Genome-wide DNA methylation profiling confirms a case of low-level mosaic Kabuki syndrome 1

Abstract

Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.

Keywords: DNA methylation; HLHS (hypoplastic left heart syndrome); KMT2D; Kabuki syndrome; episignature; mosaicism.

FIGURE 1

Clinical features of the patient described in this report at 13 months of age (4 months after initial evaluation). (a) Facial features include arched eyebrows with lateral sparseness, long palpebral fissures with eversion of lateral third of the lower eyelids, long eyelashes, broad nasal tip, short columella, and epicanthal folds. Unique features included exophthalmos due to shallow orbits, depressed nasal bridge, and a bulbous nose. (b, c) Lateral views illustrating prominent ears. Persistence of (d) fingertip and (e) toe pads

FIGURE 2

EpiSign DNA methylation analysis of peripheral blood from a patient with a somatic mosaic nonsense variant in KMT2D, the causative gene for Kabuki syndrome 1 (KS1). (a) Hierarchical clustering and (b) multidimensional scaling plots indicate that the patient (red) has a DNA methylation signature similar to subjects with a confirmed KS episignature (blue) and distinct from controls (green). Each row of the heatmap represents one CpG probe on the DNA methylation array, and each column represents one individual's sample. The heatmap color scale from blue to red represents the DNA methylation level (beta value) from 0 (no methylation) to 1 (fully methylated). (c) MVP score, a multiclass supervised classification system capable of discerning between multiple episignatures by generating a probability score for each episignature. The elevated patient score for KS compared to other syndromes suggests an episignature similar to the KS reference signature; however, the decreased probability compared to what is typically observed for constitutional KS (score >0.5) likely results from the low‐level mosaicism of the variant