Novel KMT5B de novo variants disrupt DNA damage response in intellectual disability

KMT5B encodes a histone methyltransferase critical for catalysing histone H4 lysine 20 dimethylation, an epigenetic mark essential for chromatin remodeling and DNA damage response (DDR). Heterozygous pathogenic variants in KMT5B cause autosomal dominant intellectual developmental disorder 51 (MRD51). Although haploinsufficiency is proposed as the primary disease mechanism, the functional impact of missense variants on DDR regulation remains unknown.

This study aims to explore whether two novel missense variants in the KMT5B gene disrupt the DDR pathway, thereby leading to intellectual disability (ID).

We performed whole-exome sequencing on two Chinese probands with moderate ID and their parents, followed by bioinformatics analysis to predict variant pathogenicity. In vitro, we established stable cell lines and used Western blotting and immunofluorescence to assess KMT5B protein stability and DDR-related protein expression.

Two novel missense variants in KMT5B (NM_017635.5: c.280G>A/p.Gly94Ser and c.877G>C/p.Ala293Pro) were identified in the probands. These variants, located in critical functional domains and highly conserved across evolution, significantly reduce KMT5B protein stability and expression. KMT5B knockdown in HEK293T cells resulted in the upregulation of DDR proteins, including p53, DDIT4 and γH2AX. While overexpression of wild-type KMT5B normalizes the levels of these DDR proteins, the variants fail to normalize the levels, with immunofluorescence revealing persistent upregulation of γH2AX.

These variants may destabilize KMT5B protein and disrupt the DDR pathway, suggesting a potential mechanism for ID. Our findings expand the genetic spectrum of KMT5B-related disorders and highlight the clinical value of KMT5B screening in ID diagnosis.