De Novo Mutations in CHD4, an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms.
Chromodomain helicase DNA-binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler involved in epigenetic regulation of gene transcription, DNA repair, and cell cycle progression. Also known as Mi2β, CHD4 is an integral subunit of a well-characterized histone deacetylase complex. Here we report five individuals with de novo missense substitutions in CHD4 identified through whole-exome sequencing and web-based gene matching. These individuals have overlapping phenotypes including developmental delay, intellectual disability, hearing loss, macrocephaly, distinct facial dysmorphisms, palatal abnormalities, ventriculomegaly, and hypogonadism as well as additional findings such as bone fusions. The variants, c.3380G>A (p.Arg1127Gln), c.3443G>T (p.Trp1148Leu), c.3518G>T (p.Arg1173Leu), and c.3008G>A, (p.Gly1003Asp) (GenBank: NM_001273.3), affect evolutionarily highly conserved residues and are predicted to be deleterious. Previous studies in yeast showed the equivalent Arg1127 and Trp1148 residues to be crucial for SNF2 function. Furthermore, mutations in the same positions were reported in malignant tumors, and a de novo missense substitution in an equivalent arginine residue in the C-terminal helicase domain of SMARCA4 is associated with Coffin Siris syndrome. Cell-based studies of the p.Arg1127Gln and p.Arg1173Leu mutants demonstrate normal localization to the nucleus and HDAC1 interaction. Based on these findings, the mutations potentially alter the complex activity but not its formation. This report provides evidence for the role of CHD4 in human development and expands an increasingly recognized group of Mendelian disorders involving chromatin remodeling and modification.
Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Karin
K
Weiss
Department of Genetics, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands.
Paulien A
PA
Terhal
Pediatric Genetics, Schneider Children Medical Center of Israel, Petah Tikva 49202, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
Lior
L
Cohen
Rosalind and Morris Goodman Cancer Research Center, McGill University, and Department of Medicine, McGill University Health Center, Montreal, QC H3G 2M1, Canada.
Michael
M
Bruccoleri
Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK.
Melita
M
Irving
Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Ariel F
AF
Martinez
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Jill A
JA
Rosenfeld
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Keren
K
Machol
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Yaping
Y
Yang
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Pengfei
P
Liu
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Magdalena
M
Walkiewicz
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Joke
J
Beuten
Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Natalia
N
Gomez-Ospina
Department of Pediatric Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA.
Katrina
K
Haude
Department of Pediatric Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA.
Chin-To
CT
Fong
Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Gregory M
GM
Enns
Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Jonathan A
JA
Bernstein
Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Judith
J
Fan
Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Garrett
G
Gotway
Rosalind and Morris Goodman Cancer Research Center, McGill University, and Department of Medicine, McGill University Health Center, Montreal, QC H3G 2M1, Canada.
Mohammad
M
Ghorbani
Department of Genetics, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands.
Koen
K
van Gassen
Department of Genetics, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands; Center for Molecular Medicine, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands.
Glen R
GR
Monroe
Department of Genetics, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands; Center for Molecular Medicine, Utrecht University Medical Center, Utrecht 3584 CX, the Netherlands.
Gijs
G
van Haaften
Pediatric Genetics, Schneider Children Medical Center of Israel, Petah Tikva 49202, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva 49100, Israel.
Lina
L
Basel-Vanagaite
Rosalind and Morris Goodman Cancer Research Center, McGill University, and Department of Medicine, McGill University Health Center, Montreal, QC H3G 2M1, Canada.
Xiang-Jiao
XJ
Yang
Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Montreal, QC H3T 1C4, Canada. Electronic address: p.campeau@umontreal.ca.
Philippe M
PM
Campeau
Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA. Electronic address: mmuenke@nhgri.nih.gov.
Maximilian
M
Muenke
D000015:Abnormalities, Multiple / Q000235:genetics; D000255:Adenosine Triphosphate / Q000378:metabolism*; D000293:Adolescent; D000818:Animals; D001324:Autoantigens / Q000235:genetics*; D002467:Cell Nucleus / Q000378:metabolism; D002648:Child; D002675:Child, Preschool; D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D004265:DNA Helicases / Q000235:genetics; D002658:Developmental Disabilities / Q000235:genetics; D059472:Exome / Q000235:genetics; D005145:Face / Q000002:abnormalities; D005260:Female; D006228:Hand Deformities, Congenital / Q000235:genetics; D034381:Hearing Loss / Q000235:genetics; D056284:Histone Deacetylase 1 / Q000378:metabolism; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics*; D008297:Male; D058627:Megalencephaly / Q000235:genetics; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex / Q000235:genetics*; D051379:Mice; D008844:Micrognathism / Q000235:genetics; D020125:Mutation, Missense / Q000235:genetics*; D009333:Neck / Q000002:abnormalities; D009687:Nuclear Proteins / Q000235:genetics; D013577:Syndrome; D014157:Transcription Factors / Q000235:genetics
D001324:Autoantigens; C115323:CHD4 protein, human; D009687:Nuclear Proteins; D014157:Transcription Factors; D000255:Adenosine Triphosphate; C110550:HDAC1 protein, human; D056284:Histone Deacetylase 1; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex; C084108:SMARCA4 protein, human; C509277:Mi-2beta protein, mouse; D004265:DNA Helicases