PURPOSE: Ohtahara syndrome (OS) is one of the most severe and earliest forms of 
epilepsy. STXBP1 and ARX mutations have been reported in patients with OS. In 
this study, we aimed to identify new genes involved in OS by copy number 
analysis and whole exome sequencing.
METHODS: Copy number analysis and whole exome sequencing were performed in 34 
and 12 patients with OS, respectively. Fluorescence in situ hybridization, 
quantitative polymerase chain reaction (PCR), and breakpoint-specific and 
reverse-transcriptase PCR analyses were performed to characterize a deletion. 
Immunoblotting using lymphoblastoid cells was done to examine expression of CASK 
protein.
KEY FINDINGS: Genomic microarray analysis revealed a 111-kb deletion involving 
exon 2 of CASK at Xp11.4 in a male patient. The deletion was inherited from his 
mother, who was somatic mosaic for the deletion. Sequencing of the mutant 
transcript expressed in lymphoblastoid cell lines derived from the patient 
confirmed the deletion of exon 2 in the mutant transcript with a premature stop 
codon. Whole exome sequencing identified another male patient who was harboring 
a c.1A>G mutation in CASK, which occurred de novo. Both patients showed severe 
cerebellar hypoplasia along with other congenital anomalies such as 
micrognathia, a high arched palate, and finger anomalies. No CASK protein was 
detected by immunoblotting in lymphoblastoid cells derived from two patients.
SIGNIFICANCE: The detected mutations are highly likely to cause the loss of 
function of the CASK protein in male individuals. CASK mutations have been 
reported in patients with intellectual disability with microcephaly and 
pontocerebellar hypoplasia or congenital nystagmus, and those with FG syndrome. 
Our data expand the clinical spectrum of CASK mutations to include OS with 
cerebellar hypoplasia and congenital anomalies at the most severe end.