Molecular and in silico analyses of the full-length isoform of usherin identify new pathogenic alleles in Usher type II patients

Abstract

The usherin gene (USH2A) has been screened for mutations causing Usher syndrome type II (USH2). Two protein isoforms have been identified: a short isoform of 1,546 amino acids and a more recently recognized isoform extending to 5,202 amino acids. We have screened the full length by genomic sequencing. We confirm that many mutations occur in the exons contributing solely to the longer form. USH2 is an autosomal recessive disorder and, in contrast to previous studies, both mutations were identified in 23 patients and a single mutation in 2 out of 33 patients. A total of 34 distinct mutated alleles were identified, including one complex allele with three variants and another with two. A total of 27 of these are novel, confirming that most mutations in usherin are private. Many of the mutations will lead to prematurely truncated protein but as there are a substantial number of missense variants, we have used in silico analysis to assess their pathogenicity. Evidence that they are disease-causing has been produced by protein alignments and three-dimensional (3D) structural predictions when possible. We have identified a previously unrecognized cysteine rich structural domain, containing 12 dicysteine repeats, and show that three missense mutations result in the loss of one of a pair of the defining cysteine-cysteine pairs.

Partial USH2A deletions contribute to Usher syndrome in Denmark

“…A deletion of exons 22-24 in USH2A has been described previously by Baux et al 28 and deletion breakpoints that differs only by 2 bp (AT) compared with the present case was submitted to https://grenada.lumc.nl/LOVD2/Usher_montpellier/home.php?select_db = USH2A in 2012 (DB-ID USH2A_00095; Patient data: #0000067). In two apparently unrelated patients, 70353 and 55555, we identified a deletion of exons 4-10 with Mb on one of the two alleles with very high probability is identical by decent, and thus inherited from a common ancestor.…”

Comprehensive and Rapid Genotyping of Mutations and Haplotypes in Congenital Bilateral Absence of the Vas Deferens and Other Cystic Fibrosis Transmembrane Conductance Regulator-Related Disorders

“…The single condition touchdown amplification/ sequencing strategy is now widely used in our laboratory, eg, for the comprehensive genotyping of eight genes in the Usher syndrome, for which up to 250 amplicons are analyzed. 28,29 The new fluorescent, rapid, and reliable method that we report here for the determination of alleles and haplotypes at locus IVS8-(TG)mTn will also facilitate the genotyping of the sequences that modulate the splicing efficiency of exon 9 in the mRNA and/or are major determinants of the penetrance of the T5 allele in CBAVD. The importance of IVS8-(TG)mT5 determination is supported by an international collaborative study providing evidence that the odds of pathogenicity are 28 and 34 times greater for (TG)12T5 and (TG)13T5, respectively, than for (TG)11T5.…”

Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II

“…Since the identification of the USH2A gene (Eudy et al, 1998) several research groups have scanned the USH2A gene in USH2 patients from various ethnic backgrounds (Eudy et al, 1998;Liu et al, 1999;Adato et al, 2000;Dreyer et al, 2000;Rivolta et al, 2000;Weston et al, 2000;Leroy et al, 2001;Najera et al, 2002;Bernal et al, 2003;Aller et al, 2004;Ouyang et al, 2004;Pennings et al, 2004;Seyedahmadi et al, 2004;Maubaret et al, 2005;Aller et al, 2006;Cremers et al, 2007;Kaiserman et al, 2007;Baux et al, 2007). Such investigations are a prerequisite in order to provide an accurate and unambiguous molecular diagnosis for patients with Usher syndrome type II.…”

“…The identification of additional 51 exons (van Wijk et al, 2004) as well as a novel alternatively spliced exon located after exon 70 (Adato et al, 2005) have provided obvious candidates for further mutation scanning in order to solve the incomplete molecular diagnosis of Usher syndrome type IIa. In fact, recently altogether 39 putative pathogenic mutations situated in exons 22-72 were recently reported (van Wijk et al, 2004;Aller et al, 2006, Baux et al, 2007.…”