Dissecting KMT2D missense mutations in Kabuki syndrome patients

Abstract

Kabuki syndrome is a rare autosomal dominant condition characterized by facial features, various organs malformations, postnatal growth deficiency and intellectual disability. The discovery of frequent germline mutations in the histone methyltransferase KMT2D and the demethylase KDM6A revealed a causative role for histone modifiers in this disease. However, the role of missense mutations has remained unexplored. Here, we expanded the mutation spectrum of KMT2D and KDM6A in KS by identifying 37 new KMT2D sequence variants. Moreover, we functionally dissected 14 KMT2D missense variants, by investigating their impact on the protein enzymatic activity and the binding to members of the WRAD complex. We demonstrate impaired H3K4 methyltransferase activity in 9 of the 14 mutant alleles and show that this reduced activity is due in part to disruption of protein complex formation. These findings have relevant implications for diagnostic and counseling purposes in this disease.

Update of the genotype and phenotype ofKMT2DandKDM6Aby genetic screening of 100 patients with clinically suspected Kabuki syndrome

“…We identified a deep splicing variant of KMT2D (c.14000-8C>G) in our cohort. To our knowledge, only three splicing variants of KMT2D (c.840-6delC, c.4584-6C>G, and c.10356-9G>A) have been reported to reside deeper than five nucleotides (Banka et al, 2012;Cocciadiferro et al, 2018), but no variant has been proven by RNAseq. We performed RNA-seq analysis and confirmed the presence of aberrantly spliced KMT2D mRNA in lymphocytes from the patient (Figure 2b).…”

“…p.(Glu5038Lys) was not located in any of the known functional domains, but was in a specific region (amino acids 4,995-5,090) where missense mutations in KS are particularly concentrated (Faundes et al, 2019). Many missense variants of KS patients in the C-terminal region of KMT2D have been demonstrated to impair its histone H3 lysine nine methylation activity and protein complex formation (Cocciadiferro et al, 2018). Further characterization of the protein structure and functional domains of KMT2D would enable the accurate evaluation of the pathogenicity of KMT2D missense variants in the diagnostic setting.…”

Phenotypic expansion of KMT2D‐related disorder: Beyond Kabuki syndrome

“…Focused analyses of missense variants in KMT2D have recently been published. Cocciadiferro et al () identified missense variants associated with Kabuki syndrome along the entire length of the protein and used functional studies to demonstrate that some missense variants abrogate histone methylation activity, confirming these are loss‐of‐function variants. Faundes et al () analyzed three groups of missense variants in KMT2D : 1) germline variants associated with Kabuki syndrome, 2) somatic variants found in various cancers, and 3) a compilation of “control” variants observed in ExAC (Lek et al, ) and similar databases.…”

“…Missense variants are observed in approximately 15–20% of cases, and can occur along the entire length of the protein (Bogershausen et al, ). Recent reports have attempted to categorize these variants, which appear to cluster in specific functional domains, although their pathogenicity can be more difficult to interpret (Bogershausen et al, ; Cocciadiferro et al, ; Faundes, Malone, Newman, & Banka, ).…”

Facial Dysmorphisms, Macrodontia, Focal Epilepsy, and Thinning of the Corpus Callosum: A Rare Mild Form of Kabuki Syndrome

“…This study provided evidence that some naturally occurring missense mutations in KMT2D effectively impact KMT2D interaction and H3K4 methylation activity. 17 The c.2413C > T missense variant, detected in our patient, has not been previously reported in the literature and has not been annotated in variant database (Leiden Open Variation Database [www.lovd.nl/], the PubMed database of National Center for Biotechnology Information (www.ncbi. nlm.nih.gov/), the Human Gene Mutation Database (www.…”