Interestingly, our analysis revealed a novel de novo frameshift variant c.516_517insG (p.Ala173fs: p.A173fs) in MSX2 in a Japanese patient of autism spectrum disorder (ASD) associated with a cranial malformation (cranial meningocele) who also developed partial epileptic seizures (SIZ‐894, Tables S4 and S8), which is according to our knowledge the first report of a de novo truncation variant in MSX2 in a patient with NDD. This evidence concerns the gene MSX2 and Cranial meningocele.