Abstracts

Rationale: The US National Human Genome Research Institute (NHGRI) and the American College of Medical Genetics and Genomics (ACMG) in conjunction with the Association of Molecular Pathologists (AMP) and College of American Pathologists (CAP) have recently released guidelines for interpretation and assignment of pathogenic-causality to sequence variants. Now, 11 years after the initial implication of EFHC1 as a disease-causing gene in Juvenile Myoclonic Epilepsy (JME), we reanalyze 32 purported pathogenic EFHC1 variants, found in 41 index cases across 12 international cohorts, and the 18 EFHC1 polymorphisms found across all populations, and reassess the pathogenicity of EFHC1 with respect to epilepsy.Methods: We compiled data from several lines of evidence, including results of case-control screening, experimental and functional studies, and applied information from bioinformatics and large public genome databases, such as Genome 1000, Exon Variant Server, and ExAC, that were unavailable when EFHC1 was first linked to JME. We conducted a variant reanalysis to “vet” the assignment of pathogenicity using the NHGRI and ACMG core guideline.Results: Of 32 variants implicated in JME, 6 have been replicated in multiple unrelated index cases (the most frequently detected variant, p.F229L, has been found in 10 different IGE cases across three continents), and 9 co-segregate with other affected members of the family. Within the scope of each study, 9 variants demonstrated statistically significant enrichment in cases over controls. In the large public allele frequency databases, we found 22 variants were absent in ESP6500 (6,500+ exomes), 21 were absent in 1000 Genomes Phase 3 release (~2,500 genomes), and 6 were absent the ExAC database (65,000+ exomes). The informatics predictors of pathogenicity 13 of the 29 exonic variants were predicted to have a damaging effect on the protein product by at least half of the measures from dbNSFP v2.6. Three separate variant-specific experimental studies on the original 5 EFHC1 mutants from Mexico and one variant-specific experimental study on 12 variants from India demonstrated a dominant negative function on mitosis, apoptosis and neuroblast migration. These effects result in poorly integrated neurons and overgrown synaptic and dendritic networks that demonstrate the same “microdysgenesis” and “thicker mesial frontal gray matter” observed in the MRIs of human JME patients. EFHC1-knock out models in the mouse and fly recapitulated in vivo neurodevelopment abnormalities and replicated myoclonic and grand mal seizures.Conclusions: EFHC1 meets gene-level and variant-level support for disease implication in JME. Of the 50 total EFHC1 variants published in the literature, we classify at least six as meeting the ACMG criteria as “pathogenic”, another three as “likely pathogenic”, and six are classified as “benign”. At this time, the remaining 35 variants are classified as “variants of unknown significance”. Funding: NIH R01NS055057, VACO Merit Review Grant.