Rare variants of small effect size in neuronal excitability genes influence clinical outcome in Japanese cases of SCN1A truncation-positive Dravet syndrome

Michael F Hammer,Brian Hallmark,Laurel Johnstone,Shinichi Hirose,Ryan Sprissler,Jin Zhou,Branden Lau,Alexander Tchourbanov,Joseph Watkins,Miao Zhang,Atsushi Ishii

doi:10.1371/journal.pone.0180485

Abstract

Dravet syndrome (DS) is a rare, devastating form of childhood epilepsy that is often associated with mutations in the voltage-gated sodium channel gene, SCN1A. There is considerable variability in expressivity within families, as well as among individuals carrying the same primary mutation, suggesting that clinical outcome is modulated by variants at other genes. To identify modifier gene variants that contribute to clinical outcome, we sequenced the exomes of 22 individuals at both ends of a phenotype distribution (i.e., mild and severe cognitive condition). We controlled for variation associated with different mutation types by limiting inclusion to individuals with a de novo truncation mutation resulting in SCN1A haploinsufficiency. We performed tests aimed at identifying 1) single common variants that are enriched in either phenotypic group, 2) sets of common or rare variants aggregated in and around genes associated with clinical outcome, and 3) rare variants in 237 candidate genes associated with neuronal excitability. While our power to identify enrichment of a common variant in either phenotypic group is limited as a result of the rarity of mild phenotypes in individuals with SCN1A truncation variants, our top candidates did not map to functional regions of genes, or in genes that are known to be associated with neurological pathways. In contrast, we found a statistically-significant excess of rare variants predicted to be damaging and of small effect size in genes associated with neuronal excitability in severely affected individuals. A KCNQ2 variant previously associated with benign neonatal seizures is present in 3 of 12 individuals in the severe category. To compare our results with the healthy population, we performed a similar analysis on whole exome sequencing data from 70 Japanese individuals in the 1000 genomes project. Interestingly, the frequency of rare damaging variants in the same set of neuronal excitability genes in healthy individuals is nearly as high as in severely affected individuals. Rather than a single common gene/variant modifying clinical outcome in SCN1A-related epilepsies, our results point to the cumulative effect of rare variants with little to no measurable phenotypic effect (i.e., typical genetic background) unless present in combination with a disease-causing truncation mutation in SCN1A.

Highlights

An important problem in medical genetics is identifying factors that influence the clinical outcome of Mendelian disease
This is due to the fact that human populations carry genetic variation at many genes that could influence clinical outcome of monogenic disease, and variants at modifier genes may have no affect on the phenotype of individuals when not present in combination with the primary gene variant responsible for the disease [4]
While we did not identify a single major modifier locus, our results suggest that rare pathogenic variants of small effect size in genes associated with neuronal excitability may tip the balance toward mild or severe clinical outcome in children with SCN1A truncation mutations

Summary

Introduction

An important problem in medical genetics is identifying factors that influence the clinical outcome of Mendelian disease. While studies in mice have been successful in identifying genes that modify the phenotypic expression of a mutant gene [1,2,3], the search for modifier genes in humans remains challenging. This is due to the fact that human populations carry genetic variation at many genes that could influence clinical outcome of monogenic disease, and variants at modifier genes may have no affect on the phenotype of individuals when not present in combination with the primary gene variant responsible for the disease [4]. Epilepsy disorders caused by sodium channel mutations represent a disease phenotype that may be strongly influenced by modifier genes. Studies in mice have mapped several modifiers of SCN1A, many of which turn out to be genes coding for other ion channels [3, 12, 13]

Methods

Results

Conclusion