PURPOSE: The management of epilepsy in children is particularly challenging when 
seizures are resistant to antiepileptic medications, or undergo many changes in 
seizure type over time, or have comorbid cognitive, behavioral, or motor 
deficits. Despite efforts to classify such epilepsies based on clinical and 
electroencephalographic criteria, many children never receive a definitive 
etiologic diagnosis. Whole exome sequencing (WES) is proving to be a highly 
effective method for identifying de novo variants that cause neurologic 
disorders, especially those associated with abnormal brain development. Herein 
we explore the utility of WES for identifying candidate causal de novo variants 
in a cohort of children with heterogeneous sporadic epilepsies without etiologic 
diagnoses.
METHODS: We performed WES (mean coverage approximately 40×) on 10 trios 
comprised of unaffected parents and a child with sporadic epilepsy characterized 
by difficult-to-control seizures and some combination of developmental delay, 
epileptic encephalopathy, autistic features, cognitive impairment, or motor 
deficits. Sequence processing and variant calling were performed using standard 
bioinformatics tools. A custom filtering system was used to prioritize de novo 
variants of possible functional significance for validation by Sanger 
sequencing.
KEY FINDINGS: In 9 of 10 probands, we identified one or more de novo variants 
predicted to alter protein function, for a total of 15. Four probands had de 
novo mutations in genes previously shown to harbor heterozygous mutations in 
patients with severe, early onset epilepsies (two in SCN1A, and one each in 
CDKL5 and EEF1A2). In three children, the de novo variants were in genes with 
functional roles that are plausibly relevant to epilepsy (KCNH5, CLCN4, and 
ARHGEF15). The variant in KCNH5 alters one of the highly conserved arginine 
residues of the voltage sensor of the encoded voltage-gated potassium channel. 
In vitro analyses using cell-based assays revealed that the CLCN4 mutation 
greatly impaired ion transport by the ClC-4 2Cl(-) /H(+) -exchanger and that the 
mutation in ARHGEF15 reduced GEF exchange activity of the gene product, 
Ephexin5, by about 50%. Of interest, these seven probands all presented with 
seizures within the first 6 months of life, and six of these have intractable 
seizures.
SIGNIFICANCE: The finding that 7 of 10 children carried de novo mutations in 
genes of known or plausible clinical significance to neuronal excitability 
suggests that WES will be of use for the molecular genetic diagnosis of sporadic 
epilepsies in children, especially when seizures are of early onset and 
difficult to control.