In this study, we have identified nine novel de novo truncation variants in patients of NDD: CYP1A1, C14orf119, FLI1, CYB5R4, SEL1L2, RAB11FIP2, ZMYND8, ZNF143, and MSX2. More surprisingly, we have found a recurrent hemizygous missense variant in PJA1 in a total of seven male patients with NDDs, five of which also had a mild trigonocephaly. This evidence concerns the gene MSX2 and trigonocephaly.