De novo heterozygous variants in EHMT2 genocopy Kleefstra syndrome via loss of G9a methyltransferase activity

EHMT1 and EHMT2 genes encode human euchromatin histone lysine methyltransferase 1 and 2 (EHMT1 alias GLP; EHMT2 alias G9a) that form heteromeric GLP/G9a complexes with essential roles in epigenetic regulation of gene expression. While EHMT1 haploinsufficiency was established as the cause of Kleefstra syndrome twenty years ago, the pathogenesis of G9a dysfunction in human disease remains largely unknown. Here, we report clinical and molecular correlates of six de novo EHMT2 variants in patients with clinical presentation, episignatures, histone modifications, and transcriptomic profiles similar to those of Kleefstra syndrome. In vitro studies revealed that these variants encode structurally stable G9a proteins that are catalytically incompetent due to aberrant interactions either with histone H3 tail or with S-adenosylmethionine. Heterozygous mice carrying a patient-derived variant (Ehmt2 c.3385_3396del) exhibited growth retardation, facial/skull dysmorphia, and aberrant behavior. EHMT2 variants described here likely exert dominant-negative effects on GLP/G9a complexes and thus genocopy the EHMT1 haploinsufficiency, causing Kleefstra syndrome via a distinct molecular mechanism.