De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability

Am J Med Genet A. 2019 Apr;179(4):570-578. doi: 10.1002/ajmg.a.61061. Epub 2019 Feb 7.


DDX3X (Xp11.4) encodes a DEAD-box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X-linked intellectual disability (ID) (MRX102, MIM: 300958). The phenotypes associated with DDX3X variants are heterogeneous and include brain and behavioral abnormalities, microcephaly, hypotonia, and movement disorders and/or spasticity. The majority of DDX3X variants described are de novo mutations in females with ID. In contrast, most male DDX3X variants are inherited from an unaffected mother, with one documented exception being a recently identified de novo splice site variant. It has been suggested, therefore, that DDX3X exerts its effects through haploinsufficiency in females, and that affected males carry hypomorphic alleles that retain partial function. Given the lack of male de novo DDX3X variants, loss-of-function variants in this gene are suspected to be male lethal. Through whole-exome sequencing, we identified three unrelated males with hemizygous missense DDX3X variants and ID. All three variants were confirmed by Sanger sequencing, with two established as de novo. In silico analyses were supportive of pathogenicity. We report the male phenotypes and compare them to phenotypes observed in previously reported male and female patients. In conclusion, we propose that de novo DDX3X variants are not necessarily male lethal and should be considered as a cause of syndromic ID in both males and females.

Keywords: DDX3X; developmental delay; intellectual disability; syndromic intellectual disability.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Child
  • DEAD-box RNA Helicases / genetics*
  • Female
  • Humans
  • Intellectual Disability / genetics*
  • Intellectual Disability / pathology*
  • Male
  • Mutation, Missense*
  • Phenotype
  • Sex Factors
  • Syndrome
  • Whole Exome Sequencing


  • DDX3X protein, human
  • DEAD-box RNA Helicases