De novo TANC2 variants caused developmental and epileptic encephalopathy and epilepsy

OBJECTIVE: The TANC2 gene encodes a scaffolding synaptic protein with essential roles in synaptic transmission. This study aims to explore the association between TANC2 and epilepsy and the mechanism underlying phenotypic variation. METHODS: Trio-based exome sequencing was performed in patients with epilepsy from the China Epilepsy 1.0 cohort. The association between TANC2 and epilepsy was validated with a Drosophila model. The role of TANC2 in development was investigated by single-cell RNA sequencing in cerebral organoids and spatiotemporal expression across brain regions. RESULTS: De novo TANC2 variants were identified in six unrelated cases, including four null and two missense variants. The six variants were classified as "pathogenic"/"likely pathogenic," according to the American College of Medical Genetics and Genomics guidelines. Patients with null variants exhibited severe phenotypes, including three with epilepsy and neurodevelopmental disorders (NDDs) and one with developmental and epileptic encephalopathy (DEE). In contrast, the patients with missense variants presented with only epilepsy. Genotype-phenotype correlation analysis revealed that variants associated with epilepsy and NDD were mostly null variants, whereas the missense variants were associated with NDD or epilepsy. NDD-associated missense variants exhibited more severe damage effects, compared with the epilepsy-associated missense variants. Functional studies in Drosophila suggested that knockdown TANC2 led to increased susceptibility to seizure-like behavior. TANC2 expresses highly in the brain, with three peaks in early fetal, infancy, and adulthood, coinciding with the onset ages of patients. Specifically, TANC2 exhibited the highest expression in the early fetal stage, indicating its vital role in early development. Single-cell RNA sequencing revealed an extensive expression of TANC2 in neurons in 1-month-old cerebral organoids, suggesting its vital role in neurodevelopment. SIGNIFICANCE: This study suggested TANC2 as a causative gene of epilepsy and DEE. The phenotypic spectrums of TANC2 potentially ranged from early lethality, DEE, epilepsy with NDD, NDD, to mild epilepsy, depending on the damaging effects caused by variants.