Biallelic EHMT2 Variants Identified in Second-Ever Case of Autosomal Recessive Kleefstra-Like Neurodevelopmental Syndrome
Key Insights
A 31-month-old male with global developmental delay, congenital heart disease, and dysmorphic features was found to harbor compound heterozygous EHMT2 (search) variants via trio genome sequencing.
RNA sequencing confirmed the maternally inherited intronic variant causes aberrant splicing in ~25% of transcripts, while the paternal frameshift variant showed reduced transcript abundance consistent with nonsense-mediated decay.
DNA methylation episignature analysis demonstrated the proband's profile clusters with Kleefstra syndrome type 1 (search) (KS1) patients, supporting a causal role for EHMT2 (search) in neurodevelopmental disease.
A multinational team of researchers has identified compound heterozygous variants in EHMT2 (search) in a 31-month-old male presenting with a constellation of features overlapping Kleefstra syndrome type 1 (search) (KS1), providing the second documented case of autosomal recessive inheritance for this emerging neurodevelopmental disorder. The findings, published in Frontiers in Genetics, strengthen the case for EHMT2 as a disease-causing gene and clarify the molecular consequences of biallelic variants through integrated multi-omics analysis.
The proband, of Russian and Eastern European descent, was referred for genetics evaluation following abnormal prenatal ultrasounds suggestive of small omphalocele, ventricular septal defect, short corpus callosum, inferior vermis hypoplasia, absent nasal bone, and absent gallbladder. Postnatal evaluation confirmed tricuspid valve dysplasia, ventricular septal defect, type B interrupted aortic arch, umbilical hernia, low-lying conus, right cryptorchidism, and chordee. Brain MRI revealed thickening of the superior cerebellar peduncles with vermian hypodysplasia.
Clinical Phenotype Aligns with Kleefstra Syndrome Spectrum
At 19 months, the patient exhibited hypotonia, recurrent otitis media requiring myringotomy tube placement, obstructive sleep apnea necessitating nocturnal CPAP, recurrent respiratory infections, nephrocalcinosis, and scoliosis. Global developmental delay was evident, with independent sitting achieved at 11 months and independent walking at 28 months. He was diagnosed with autism spectrum disorder at 18 months. Physical examination revealed plagiocephaly, square face, midface flattening, arched eyebrows, hypertelorism, wide nasal root, open-mouth posturing with protruding tongue, everted lower lip vermilion, and prognathia.
Growth parameters at 19 months showed weight at 14.9 kg (>99th percentile), height at 86.5 cm (80th percentile), and head circumference at 44 cm (<1st percentile, corresponding to the 50th percentile for a 6-month-old).
Trio Genome Sequencing Reveals Biallelic EHMT2 (search) Variants
Following non-diagnostic prenatal microarray and trio exome sequencing — which identified only a maternally inherited pathogenic CEP290 variant considered consistent with carrier status — trio genome sequencing at Baylor Genetics Laboratory (search) uncovered biallelic variants of uncertain significance in EHMT2 (search). The paternally inherited variant, NM_006709.5:c.2648_2649del p.(Glu883Glyfs*48), is a frameshift in the ankyrin repeat domain. The maternally inherited variant, NM_006709.5:c.2344-19_2344-16del r.spl, is a 4-bp deletion in intron 18 predicted by SpliceAI to create a cryptic acceptor site (acceptor gain Δ score = 0.29).
RNA Sequencing Confirms Aberrant Splicing and Reduced Transcript Abundance
Targeted reflex RNA sequencing from peripheral blood demonstrated that the maternally inherited variant results in multiple aberrant splice isoforms in approximately 25% of reads, including an event causing retention of 291 nucleotides of intron 18 that generates a nonsense variant in the canonical EHMT2 (search) transcript [NM_006709.5:r.2343_2344ins291; p.(Asp782*)], likely triggering nonsense-mediated decay. The paternally inherited frameshift variant was not associated with alternate splicing events, but analysis revealed reduced abundance of the variant-bearing transcript, consistent with partial nonsense-mediated decay.
DNA Methylation Episignature Matches KS1
DNA methylation episignature profiling using the clinically validated EpiSign v5 test demonstrated that the proband's methylation profile clustered with KS1 patients, while both parents clustered with healthy controls. The methylation variant pathogenicity (MVP) scores indicated high overlap between the proband's episignature and the KS1 profile, with very low overlap with other rare syndromes in the EpiSign Knowledge Database.
Comparative Analysis Across Reported EHMT2 (search) Cases
The authors systematically compared the proband's phenotype with seven previously reported individuals harboring de novo heterozygous EHMT2 (search) variants and one individual with a homozygous splice variant. All reported patients displayed a DNA methylation episignature overlapping with KS1. Key phenotypic features in the autosomal recessive cases included brachycephaly (2/2, 100%), midface flattening (2/2, 100%), eyebrow anomalies (2/2, 100%), prognathism (2/2, 100%), ptosis (2/2, 100%), congenital heart disease (2/2, 100%), hypotonia (2/2, 100%), developmental delay/intellectual disability (2/2, 100%), umbilical hernia (2/2, 100%), and spine anomalies (2/2, 100%).
In contrast, the seven autosomal dominant cases showed dental anomalies in all patients (7/7, 100%), a feature absent in both recessive cases (0/2, 0%). The dominant cases carried missense variants or in-frame deletions clustered in the SET domain, with a suspected dominant-negative mechanism, while the recessive cases harbored biallelic splice or frameshift variants with a suspected hypomorphic, loss-of-function mechanism.
"Though these reports support a role for EHMT2 (search) in a novel syndromic neurodevelopmental disorder, this gene is not yet recognized as disease-causing in the Online Mendelian Inheritance in Man (OMIM) database and the mode of inheritance (autosomal dominant versus recessive) is unclear," the authors noted, underscoring the importance of describing additional cases.
The findings allowed for anticipatory guidance regarding recurrence risk for the family, a critical benefit of establishing the autosomal recessive inheritance pattern. The EHMT2 (search) variants have been submitted to ClinVar under accession numbers SCV007495237 and SCV007516937.