Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders

Abstract

Background We aimed to define the clinical and mutational spectrum, and to provide novel molecular insights into DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through family support group, GeneMatcher and our network of collaborators. Novel missense variants were investigated by in-vitro and in-vivo assays. These analyses included investigation of stress granule formation, global translation, ATPase and helicase activity, as well as the effect of selected variants on embryonal development in Zebrafish. Results We identified altogether 25 previously unreported individuals. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30 and global translation, trigger stress granule formation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented a milder clinical course, similar to an individual bearing a de novo mosaic missense variant within HCM. Late-onset severe ataxia was observed in an individual with a de novo missense variant within the ratchet-like domain, and early-onset lethal epileptic encephalopathy in an individual with a homozygous missense variant within the helicase core region but not within a HCM. We report ten novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. Functional analyses confirmed pathogenicity of all missense variants, and suggest the existence of clinically distinct subtypes that correlate with their location and nature. Moreover, we established here DHX30 as an ATP-dependent RNA helicase. Conclusions Our study highlights the usefulness of social media in order to define novel Mendelian disorders, and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected, clinicians, molecular genetics diagnostic laboratories and research laboratories.

De novo pathogenic DHX30 variants in two cases

“…At least 16 heterozygous pathogenic variants in DHX30 have been reported so far. [1][2][3] Here, we report two unrelated patients (Figure 1) with de novo missense DHX30 variants detected by whole exome sequencing and subsequent Sanger sequencing, as reported previously. 4 This study was approved by the Institutional Review Board of Yokohama City University School of Medicine.…”

“…3 Both patients showed microcephaly, profound developmental delay, hypotonia, speech impairment, no independent walking, autistic behavior, stereotypic movements, scoliosis, cerebral atrophy, dilated ventricles, and delayed myelination, which is similar to DHX30-related disease. [1][2][3] Patient 1 (a 19-year-old Brazilian female) was born at term to non-consanguineous parents with unremarkable prenatal and family histories. She had a birth weight of 3045 g (À0.78 SD), length of 47 cm (À1.51 SD), and head circumference of 34 cm (À0.51 SD).…”

“…3 Both variants reduce ATPase activity, while p.Ser737Phe also impairs RNA helicase activity. 3 Both patients showed microcephaly, profound developmental delay, hypotonia, speech impairment, no independent walking, autistic behavior, stereotypic movements, scoliosis, cerebral atrophy, dilated ventricles, and delayed myelination, which is similar to DHX30-related disease. [1][2][3] Patient 1 (a 19-year-old Brazilian female) was born at term to non-consanguineous parents with unremarkable prenatal and family histories.…”

“…The detected variants are: c.2210C > T, p.Ser737Phe in Patient 1, which has been previously reported, 2,3 and c.2345G > A, p.Arg782Gln in Patient 2, whichwas novel but has since been described. 3 Both variants reduce ATPase activity, while p.Ser737Phe also impairs RNA helicase activity. 3 Both patients showed microcephaly, profound developmental delay, hypotonia, speech impairment, no independent walking, autistic behavior, stereotypic movements, scoliosis, cerebral atrophy, dilated ventricles, and delayed myelination, which is similar to DHX30-related disease.…”

Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans

“…neurodevelopmental disorders shows that often missense variants cause a more severe phenotype than loss-of-function variants. This happens when variants do not disrupt folding and overall abundance of the gene product, but rather interfere with one specific and important molecular interaction while leaving others intact [68][69][70]. For Shank2 variants described here, other interactions outside PDZ (for p.G643R) and SAM (for p.L1800W) domains are not affected; targeting of the mutant protein to postsynaptic sites is reduced but not abolished.…”