De Novo Mutations in CHD4, an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms

Am J Hum Genet. 2016 Oct 6;99(4):934-941. doi: 10.1016/j.ajhg.2016.08.001. Epub 2016 Sep 8.


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.

MeSH terms

  • Abnormalities, Multiple / genetics
  • Adenosine Triphosphate / metabolism*
  • Adolescent
  • Animals
  • Autoantigens / genetics*
  • Cell Nucleus / metabolism
  • Child
  • Child, Preschool
  • Chromatin Assembly and Disassembly / genetics*
  • DNA Helicases / genetics
  • Developmental Disabilities / genetics
  • Exome / genetics
  • Face / abnormalities
  • Female
  • Hand Deformities, Congenital / genetics
  • Hearing Loss / genetics
  • Histone Deacetylase 1 / metabolism
  • Humans
  • Intellectual Disability / genetics*
  • Male
  • Megalencephaly / genetics
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex / genetics*
  • Mice
  • Micrognathism / genetics
  • Mutation, Missense / genetics*
  • Neck / abnormalities
  • Nuclear Proteins / genetics
  • Syndrome
  • Transcription Factors / genetics


  • Autoantigens
  • CHD4 protein, human
  • Nuclear Proteins
  • Transcription Factors
  • Adenosine Triphosphate
  • HDAC1 protein, human
  • Histone Deacetylase 1
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex
  • SMARCA4 protein, human
  • Mi-2beta protein, mouse
  • DNA Helicases

Supplementary concepts

  • Coffin-Siris syndrome