Variants in CSMD2 and CSMD3, genes involved in synaptogenesis, are associated with epilepsies

Abstract Objective The CSMD genes, including CSMD1 , CSMD2 , and CSMD3 , encoding synaptic transmembrane proteins, play important roles in neuronal maturation, growth of dendrites, and processes of synapses. Our recent study showed that CSMD1 was associated with developmental epileptic encephalopathy (DEE) and generalized epilepsy. The significance of CSMD2 and CSMD3 in human disease is unknown. Methods Trio‐based whole‐exome sequencing was performed in patients with focal epilepsy without acquired etiologies. The gene–disease association was validated by excess and damaging effect of variants, genotype–phenotype correlation, and studies on spatial–temporal and single‐cell expression. Results CSMD2 variants were identified in six and CSMD3 variants were identified in four cases with focal epilepsy. Additional CSMD3 variants were identified in three cases with febrile seizures plus and one case with infantile spasms. The variants included 1 de novo , 1 homozygous, and 12 pairs of compound heterozygous variants. All variants were missense except one and presented no or extremely low minor allele frequencies, which were significantly lower than that of benign variants and higher in excess by multiple statistical analyses. The gene–disease association was further supported by correlation between damage scoring of variants and phenotype severity. The three CSMD genes are expressed predominantly at early development stages, correlated with the neurodevelopment abnormalities/DEE. CSMD1 expression increases significantly starting with later childhood, consistent with the poor prognosis of DEE. CSMD2 presented the highest expression in the developing brain, with predominance in inhibitory neurons, explaining the focal epilepsy and focal cortical dysplasia (FCD). CSMD3 expressed in relatively low levels with less neuron‐specificity explained the heterogeneous phenotypes. Significance The CSMD genes are associated with epilepsies, CSMD2 with focal epilepsy/FCD, and CSMD3 with a phenotype spectrum that includes focal epilepsy, febrile seizures, and DEE. The distinct phenotypes of CSMD genes are explained by their features of genetic dependent stage and the development‐dependent expression pattern of neuron specificity.