Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes

Abstract

Trithorax-related H3K4 methyltransferases, KMT2C and KMT2D, are critical epigenetic modifiers. Haploinsufficiency of KMT2C was only recently recognized as a cause of neurodevelopmental disorder (NDD), so the clinical and molecular spectrums of the KMT2C-related NDD (now designated as Kleefstra syndrome 2) are largely unknown. We ascertained 98 individuals with rare KMT2C variants, including 75 with protein-truncating variants (PTVs). Notably, ∼15% of KMT2C PTVs were inherited. Although the most highly expressed KMT2C transcript consists of only the last four exons, pathogenic PTVs were found in almost all the exons of this large gene. KMT2C variant interpretation can be challenging due to segmental duplications and clonal hematopoesis-induced artifacts. Using samples from 27 affected individuals, divided into discovery and validation cohorts, we generated a moderate strength disorder-specific KMT2C DNA methylation (DNAm) signature and demonstrate its utility in classifying non-truncating variants. Based on 81 individuals with pathogenic/likely pathogenic variants, we demonstrate that the KMT2C-related NDD is characterized by developmental delay, intellectual disability, behavioral and psychiatric problems, hypotonia, seizures, short stature, and other comorbidities. The facial module of PhenoScore, applied to photographs of 34 affected individuals, reveals that the KMT2C-related facial gestalt is significantly different from the general NDD population. Finally, using PhenoScore and DNAm signatures, we demonstrate that the KMT2C-related NDD is clinically and epigenetically distinct from Kleefstra and Kabuki syndromes. Overall, we define the clinical features, molecular spectrum, and DNAm signature of the KMT2C-related NDD and demonstrate they are distinct from Kleefstra and Kabuki syndromes highlighting the need to rename this condition.

Keywords: DNA methylation; EHMT1; KMT2C; KMT2D; Kabuki syndrome; Kleefstra syndrome; neurodevelopmental disorder.

Figure 1

KMT2C variant spectrum among the recruited individuals and population (A) Likely pathogenic and pathogenic single-nucleotide, indel, and copy number variants identified in this study are shown on the linear structure of KMT2C. (B) Likely pathogenic and pathogenic as well as benign copy number variants identified in this study in comparison shown on the KMT2C genomic region with segmental duplications (gray), as well as populational deletions and duplications from DGV and gnomAD databases.

Figure 2

DNAm signature classification results (A) PCA plot for the discovery cohort of 16 individuals with KMT2C-related NDD (red) and 50 controls (blue). (B) Heatmap plot with hierarchical clustering for the discovery cohort of 16 individuals with KMT2C-related NDD (red) and 50 controls (blue), with hypermethylated sites shown in yellow and hypomethylated sites in blue. (C) Differentially methylated region that maps to several WT1 CpG islands (green) and one of the promoters (purple) (data obtained from the UCSC genome browser) where each dot shows methylation level at a CpG site in the region for each discovery cohort sample, and the line depicts the mean methylation for controls (blue) and cases (red). (D) SVM model classification results for different groups: 16 discovery KMT2C-related NDD cases (red), 50 controls (magenta), validation KMT2C-related NDD cases (light blue) and their matched controls (dark blue), KMT2C VUSs (black), Kleefstra syndrome individuals (green), and Kabuki syndrome individuals (gray). (E) KMT2C-related NDD classification results against 17 other DNAm signatures.

Figure 3

Photos of individuals with the KMT2C-related NDD y.o., years old—the age of the individuals.