Background Submicroscopic deletions in 14q12 spanning FOXG1 or intragenic mutations have been reported in patients with a developmental disorder described as a congenital variant of Rett syndrome. We aimed to further characterize and delineate the phenotype of FOXG1-mutation positive patients. Method We mapped the breakpoints of a 2;14 translocation by fluorescence in situ hybridization and analyzed three chromosome rearrangements in 14q12 by cytogenetic analysis and/or array CGH. We sequenced the FOXG1 gene in 210 patients, including 129 patients with unexplained developmental disorders and 81 MECP2-mutation negative individuals. Results We report one known mutation, seen in 2 patients, and 9 novel mutations of FOXG1 including 2 deletions, 2 chromosome rearrangements disrupting or displacing putative cis-regulatory elements from FOXG1, and 7 sequence changes. Analysis of our 11 patients, and further 15 patients reported in the literature, demonstrates a complex constellation of features including mild postnatal growth deficiency, severe postnatal microcephaly, severe mental retardation with absent language development, deficient social reciprocity resembling autism, combined stereotypies and frank dyskinesias, epilepsy, poor sleep patterns, irritability in infancy, unexplained episodes of crying, recurrent aspiration, and gastroesophageal reflux. Brain imaging studies reveal simplified gyral pattern and reduced white matter volume in the frontal lobes, corpus callosum hypogenesis, and variable mild frontal pachgyria. Conclusions We significantly expanded the number of FOXG1 mutations and identified two affecting possible cis-regulatory elements. While the phenotype of the patients overlaps both classic and congenital Rett syndrome, extensive clinical evaluation demonstrates a distinctive and clinically recognizable phenotype which we suggest to designate as the FOXG1 syndrome.

CASK is a multi-domain scaffolding protein that interacts with the transcription factor TBR1 and regulates expression of genes involved in cortical development such as RELN. Here we describe a previously unreported X-linked brain malformation syndrome caused by mutations of CASK. All five affected individuals with CASK mutations had congenital or postnatal microcephaly, disproportionate brainstem and cerebellar hypoplasia, and severe mental retardation.