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Abstract
Chromatin remodeling is of crucial importance during brain development. Pathogenic alterations of several chromatin remodeling ATPases have been implicated in neurodevelopmental disorders. We describe an index case with a de novo missense mutation in CHD3, identified during whole genome sequencing of a cohort of children with rare speech disorders. To gain a comprehensive view of features associated with disruption of this gene, we use a genotype-driven approach, collecting and characterizing 35 individuals with de novo CHD3 mutations and overlapping phenotypes. Most mutations cluster within the ATPase/helicase domain of the encoded protein. Modeling their impact on the three-dimensional structure demonstrates disturbance of critical binding and interaction motifs. Experimental assays with six of the identified mutations show that a subset directly affects ATPase activity, and all but one yield alterations in chromatin remodeling. We implicate de novo CHD3 mutations in a syndrome characterized by intellectual disability, macrocephaly, and impaired speech and language.
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1 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
2 CHU Sainte-Justine Research Center, Montreal, Canada
3 National Institute of Environmental Health Sciences, Research Triangle Park, USA
4 Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
5 Division of Genetics and Genomics, Boston Children’s Hospital, Boston, USA
6 Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, USA
7 Department of Medical Genetics, Massachusetts General Hospital, Boston, USA
8 Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
9 Nemours Childrens Clinic, Orlando, USA
10 Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, USA
11 Valley Children’s Hospital, Madera, USA
12 British Columbia Children’s Hospital Research Institute, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada
13 Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
14 Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust (Heavitree), Exeter, UK
15 Division of Genetics, Department of Medicine, University of Tennessee Medical Center, Knoxville, USA
16 Greenwood Genetic Center, Greenwood, USA
17 GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris ; Department of Medical Genetics and Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, France
18 AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France; Groupe de Recherche Clinique (GRC) ‘déficience intellectuelle et autisme’ UPMC, Paris, France
19 AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France; Groupe de Recherche Clinique (GRC) ‘déficience intellectuelle et autisme’ UPMC, Paris, France; INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
20 AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
21 GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department Child Neurology and Reference Center for Neuromuscular Diseases “Nord/Est/Ile-de-France”, FILNEMUS, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, France
22 GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, Paris, France
23 Clinical Genetics Division, Virginia Commonwealth University Health System, Richmond, USA
24 Clinical Genetics Department, University Medical Center Groningen, Groningen, The Netherlands
25 Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
26 Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, Republic of Korea
27 Oxford University Hospitals NHS Foundation Trust, Oxford, UK
28 GeneDx, Gaithersburg, USA
29 Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
30 Northwell Health, Division of Medical Genetics and Genomics, Great Neck, USA
31 Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
32 University Hospitals Bristol, Department of Clinical Genetics, St Michael’s Hospital, Bristol, UK
33 Department of Clinical Genetics, University Children’s Hospital, Paracelsus Medical University, Salzburg, Austria
34 Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria
35 Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria; Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
36 Communication Sciences and Disorders, Augustana College, Rock Island, USA
37 Department of Neurology, Mayo Clinic, Rochester, USA
38 Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
39 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
40 MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
41 Department of Engineering Science, University of Oxford, Parks Road, Oxford, UK
42 Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wiltshire, UK; Faculty of Medicine, University of Southampton, Southampton, UK
43 South West Thames Regional Genetics Centre, St George’s Healthcare NHS Trust, St George’s, University of London, London, UK
44 Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK; Department of Clinical Genetics, Block 12, Glan Clwyd Hospital, Rhyl, Denbighshire, UK
45 East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
46 Sheffield Regional Genetics Services, Sheffield Children’s NHS Trust, Sheffield, UK
47 Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHSFoundation Trust, Manchester Academic Health Science Centre, Manchester, UK
48 North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London, UK
49 North of Scotland Regional Genetics Service, NHS Grampian, Department of Medical Genetics Medical School, Aberdeen, UK
50 East of Scotland Regional Genetics Service, Human Genetics Unit, Pathology Department, NHS Tayside, Ninewells Hospital, Dundee, UK
51 Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
52 North West Thames Regional Genetics Centre, North West London Hospitals NHS Trust, The Kennedy Galton Centre, Northwick Park and St Mark’s NHS Trust Watford Road, Harrow, UK
53 Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford, UK
54 West Midlands Regional Genetics Service, Birmingham Women’s NHS Foundation Trust, Birmingham Women’s Hospital, Edgbaston, Birmingham, UK
55 Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, UK
56 Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, UK
57 Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Clinical Genetics Department, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
58 South East Thames Regional Genetics Centre, Guy’s and St Thomas’ NHS Foundation Trust, Guy’s Hospital, London, UK
59 Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary (NHS Trust), Leicester, UK
60 Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, The Gables, Nottingham, UK
61 West of Scotland Regional Genetics Service, NHS Greater Glasgow and Clyde, Institute of Medical Genetics, Yorkhill Hospital, Glasgow, UK
62 Bristol Genetics Service (Avon, Somerset, Gloucs and West Wilts), University Hospitals Bristol NHS Foundation Trust, St Michael’s Hospital, St Michael’s Hill, Bristol, UK
63 Merseyside and Cheshire Genetics Service, Liverpool Women’s NHS Foundation Trust, Department of Clinical Genetics, Royal Liverpool Children’s Hospital Alder Hey, Liverpool, UK
64 National Centre for Medical Genetics, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
65 Department of Clinical Genetics, Block 12, Glan Clwyd Hospital, Rhyl, Denbighshire, Wales, UK
66 Nuffield Department of Obstetrics & Gynaecology, University of Oxford, Level 3, Women’s Centre, John Radcliffe Hospital, Oxford, UK; Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
67 The Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
68 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
69 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
70 Waseda University, Tokyo, Japan
71 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
72 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
73 Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
74 Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche Comté, Dijon, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d’Enfants, CHU Dijon et Université de Bourgogne, Dijon, France
75 Waisman Center, Phonology Project, Madison, USA
76 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
77 Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
78 CHU Sainte-Justine Research Center, Montreal, Canada; Sainte-Justine Hospital, University of Montreal, Montreal, Canada