Decoding Abnormal Splicing Code in Human Diseases

Ohno, Kinji; Rahman, Mohammad Alinoor; Nasrin, Farhana; Matsubara, Akio

doi:10.15406/jig.2015.02.00016

Cited by 4 publications

(2 citation statements)

References 192 publications

(90 reference statements)

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“…Mature mRNA comprises only the coding sequence because introns are removed from the transcript during the splicing process (25). In most situations, adjacent pre-mRNA regulatory sequences, called ESEs or ESSs, influence splice site recognition and selection, which can have positive or negative effects on splice site utilization.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants

et al. 2022

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【Background】 Alport syndrome is an inherited disorder characterized by progressive renal disease, variable sensorineural hearing loss, and ocular abnormalities. Although many pathogenic variants in COL4A3 and COL4A4 have been identified in autosomal Alport syndrome cases, synonymous mutations in these genes have rarely been identified. 【Methods】 We conducted in silico splicing analysis using the Human Splicing Finder (HSF) and Alamut to predict splicing domain strength and disruption of the sites. Furthermore, we performed in vitro splicing assays using minigene constructs and mRNA analysis of patient samples to determine the pathogenicity of 4 synonymous variants detected in 4 patients with suspected autosomal dominant Alport syndrome (COL4A3 (c.693G>A (p.Val231=) and COL4A4 (c.1353C>T (p.Gly451=), c.735G>A (p.Pro245=), and c.870G>A (p.Lys290=))). 【Results】 Both in vivo and in vitro splicing assays showed exon skipping in 2 out of the 4 synonymous variants identified (c.735G>A and c.870G>A in COL4A4). Prediction analysis of wild-type and mutated COL4A4 sequences using the HSF and Alamut suggested that these 2 variants may lead to the loss of binding sites for several splicing factors, e.g., in acceptor sites and exonic splicing enhancers. The other 2 variants did not induce aberrant splicing. 【Conclusions】 This study highlights the pitfalls of classifying the functional consequences of variants by a simple approach. Certain synonymous variants, although they do not alter the amino acid sequence of the encoded protein, can dramatically affect pre-mRNA splicing as shown in 2 of our cases. Our findings indicate that transcript analysis should be carried out to evaluate synonymous variants detected in autosomal dominant Alport syndrome cases.

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Section: Discussionmentioning

confidence: 99%

Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants

et al. 2022

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“…As can be expected, this process is regulated and involves donor and acceptor splice sites, branch point and polypyrimidine tract sequences, splicing silencers/enhancers and other regulatory elements. Donor and acceptor sites are highly conserved and contain GT and AG motifs at intronic ends [21,22]. Any errors during splicing will lead to improper intron removal and can alter the reading frame or activate cryptic splice sites.…”

Section: Discussionmentioning

confidence: 99%

Novel splicing (c.6529-1G>T) and missense (c.1667G>A) mutations causing factor V deficiency

Maharaj¹,

Ayala

et al. 2021

Blood Coagulation &Amp; Fibrinolysis

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Congenital factor V deficiency (FVD) is a rare bleeding disorder. In this study, we investigated the genetic basis in an African American patient with factor V activity 3%. Custom sequence capture and targeted next-generation (NGS) sequencing of the F5 gene were undertaken followed by PCR and Sanger sequencing. Two novel variants were identified. In silico analyses correlated clinically with the patient's factor V activity and hemorrhagic tendency. A review of the literature regarding these genomic alterations is presented. We described two novel mutations causing moderate FVD. The first, Chr1:g.169483698C>A with cDNA change (F5):c.6529-1G>T, occurred in a conserved nucleotide at the canonical acceptor splice site of intron 24. The second, Chr1:g.169515775C>T with cDNA change (F5):c.1667G>A, was a missense variant of exon 11, affecting a highly conserved amino acid in the A2 domain. Further research into the mechanisms of F5 mutations leading to FVD and residual factor V expression are needed.

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Exonic Deletions and Deep Intronic Variants of the SLC26A4 Gene Contribute to the Genetic Diagnosis of Unsolved Patients With Enlarged Vestibular Aqueduct

Tian,

Liu,

et al. 2024

Human Mutation

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Enlarged vestibular aqueduct (EVA) is a frequently occurring inner ear malformation that associates with sensorineural hearing loss (SNHL), with SLC26A4 being the responsible gene. Based on multiplex PCR enrichment and sequencing of the exonic and flanking regions of the SLC26A4 gene, we developed a panel specifically for EVA and found that up to 95% of EVA patients in our Chinese cohorts carried biallelic SLC26A4 pathogenic variants (M2). In this study, we tried to investigate the genetic etiology of 13 previously undiagnosed EVA patients with monoallelic (M1) or none (M0) SLC26A4 variant using a stepwise approach, including copy number variation (CNV) analysis of multiplex PCR enrichment and next‐generation sequencing data, single‐molecule real‐time (SMRT) sequencing of the whole SLC26A4 gene, whole exome sequencing (WES), and whole genome sequencing (WGS). CNV analysis revealed deletions in Exons 1–3, Exons 5–6, and Exons 9–10 of the SLC26A4 gene in seven patients, and SMRT sequencing identified the same heterozygous deep intronic variant (NM_000441.2:c.304+941C>T) in two patients, resulting in a final diagnosis in 9/13 patients. Notably, the variants of Exons 9–10 deletion and c.304+941C>T have not been reported previously. We further showed that the variant c.304+941C>T led to the exonization of partial AluSz6 element (126 bp) where the variant is located through sequencing of the mRNA extracted from the blood of a heterozygous variant carrier. In conclusion, our stepwise approach improved the diagnosis rate of EVA, expanded the mutational spectrum of the SLC26A4 gene, and highlighted the contribution of exonic deletions and deep intronic variants to EVA.

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Decoding Abnormal Splicing Code in Human Diseases

Cited by 4 publications

References 192 publications

Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants

Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants

Novel splicing (c.6529-1G>T) and missense (c.1667G>A) mutations causing factor V deficiency

Exonic Deletions and Deep Intronic Variants of the SLC26A4 Gene Contribute to the Genetic Diagnosis of Unsolved Patients With Enlarged Vestibular Aqueduct

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