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Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability
  1. Genay O Pilarowski1,2,
  2. Hilary J Vernon2,3,4,
  3. Carolyn D Applegate2,
  4. Leandros Boukas1,2,
  5. Megan T Cho5,
  6. Christina A Gurnett6,
  7. Paul J Benke7,
  8. Erin Beaver8,
  9. Jennifer M Heeley8,
  10. Livija Medne9,
  11. Ian D Krantz9,
  12. Meron Azage10,
  13. Dmitriy Niyazov10,
  14. Lindsay B Henderson5,
  15. Ingrid M Wentzensen5,
  16. Berivan Baskin5,
  17. Maria J Guillen Sacoto5,
  18. Gregory D Bowman11,12,
  19. Hans T Bjornsson2,4,13
  1. 1 Predoctoral Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  2. 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
  3. 3 Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
  4. 4 Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
  5. 5 GeneDx, Gaithersburg, Maryland, USA
  6. 6 Department of Neurology, Division of Pediatric Neurology, Washington University School of Medicine, Saint Louis, Missouri, USA
  7. 7 Joe DiMaggio Children’s Hospital, Florida Atlantic School of Medicine, Hollywood, Florida, USA
  8. 8 Mercy Kids Genetics, Mercy Hospital, Saint Louis, Missouri, USA
  9. 9 Division of Human Genetics, Department of Pediatrics, Individualized Medical Genetics Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  10. 10 Department of Pediatrics, Ochsner Clinic, New Orleans, Louisiana, USA
  11. 11 T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
  12. 12 Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
  13. 13 Faculty of Medicine, University of Iceland, Reykjavik, Iceland
  1. Correspondence to Dr Hans T Bjornsson, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, 733 N Broadway, MRB 435, Baltimore, MD 21205, USA; hbjorns1{at}


Background The list of Mendelian disorders of the epigenetic machinery has expanded rapidly during the last 5 years. A few missense variants in the chromatin remodeler CHD1 have been found in several large-scale sequencing efforts focused on uncovering the genetic aetiology of autism.

Objectives To explore whether variants in CHD1 are associated with a human phenotype.

Methods We used GeneMatcher to identify other physicians caring for patients with variants in CHD1. We also explored the epigenetic consequences of one of these variants in cultured fibroblasts.

Results Here we describe six CHD1 heterozygous missense variants in a cohort of patients with autism, speech apraxia, developmental delay and facial dysmorphic features. Importantly, three of these variants occurred de novo. We also report on a subject with a de novo deletion covering a large fraction of the CHD1 gene without any obvious neurological phenotype. Finally, we demonstrate increased levels of the closed chromatin modification H3K27me3 in fibroblasts from a subject carrying a de novo variant in CHD1.

Conclusions Our results suggest that variants in CHD1 can lead to diverse phenotypic outcomes; however, the neurodevelopmental phenotype appears to be limited to patients with missense variants, which is compatible with a dominant negative mechanism of disease.

  • human disease
  • neurological dysfunction
  • epigenetic machinery
  • chromatin
  • speech apraxia

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  • Contributors HTB and HJV conceived study; GOP, HTB and GDB wrote the paper; GOP performed cell culture experiments; LB performed computational analysis; GDB performed structural analysis; HJV, CDA, MTC, CAG, PJB, EB, JMH, LM, IDK, MA, DN, LBH, IMW, BB, MJGS and HTB provided clinical information regarding patients.

  • Competing interests None declared.

  • Patient consent Obtained.

  • Ethics approval All work was completed in compliance with respective institutions' Institutional Review Board and proper consent was obtained from each patient/patient family included in the study.

  • Provenance and peer review Not commissioned; externally peer reviewed.