Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals

Abstract

Both mild and severe epilepsies are influenced by variants in the same genes, yet an explanation for the resulting phenotypic variation is unknown. As part of the ongoing Epi25 Collaboration, we performed a whole-exome sequencing analysis of 13,487 epilepsy-affected individuals and 15,678 control individuals. While prior Epi25 studies focused on gene-based collapsing analyses, we asked how the pattern of variation within genes differs by epilepsy type. Specifically, we compared the genetic architectures of severe developmental and epileptic encephalopathies (DEEs) and two generally less severe epilepsies, genetic generalized epilepsy and non-acquired focal epilepsy (NAFE). Our gene-based rare variant collapsing analysis used geographic ancestry-based clustering that included broader ancestries than previously possible and revealed novel associations. Using the missense intolerance ratio (MTR), we found that variants in DEEaffected individuals are in significantly more intolerant genic sub-regions than those in NAFE-affected individuals. Only previously reported pathogenic variants absent in available genomic datasets showed a significant burden in epilepsy-affected individuals compared with control individuals, and the ultra-rare pathogenic variants associated with DEE were located in more intolerant genic sub-regions than variants associated with non-DEE epilepsies. MTR filtering improved the yield of ultra-rare pathogenic variants in affected individuals compared with control individuals. Finally, analysis of variants in genes without a disease association revealed a significant burden of loss-of-function variants in the genes most intolerant to such variation, indicating additional epilepsy-risk genes yet to be discovered. Taken together, our study suggests that genic and sub-genic intolerance are critical characteristics for interpreting the effects of variation in genes that influence epilepsy.

Distinct gene-set burden patterns underlie common generalized and focal epilepsies

“…S11). A previous similar analysis of this [10] and related [11] datasets examined loss-of-function intolerant genes and demonstrated an increased burden in ultra-rare constrained as well as protein truncating variants (PTVs). Here, the examination of brain-expressed intolerant genes showed, similarly, a marked enrichment in PTVs in addition to a burden in highly constrained missense variants that is comparable to what is seen exome-wide ( Figs.…”

“…We analyzed subjects from recruitment years 1 and 2 ( n = 13,197 before filtering) targeting individuals diagnosed with DEE ( n = 1,474), GGE ( n = 4,510), NAFE ( n = 5,321). The epilepsy classification, phenotyping and consent procedures have been previously described [ 10 , 11 ]. Five control cohorts [ 10 , 12 ] were available for this analysis ( n = 13,299), including Italian controls from the Epi25 Collaborative ( n = 300), the Swedish Schizophrenia Study controls ( n = 6,242), and three Myocardial Infarction Genetics (MIGen) Consortium cohorts: Leicester UK Heart Study ( n = 1,165), Ottawa Heart Study ( n = 1,915) and the Italian Atherosclerosis, Thrombosis, and Vascular Biology (ATVB) Study ( n = 3,677).…”

“…The variants were annotated using snpEff [23] v4.3 and Annovar [24] v20191024. We focused on URVs as these have shown a strong burden of deleterious pathogenic variants in multiple studies of epilepsy and other neurological disorders [ 8 , 10 , 11 , [25] , [26] , [27] , [28] , [29] ]. URVs were defined based on their Minor Allele Counts (MACs) in the study dataset (internal allele count/frequency) and their estimated frequency in the general population (external Minor Allele Frequencies, MAFs).…”

“…The role of genetic causality is apparent in the developmental and epileptic encephalopathies (DEEs) [1] , [2] , [3] , sometimes with consequences on precision treatments [4] , [5] , [6] , [7] . In contrast, only few individuals with familial or sporadic genetic generalized epilepsies (GGEs) or non-acquired focal epilepsies (NAFEs) harbour monogenic causative variations [8] , [9] , [10] , [11] . Therefore, methodologies investigating the mutational burden of neurobiologically meaningful gene-sets improve the prospects to dissect the joint effects of multiple genetic factors underlying the complex genetic architecture of these common epilepsy syndromes.…”

Recurrent de novo single point mutation on the gene encoding Na+/K+ pump results in epilepsy

“…To date, thousands of genes have been reported as associated with epileptic conditions(Epi25 Collaborative. Electronic address & Epi, 2021;Fatima et al, 2021;Fry et al, 2021;Li et al, 2021;Lindy et al, 2018;Liu et al, 2018;Parrini et al, 2017;Tidball et al, 2020;Usmani et al, 2021), but most of them are not experimentally confirmed (Ran et al, 2015;Stenson et al, 2017;Takata et al, 2019;. Considering that comprehensive epilepsy panels including hundreds of genes are offered by companies for genetic counseling (Poduri, 2017;, it is imperative to perform mechanistic studies and confirm genotype-phenotype associations to assist clinicians in proper diagnosis and therapeutic decisionmaking (Ellis et al, 2020).…”