A mutation in OTOF, encoding otoferlin, a FER-1-like protein, causes DFNB9, a nonsyndromic form of deafness

International audienceUsing a candidate gene approach, we identified a novel human gene, OTOF, underlying an autosomal recessive, nonsyndromic prelingual deafness, DFNB9. The same nonsense mutation was detected in four unrelated affected families of Lebanese origin. OTOF is the second member of a mammalian gene family related to Caenorhabditis elegans fer-1. It encodes a predicted cytosolic protein (of 1,230 aa) with three C2 domains and a single carboxy-terminal transmembrane domain. The sequence homologies and predicted structure of otoferlin, the protein encoded by OTOF, suggest its involvement in vesicle membrane fusion. In the inner ear, the expression of the orthologous mouse gene, mainly in the sensory hair cells, indicates that such a role could apply to synaptic vesicles

Molecular Genetics of the Usher Syndrome in Lebanon: Identification of 11 Novel Protein Truncating Mutations by Whole Exome Sequencing

<div><p>Background</p><p>Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II.</p><p>Methods</p><p>Whole exome sequencing followed by expanded familial validation by Sanger sequencing.</p><p>Results</p><p>We identified disease-causing mutations in all the analyzed patients in four USH genes, <i>MYO7A</i>, <i>USH2A</i>, <i>GPR98</i> and <i>CDH23</i>. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in <i>GPR98</i>.</p><p>Conclusion</p><p>Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.</p></div

Summary of the identified mutations in the four Usher genes.

<p>Summary of the identified mutations in the four Usher genes.</p

Exome sequencing coverage, conservation of one mutation in <i>USH2A</i>, and diagram of the 14,042 bp deletion in <i>GPR98</i>.

<p><b>A.</b> Image showing the coverage of the reads at >30X and >5X of the 10 Usher genes in the 11 patients studied using whole exome sequencing. <b>B.</b> Conservation of the Arginine (R) at amino acid 2894 in USH2A in different species is shown. <b>C.</b> Diagram of the rearrangement deleting exon 83 of <i>GPR98</i> in family USHLB2. Arrows indicate the proximal and distal breakpoints of the 14,042 bp deletion. Horizontal arrow shows the AluSC8 repeat overlapping the proximal breakpoint. The 17 bp insertion is shown in a rectangle between the flanking sequences. Primers used for amplifying the 5.5 kb fragment are shown. <b>D.</b> Shows the 5.5 kb fragment amplified in the two patients III-2 and III-3 from family USHLB2. The fragment was not amplified in the two control samples due to its large size.</p

Clinical examination.

<p><b>A.</b> Posterior pole of the right eye of patient USHLB13-II.3 showing atrophy of the retina and choroid with pigment spicules (arrows) anterior to the arcades. <b>B.</b> Spectral domain optical coherence tomography of the right eye of the same patient showing significant thinning of the retina (space delineated by double arrow) compared to normal controls.</p