Variable patterns of mutation density among Na(V)1.1, Na(V)1.2 and Na(V)1.6 point to channel-specific functional differences associated with childhood epilepsy

Variants implicated in childhood epilepsy have been identified in all four voltage-gated sodium channels that initiate action potentials in the central nervous system. Previous research has focused on the functional effects of particular variants within the most studied of these channels (Na(V)1.1, Na(V)1.2 and Na(V)1.6); however, there have been few comparative studies across channels to infer the impact of mutations in patients with epilepsy. Here we compare patterns of variation in patient and public databases to test the hypothesis that regions of known functional significance within voltage-gated sodium (Na(V)) channels have an increased burden of deleterious variants. We assessed mutational burden in different regions of the Na(v) channels by (1) performing Fisher exact tests on odds ratios to infer excess variants in domains, segments, and loops of each channel in patient databases versus public “control” databases, and (2) comparing the cumulative distribution of variant sites along DNA sequences of each gene in patient and public databases (i.e., independent of protein structure). Patient variant density was concordant among channels in regions known to play a role in channel function, with statistically significant higher patient variant density in S4-S6 and DIII-DIV and an excess of public variants in SI-S3, DI-DII, DII-DIII. On the other hand, channel-specific patterns of patient burden were found in the Na(V)1.6 inactivation gate and Na(V)1.1 S5-S6 linkers, while Na(V)1.2 and Na(V)1.6 S4-S5 linkers and S5 segments shared patient variant patterns that contrasted with those in Na(V)1.1. These different patterns may reflect different roles played by the Na(V)1.6 inactivation gate in action potential propagation, and by Na(V)1.1 S5-S6 linkers in loss of function and haploinsufficiency. Interestingly, Na(V)1.2 and Na(V)1.6 both lack amino acid substitutions over significantly long stretches in both the patient and public databases suggesting that new mutations in these regions may cause embryonic lethality or a non-epileptic disease phenotype.