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X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

2015; Springer Nature; Volume: 21; Issue: 1 Linguagem: Inglês

10.1038/mp.2014.193

1476-5578

Hao Hu, Stefan A. Haas, Jamel Chelly, Hilde Van Esch, Martine Raynaud, Arjan P.M. de Brouwer, Stefanie Weinert, Guy Froyen, Suzanna G.M. Frints, Frédéric Laumonnier, Tomasz Żemojtel, Michael I. Love, Hugues Richard, A-K Emde, Melanie Bienek, Corinna Jensen, M Hambrock, Utz Fischer, Claudia Langnick, Mirjam Feldkamp, W.M. Wissink-Lindhout, Nicolas Lebrun, L. Castelnau, J. Rucci, Rodrick Montjean, Olivier Dorseuil, Pierre Billuart, Till Stuhlmann, M Shaw, Mark Corbett, Alison Gardner, Saffron A.G. Willis‐Owen, Chuan Tan, Kathryn Friend, Stefanie Belet, Kees E. P. van Roozendaal, M Jimenez-Pocquet, M.‐P. Moizard, Nathalie Ronce, Ren Sun, Sean O’Keeffe, R Chenna, Alena van Bömmel, Jonathan Göke, Anna Hackett, Michael Field, Louise Christie, Jackie Boyle, Eric Haan, John W. Nelson, Gillian Turner, Gareth Baynam, Gabriele Gillessen‐Kaesbach, Ulrich Müller, Daniela Steinberger, Bartłomiej Budny, Magdalena Badura‐Stronka, Anna Latos‐Bieleńska, Lilian Bomme Ousager, Peter Wieacker, Germán Rodríguez Criado, M.-L. Bondeson, Göran Annerén, Andreas Dufke, Monika Cohen, Lionel Van Maldergem, C. Vincent‐Delorme, Bernard Échenne, Brigitte Simon‐Bouy, Tjitske Kleefstra, Marjolein H. Willemsen, J-P. Fryns, Koenraad Devriendt, Reinhard Ullmann, Martin Vingron, Klaus Wrogemann, Thomas F. Wienker, Andreas Tzschach, Hans van Bokhoven, Jozef Gécz, Thomas J. Jentsch, W. Chen, H‐H Ropers, Vera M. Kalscheuer,

RNA modifications and cancer

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4−/− mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.