A novel KDM5C mutation associated with intellectual disability: molecular mechanisms and clinical implications

Among the disease-causing genes associated with X-linked intellectual disability (XLID), KDM5C is one of the most frequently mutated ones. KDM5C is a widely expressed gene that is most highly expressed in the brain. KDM5C modulates the transcriptional activity of genes through demethylation of H3K4, thereby regulating neural development and normal function. We identified a gene from a Chinese family and found that a nonsense mutation of KDM5C was co-segregated with the intellectual disability (ID).

The candidate mutant genes of patients with ID phenotype were screened by Whole Exome Sequencing (WES), and DNA Sanger sequencing was performed for genetic analysis. Pathogenicity prediction tools were used to evaluate the pathogenicity of new mutations. The fusion plasmid was constructed and transfected into the cells, and the changes of mRNA and protein levels of the mutants were detected by semi-qRT-PCR and Western Blot, and the subcellular localization changes of mutant proteins were detected by Immunofluorescence technique.

The nonsense mutation in KDM5C (c.2785 C > T, p. R929X) was identified by whole exome sequencing (WES) and confirmed by Sanger sequencing, resulting in a truncated protein. The mutation was determined by pathogenicity prediction tool able to find non-sense mediated mRNA decay (NMD). Semi-qRT-PCR and Western Blot showed that the mRNA levels of the mutant gene were down-regulated, while the protein level was up-regulated. Additionally, the subcellular localization of the mutant protein changed.

The KDM5C mutation found in our study leads to changes in protein levels through NMD and/or protein degradation, and produces residues lacking nuclear localization, thus altering the subcellular localization of the protein. These results may lead to changes in the expression of KDM5C target genes, ultimately contributing to the clinical phenotype observed in the patients.