Epileptic encephalopathy linked to a DALRD3 missense variant impaired in tRNA modification function

Abstract

Epileptic encephalopathies are severe epilepsy syndromes characterized by early onset and progressive cerebral dysfunction. A nonsense variant in the DALR Anticodon Binding Domain Containing 3 (DALRD3) gene has been implicated in epileptic encephalopathy but no other disease-associated variants in DALRD3 have been described. In human cells, the DALRD3 protein forms a complex with the METTL2 methyltransferase to generate the 3-methylcytosine (m3C) modification in specific arginine tRNAs. Here, we identify a patient with a homozygous missense variant in DALRD3 who displays developmental delay, cognitive deficiencies, and multifocal epilepsy. The missense variant substitutes an arginine residue to cysteine (R517C) within the DALR domain of DALRD3 that is required for binding tRNAs. Patient cells homozygous for the DALRD3-R517C variant exhibit reduced levels of m3C modification in arginine tRNAs, indicating that the R517C variant impairs DALRD3 function. Notably, the DALRD3-R517C variant displays reduced association with METTL2 and loss of interaction with substrate tRNAs. Our results uncover a novel pathogenic variant in DALRD3 that links DALRD3 loss-of-function to epileptic encephalopathy disorders. Importantly, these findings underscore DALRD3-dependent tRNA modification as a key contributor to proper brain development and function.