical splice sites. It is worth mentioning that this is the largest study on pre-mRNA splicing of SLC12A3 exonic variants. In addition, our study emphasizes the importance of detecting splicing function at the mRNA level in GS and indicates that minigene analysis is a valuable tool for splicing functional assays of variants in vitro.

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“…The literature reveals that the exonic sequences are involved in the regulation of pre-mRNA splicing in addition to their protein-coding potential (53)(54)(55). Because exons contain cis-regulatory elements, such as exonic splicing enhancers (ESEs) and exonic splicing silencers (ESSs) which promote or inhibit the recognition of the neighboring splice sites, respectively (53).…”

Section: Discussionmentioning

confidence: 99%

Identification of splicing defects caused by novel exonic mutations in LEF1 in Sudanese B- chronic lymphocytic leukemia patients: computational approach

Eltayeb

Hassan

Idris

et al. 2022

Preprint

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BackgroundLymphocyte enhancer factor-1 (LEF-1) is a member of the LEF-1/TCF family of transcription factors that are critically involved in canonical Wnt/β-catenin Signaling to regulate B Lymphocyte proliferation and survival. Alteration of LEF1 expression and function leads to leukemogenesis as well as other several neoplasms.Aimsto identify mutations in exons two and three of the LEF1 among B-CLL Sudanese patients. Also, to functionally analyze the detected SNPs using different in silico tools.Materials and methodsImmuno-phenotype for the detection of B cells CD5 and CD19 markers was performed on 128 B-CLL Sudanese patients by using a flow cytometry technique. DNA extraction, conventional PCR, and Sanger sequencing were applied to the LEF1 gene. Also, we performed a mutational analysis for identified SNPs using bioinformatics tools.ResultsA positive CD5 & CD19 expression was found in B-CLL patients. No mutation was observed in exon two. While four mutations were observed in exon three; two of them were not reported in previous studies. Interestingly, splicing analysis predicted that these mutations could lead to splicing defects in LEF1 pre-mRNA due to their potential effects on splicing regulatory elements (i.e. ESE).Conclusionthe two mutations Pro134Pro and Ile135Asn (novel mutation) were detected in all enrolled CLL patients and they could be used as diagnostic and/or prognostic markers for CLL. Therefore, further in vitro and in vivo functional studies with a large sample size are required to verify the splicing effect of the detected mutations in LEF1 pre-mRNA.

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

Cited by 23 publications

References 63 publications

Aberrant Splicing Is the Pathogenicity Mechanism of the p.Glu314Lys Variant in CYP11A1 Gene

Aberrant Splicing Is the Pathogenicity Mechanism of the p.Glu314Lys Variant in CYP11A1 Gene

Minigene splicing assays reveal new insights into exonic variants of the SLC12A3 gene in Gitelman Syndrome.

Identification of splicing defects caused by novel exonic mutations in LEF1 in Sudanese B- chronic lymphocytic leukemia patients: computational approach

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