Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity

Abstract

Mutations in KDM, C are an important cause of X-linked intellectual disability in males. KDM, C encodes a histone demethylase, suggesting that alterations in chromatin landscape may contribute to disease. We used primary patient cells and biochemical approaches to investigate the effects of patient mutations on KDM, C expression, stability and catalytic activity. We report and characterize a novel nonsense mutation, c., delG, p.V, Yfs, which leads to loss of KDM, C protein. We also characterize two KDM, C missense mutations, c., C, T, p.P, L, and c., G, T, p.D, Y, that are compatible with protein production, but compromise stability and enzymatic activity. Finally, we demonstrate that a c., T, C mutation in the translation initiation codon of KDM, C results in translation re-start and production of a N-terminally truncated protein, p.M, E, del, that is unstable and lacks detectable demethylase activity. Patient fibroblasts do not show global changes in histone methylation but we identify several up-regulated genes, suggesting local changes in chromatin conformation and gene expression. This thorough examination of KDM, C patient mutations demonstrates the utility of examining the molecular consequences of patient mutations on several levels, ranging from enzyme production to catalytic activity, when assessing the functional outcomes of intellectual disability mutations.