Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome

Novel Phenotypes and Genotype-Phenotype Correlations in a Large Clinical Cohort of Patients With Kleefstra Syndrome

Kleefstra syndrome (KLEFS) is a genetic neurodevelopmental disorder caused by haploinsufficiency of EHMT1. The full spectrum of clinical features and genotype-phenotype correlations is currently not fully understood. We performed a retrospective chart review of patients with KLEFS evaluated at the Boston Children's Hospital Kleefstra Clinic. There were 65 individuals (40 females, 25 males, mean age 9.3 years). 17% had large 9q34 deletions (≥ 1 Mb), 29% had small 9q34 deletions (< 1 Mb), and 54% had sequence variants. Global developmental delay (GDD) or intellectual disability (ID) was present in 77%. Behavioral disorders, such as autism spectrum disorder (38%), were common. Epilepsy affected 15%. Systemic health issues included structural cardiac defects (40%), hearing loss (32%), and constipation (31%). Novel features including subgroups with significant motor impairment (24%) and refractory epilepsy (9%), as well as small numbers with opsoclonus-like eye movements (n = 2), thrombocytopenia (n = 2), progressive cerebral atrophy (n = 1), and adrenal carcinoma (n = 1). 9q34 deletion subgroups had higher rates of GDD/ID (p = 0.037), significant motor impairment (p = 0.01), epilepsy (p = 0.004), and cortical visual impairment (p = 0.003) compared to the subgroup with sequence variants. This information may be used to improve clinical care as well as inform research and future therapeutic initiatives.

EHMT2 as a Candidate Gene for an Autosomal Recessive Neurodevelopmental Syndrome

Neurodevelopmental disorders (NDD) comprise clinical conditions with high genetic heterogeneity and a notable enrichment of genes involved in regulating chromatin structure and function. The EHMT1/2 epigenetic complex plays a crucial role in repression of gene transcription in a highly tissue- and temporal-specific manner. Mutations resulting in heterozygous loss-of-function (LoF) of EHMT1 are implicated in Kleefstra syndrome 1 (KS1). EHMT2 is a gene acting in epigenetic regulation; however, the involvement of mutations in this gene in the etiology of NDDs has not been established thus far. A homozygous EHMT2 LoF variant [(NM_006709.5):c.328 + 2 T > G] was identified by exome sequencing in an adult female patient with a phenotype resembling KS1, presenting with intellectual disability, aggressive behavior, facial dysmorphisms, fused C2-C3 vertebrae, ventricular septal defect, supernumerary nipple, umbilical hernia, and fingers and toes abnormalities. The absence of homozygous LoF EHMT2 variants in population databases underscores the significant negative selection pressure exerted on these variants. In silico evaluation of the effect of the EHMT2(NM_006709.5):c.328 + 2 T > G variant predicted the abolishment of intron 3 splice donor site. However, manual inspection revealed potential cryptic donor splice sites at this EHMT2 region. To directly access the impact of this splice site variant, RNAseq analysis was employed and disclosed the usage of two cryptic donor sites within exon 3 in the patient's blood, which are predicted to result in either an out-of-frame or in-frame effect on the protein. Methylation analysis was conducted on DNA from blood samples using the clinically validated EpiSign assay, which revealed that the patient with the homozygous EHMT2(NM_006709.5):c.328 + 2 T > G splice site variant is conclusively positive for the KS1 episignature. Taken together, clinical, genetic, and epigenetic data pointed to a LoF mechanism for the EHMT2 splice variant and support this gene as a novel candidate for an autosomal recessive Kleefstra-like syndrome. The identification of additional cases with deleterious EHMT2 variants, alongside further functional validation studies, is required to substantiate EHMT2 as a novel NDD gene.

A Novel Frameshift Variant and a Partial EHMT1 Microdeletion in Kleefstra Syndrome 1 Patients Resulting in Variable Phenotypic Severity and Literature Review

BACKGROUND

Kleefstra syndrome 1(KLEFS1, OMIM#610253) is a rare neurodevelopmental disorder (NDD) instigated by heterozygous variants or microdeletions occurring in the 9q34.4 genomic region of the euchromatic histone methyltransferase-1 (EHMT1) gene and is inherited in an autosomal dominant (AD) manner. The clinical phenotype of KLEFS1 includes moderate to severe intellectual disability (ID), hypotonia, and distinctive facial features and additionally involves other organ systems (heart, renal, genitourinary, sensory) albeit with phenotypic heterogeneity between patients. The purpose of this study is to expand the genotypic spectrum of KLEFS1 and compare phenotypic features of the syndrome of already published cases.

METHODS

Exome sequencing (ES), chromosomal microarray analysis (CMA), as well as sanger sequencing, for confirmation of the de novo status of the frameshift variant, were used.

RESULTS

Here we describe two more cases, both males with a similar age and carriers of novel variants; one with a frameshift variant involving exon 13: p.Val692Glyfs*64 and the other with the smallest so far described, 11 Kb (exons 19-25), 9q34.4 microdeletion: 9q34.3 (140703393-140714454). Both presented with an NDD disorder with one showing more severe ID with significant social disabilities, while the other with the microdeletion had mild ID and following a normal education curriculum. Neither of them were obese nor had any other significant organ system disorder.

CONCLUSIONS

The observed phenotypic variability due to genotypic differences in the two children contributes to the expanding spectrum of KLEFS1 disease phenotypes.

Highlighting cardiovascular manifestations of kleefstra syndrome: literature review and clinical insights

Kleefstra syndrome (KLEFS1) is a rare genetic disorder primarily caused by the deletion of the chromosome 9q34.3 genomic segment or pathogenic mutations in the euchromatin histone methyltransferase 1 (EHMT1) gene. It is characterized by intellectual disability or impairment, childhood hypotonia, and distinct facial features. Notably, cardiovascular defects especially congenital heart diseases also represent a major feature of KLEFS1. While the neuropsychiatric aspects of KLEFS1 have been extensively documented and researched, the cardiovascular manifestations have not received adequate attention. The majority of KLEFS1 patients often present with a spectrum of cardiovascular defects, including abnormal cardiac structure, arrhythmias, valve abnormalities, cardiomyopathy, and coronary artery abnormalities. Here, we systematically searched and reviewed previously published articles and case reports related to KLEFS1, conducting a comprehensive analysis of the existing literature to highlight the cardiovascular manifestations of this genetic disorder and explore the potential correlations between the cardiac phenotype and KLEFS1. Clinical trial number: Not applicable.