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Background  De novo pathogenic variants in the  DDX3X  gene are reported to account for 1–3% of unexplained intellectual disability (ID) in females, leading to the rare disease known as  DDX3X  syndrome (MRXSSB, OMIM #300958). Besides ID, these patients manifest a variable clinical presentation, which includes neurological and behavioral defects, and abnormal brain MRIs.    Case presentation  We report a 10-year-old girl affected by delayed psychomotor development, delayed myelination, and polymicrogyria (PMG). We identified a novel de novo missense mutation in the  DDX3X  gene (c.625C > G) by whole exome sequencing (WES). The  DDX3X  gene encodes a DEAD-box ATP-dependent RNA-helicase broadly implicated in gene expression through regulation of mRNA metabolism. The identified mutation is located just upstream the helicase domain and is suggested to impair the protein activity, thus resulting in the altered translation of DDX3X-dependent mRNAs. The proband, presenting with the typical PMG phenotype related to the syndrome, does not show other clinical signs frequently reported in presence of missense  DDX3X  mutations that are associated with a most severe clinical presentation. In addition, she has brachycephaly, never described in female  DDX3X  patients, and macroglossia, that has never been associated with the syndrome.    Conclusions  This case expands the knowledge of  DDX3X  pathogenic variants and the associated  DDX3X  syndrome phenotypic spectrum.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13052-021-01033-4.

A novel de novo DDX3X missense variant in a female with brachycephaly and intellectual disability: a case report