A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative features

Abstract

Background: Intellectual disability (ID) is a common condition with a population prevalence frequency of 1-3% and an enrichment for males, driven in part by the contribution of mutant alleles on the X-chromosome. Among the more than 500 genes associated with ID, DDX3X represents an outlier in sex specificity. Nearly all reported pathogenic variants of DDX3X are de novo, affect mostly females, and appear to be loss of function variants, consistent with the hypothesis that haploinsufficiency at this locus on the X-chromosome is likely to be lethal in males.

Results: We evaluated two male siblings with syndromic features characterized by mild-to-moderate ID and progressive spasticity. Quad-based whole-exome sequencing revealed a maternally inherited missense variant encoding p.R79K in DDX3X in both siblings and no other apparent pathogenic variants. We assessed its possible relevance to their phenotype using an established functional assay for DDX3X activity in zebrafish embryos and found that this allele causes a partial loss of DDX3X function and thus represents a hypomorphic variant.

Conclusions: Our genetic and functional data suggest that partial loss of function of DDX3X can cause syndromic ID. The p.R79K allele affects a region of the protein outside the critical RNA helicase domain, offering a credible explanation for the observed retention of partial function, viability in hemizygous males, and lack of pathology in females. These findings expand the gender spectrum of pathology of this locus and suggest that analysis for DDX3X variants should be considered relevant for both males and females.

Fig. 1

Brain MRI of both affected syndromic ID cases. a Family pedigree showing the two affected brothers and the family pedigree. b (i) Axial T2 FLAIR of sibling 1 at age 16 demonstrates mild enlargement of the lateral ventricles and mild confluent hyperintensity in the adjacent white matter. (ii) Axial T2 FLAIR of sibling 1 2 years later demonstrates interval enlargement of the lateral ventricles and mild progression of the confluent hyperintensity in the adjacent white matter suggesting progressive damage to the central white matter and volume loss. (iii) Sagittal T1 demonstrates generalized volume loss in the corpus callosum that is more prominent in the genu and anterior body, further supporting central white matter volume loss that is more severe anteriorly. (iv) Axial T2 FLAIR of sibling 2 at age 15 demonstrates mild enlargement of the lateral ventricles and mild, symmetric hyperintensity in the adjacent white matter, suggesting central white matter volume loss and gliosis. (v) Axial T2 FLAIR of sibling 2 2 years later demonstrates mild interval increase in size of the lateral ventricles suggesting mild progression of central white matter volume loss, but no significant change in the periventricular hyperintensity. (vi) Sagittal T1 image is also comparable in appearance to his sibling, with prominent volume loss in the corpus callosum that is more striking anteriorly

Fig. 2

Discovery of a maternally transmitted DDX3X variant in male ID. a Protein sequence alignment of DDX3X across vertebrate species; the mutated residue is shown by arrow. b Location of all functionally tested amino acid substitutions in DDX3X. Reported male alleles (top); alleles found in females (bottom). The helicase ATP-binding domain and a helicase C-terminal domain are also shown (green)

Fig. 3

Functional testing of DDX3X variants. a–c Representative lateral images of zebrafish embryos at 2 dpf that are either uninjected (a) or injected with human WNT3A without (b) or with (c) human DDX3X show a range of ventralized phenotypes. These were scored according to established criteria as normal, class I, or class II ventralization. No injection condition resulted in severe ventralization (class III or IV) [3]. d DDX3X variants were tested for their effect on increasing WNT3A-mediated ventralization using 550 fg of WNT3A mRNA and 30 pg of DDX3X mRNA per embryo. P values: < 0.0001 (four asterisks); 0.0001 to 0.001 (three asterisks); 0.001 to 0.01 (two asterisks); 0.01 to 0.05 (one asterisk); ≥ 0.05 not significant (ns)