Genetic diagnosis for epilepsy and other neurological disorders are not optimized

to detect somatic mutations, representing a significant unsolved challenge in neurology. Our

group identified candidate somatic variants from the Epi4K consortium, a large cohort of

epilepsy trio exomes, using MosaicHunter, a sensitive framework to identify candidate somatic

variants. Here, we analyze a specific loss-of-function somatic single nucleotide variant (sSNV)

in ARHGAP31 to determine its functional effect as a potential novel epilepsy gene.

Once somatic variants have been identified and characterized in-silico, their

functional and biological consequences must be experimentally validated. Here, we describe a

clinical case with somatic candidate stop-gain variant in ARHGAP31, and use a patient cell line

to investigate ARHGAP31, a gene that plays a key role in cellular signaling by regulating

To determine the effect of our ARHGAP31 variant on ARHGAP31 gene

expression, concurrent genotyping and RNA expression analysis of individual patient-derived

lymphoblasts was performed using a single-cell workflow with primers for Sanger sequencing

and probes for digital droplet PCR (ddPCR). Additionally, we analyzed Epi25K, a cohort of

exome sequencing data from epilepsy cases and controls, to determine whether ARHGAP31

somatic variants are preferentially present in epilepsy cohorts.

We hypothesized that wild-type cells express ARHGAP31 at a higher level than

cells carrying the sSNV and report that in a population of 13 patient single-cells expressing

ARHGAP31 at the highest level, 100% (13/13) were wild-type genotype (p-value = 0.00005).

Additionally, we report several loss-of-function somatic variants in ARHGAP31 in large cohort

analysis from Epi25K.