REPORT Mutations in CDC14A, Encoding a Protein Phosphatase Involved in Hair Cell Ciliogenesis, Cause Autosomal-Recessive Severe to Profound Deafness Sedigheh Delmaghani, 1,2,3 Asadollah Aghaie, 2,3,4 Yosra Bouyacoub, 5,6 Hala El Hachmi, 7 Crystel Bonnet, 2,3,4 Zied Riahi, 2,3,4 Sebastien Chardenoux, 1,2,3 Isabelle Perfettini, 1,2,3 Jean-Pierre Hardelin, 1,2,3 Ahmed Houmeida, 7 Philippe Herbomel, 3,8,9 and Christine Petit 1,2,3,4,10, * By genetic linkage analysis in a large consanguineous Iranian family with eleven individuals affected by severe to profound congenital deafness, we were able to define a 2.8 Mb critical interval (at chromosome 1p21.2-1p21.1) for an autosomal-recessive nonsyndromic deafness locus (DFNB). Whole-exome sequencing allowed us to identify a CDC14A biallelic nonsense mutation, c.1126C>T (p.Arg376*), which was present in the eight clinically affected individuals still alive. Subsequent screening of 115 unrelated individuals affected by severe or profound congenital deafness of unknown genetic cause led us to identify another CDC14A biallelic nonsense mu- tation, c.1015C>T (p.Arg339*), in an individual originating from Mauritania. CDC14A encodes a protein tyrosine phosphatase. Immu- nofluorescence analysis of the protein distribution in the mouse inner ear showed a strong labeling of the hair cells’ kinocilia. By using a morpholino strategy to knockdown cdc14a in zebrafish larvae, we found that the length of the kinocilia was reduced in inner-ear hair cells. Therefore, deafness caused by loss-of-function mutations in CDC14A probably arises from a morphogenetic defect of the auditory sensory cells’ hair bundles, whose differentiation critically depends on the proper growth of their kinocilium. Almost 90% of all cases of nonsyndromic, severe to pro- found congenital deafness display an autosomal-recessive mode of transmission (DFNB forms). Sixty genes have already been identified, but many others remain to be discovered according to the much larger number of DFNB loci reported (Hereditary Hearing Loss website; see Web Resources). 1 With high-throughput sequencing techniques becoming available and the whole-exome sequencing approach in affected individuals, the pace of gene discovery has accelerated. Here we used a combi- nation of genetic linkage analysis and whole-exome sequencing to identify two different nonsense mutations in CDC14A (OMIM: 603504). Informed consent was obtained from all study partici- pants. Of the eight affected individuals still alive in a consanguineous Iranian family (Figure 1A), the six that could be tested for auditory function (V.1, V.6, V.8, V.14, V.15, and V.18), aged 21–69 years, all suffered from prelin- gual, severe to profound deafness of cochlear origin, as shown by the markedly increased detection thresholds in pure-tone audiometry (both with air- and bone-trans- mitted sounds) and auditory brainstem responses and by the absence of transient evoked otoacoustic emissions (Figure 1B and data not shown). 2,3 Otoscopic examination and tympanometry with acoustic reflex testing did not show evidence of a conductive hearing impairment. General clinical examination did not find any feature of syndromic deafness, and normal age of walking onset allowed us to exclude severe congenital vestibular dysfunction. Genetic linkage analysis was carried out on 21 family members. SNP array analysis (700k Illumina OmniExpress-12) and homozygosity mapping defined a single critical region of 2.8 Mb between rs7537296 and rs950060 at chromosome 1p21.2–1p21.1 (Figure 1A). This locus (DFNB105 [OMIM: 616958]) does not match any of the previously reported human deafness loci, and the murine syntenic region at chromosome 3qF3–3qG1 does not contain a reported deafness locus either. We then carried out whole-exome sequencing in three affected individuals (V.6, V.8, and V.14) and identified a biallelic nonsense mutation in exon 11 of CDC14A (cell division cycle 14A; NCBI ID 8556), c.1126C>T (p.Arg376*) (NCBI RefSeq: NM_033312.2). Incidentally, one nonsynonymous and six synonymous sequence variants were also found in the critical interval; all of these were present in HapMap, 1000 Genomes, and Exome Variant Server databases. Sanger sequencing of CDC14A exon 11 confirmed the presence of the biallelic nonsense mutation in the eight clinically affected individuals only. In addition, all tested clinically unaffected individuals except three (V.4, V.10, and V.17) carried the mutation at the heterozygous state, as expected from the genetic linkage analysis (Figure 1A). This mutation was absent from the 1000 Genomes and Exome Variant Server databases and was not detected in 1 Unite ´ de Ge ´ne ´tique et Physiologie de l’Audition, Institut Pasteur, 75015 Paris, France; 2 UMRS 1120, Institut National de la Sante ´ et de la Recherche Me ´d- icale, 75015 Paris, France; 3 Sorbonne Universite ´s, Universite ´ Pierre et Marie Curie, Complexite ´ du Vivant, 75005 Paris, France; 4 Syndrome de Usher et Autres Atteintes Re ´tino-Cochle ´aires, Institut de la Vision, 75012 Paris, France; 5 Institut Pasteur de Tunis, LR11IPT05, Biomedical Genomics and Oncoge- netics Laboratory, Tunis 1002, Tunisia; 6 Universite ´ de Monastir, Institut Supe ´rieur de Biotechnologie, BP 56 Monastir 5000, Tunisia; 7 Laboratoire de Biochimie et Biologie Mole ´culaire, Faculte ´ des Sciences et Techniques, Nouakchott 5026, Mauritania; 8 Unite ´ des Macrophages et De ´veloppement de l’Immunite ´, Institut Pasteur, 75015 Paris, France; 9 UMR 3738, Centre National de la Recherche Scientifique, 75015 Paris, France; 10 Colle `ge de France, 75005 Paris, France *Correspondence: christine.petit@pasteur.fr http://dx.doi.org/10.1016/j.ajhg.2016.04.015. 1266 The American Journal of Human Genetics 98, 1266–1270, June 2, 2016 Ó 2016 American Society of Human Genetics.