A recurrentPJA1variant in trigonocephaly and neurodevelopmental disorders

Objective: Neurodevelopmental disorders (NDDs) often associate with epilepsy or craniofacial malformations. Recent large-scale DNA analyses identified hundreds of candidate genes for NDDs, but a large portion of the cases still remain unexplained. We aimed to identify novel candidate genes for NDDs. Methods: We performed exome sequencing of 95 patients with NDDs including 51 with trigonocephaly and subsequent targeted sequencing of additional 463 NDD patients, functional analyses of variantin vitro,and evaluations of autism spectrum disorder (ASD)-like phenotypes and seizure-related phenotypesin vivo. Results: We identifiedde novotruncation variants in nine novel genes;CYP1A1,C14orf119,FLI1,CYB5R4,SEL1L2, RAB11FIP2, ZMYND8, ZNF143,andMSX2. MSX2variants have been described in patients with cranial malformations, and our present patient with theMSX2 de novotruncation variant showed cranial meningocele and partial epilepsy. MSX2 protein is known to be ubiquitinated by an E3 ubiquitin ligase PJA1, and interestingly we found aPJA1hemizygous p.Arg376Cys variant recurrently in seven Japanese NDD patients; five with trigonocephaly and one with partial epilepsy, and the variant was absent in 886 Japanese control individuals.Pja1knock-in mice carrying p.Arg365Cys, which is equivalent to p.Arg376Cys in human, showed a significant decrease in PJA1 protein amount, suggesting a loss-of-function effect of the variant.Pja1knockout mice displayed moderate deficits in isolation-induced ultrasonic vocalizations and increased seizure susceptibility to pentylenetetrazole. Interpretation: These findings propose novel candidate genes includingPJA1andMSX2for NDDs associated with craniofacial abnormalities and/or epilepsy.