Biallelic EZH1 Nonsense Novel Variant in Two Siblings with Neurodevelopmental Disorder and Central Precocious Puberty: A Case Report from a Consanguineous Saudi Family
Aug 2026· International Journal of Molecular Sciences· Vol 27· 0 citations· 38 references
Medicine
TL;DR
This study expands the clinical, genetic, and molecular spectrum of EZH1-associated neurodevelopmental disorders by demonstrating that reduced EZH1 expression is consistent with a loss-of-function disease mechanism.
Abstract
Neurodevelopmental disorders (NDDs) are a group of conditions that impair the development and function of the central nervous system. Recently, variants in the EZH1 gene have been associated with neurodevelopmental disorders. Here, using whole-exome sequencing coupled with confirmatory Sanger sequencing, we identified a homozygous nonsense variant in EZH1 in two affected siblings. Both parents were heterozygous carriers of the variant. The variant is predicted to result in a 44-amino acid C-terminal truncation within the catalytic SET domain, leading to loss of protein function. RT-qPCR analysis revealed significantly reduced EZH1 mRNA expression in patient-derived peripheral blood cells. The index patient (female) also exhibited elevated gamma-glutamyl transferase (GGT) levels and hypoalbuminemia, whereas the affected male presented with central precocious puberty. This study further expands the clinical, genetic, and molecular spectrum of EZH1-associated neurodevelopmental disorders by demonstrating that reduced EZH1 expression is consistent with a loss-of-function disease mechanism.
Consanguinity increases the risk of autosomal recessive disorders and may result in the co-segregation of multiple pathogenic variants within the same family. Although most affected families are explained by a single genetic diagnosis, multilocus pathogenic variation can produce complex and overlapping clinical phenotypes. We investigated a consanguineous Pakistani family with three affected siblings, including dizygotic twins presenting with neurodevelopmental disorder and hearing loss, using detailed clinical evaluation, long-read whole-genome sequencing, bulk transcriptomics, protein profiling, and segregation analysis to determine the underlying molecular diagnoses. One sibling presented with isolated non-syndromic hearing loss, whereas the dizygotic twins exhibited severe neurodevelopmental impairment characterized by global developmental delay, spastic quadriplegic cerebral palsy, microcephaly, and white matter abnormalities. Long-read whole-genome sequencing identified a homozygous start-loss variant in HPDL (c.3G>C) in both twins, consistent with HPDL-related neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities (NEDSWMA). In addition, a novel homozygous nonsense variant in EPS8 (c.1294C>T) was identified in one twin and the sibling with isolated hearing loss, explaining the auditory phenotype. Long-read transcriptomic analysis demonstrated absence of detectable EPS8 transcripts in both individuals homozygous for the nonsense variant, providing transcript-level evidence consistent with a loss-of-function mechanism. Genome-wide comprehensive proteomic profiling (SomaScan) identified distinct protein abundance profiles across family members, with the most pronounced alterations observed in the twins affected by HPDL-related neurodevelopmental disease, particularly the individual harboring pathogenic variants in both EPS8 and HPDL. This study expands the mutational spectrum of EPS8 and highlights the independent segregation of two autosomal recessive disorders within the complex consanguineous family, resulting in distinct and blended phenotypes.
Bassam Jamalalail, Ahmed A. Khalifa, Bipin Balan et al.· bioRxiv· 0 citations
Biallelic variants in a family with sequence similarity 149 member B1 gene (FAM149B1, OMIM #618413) causes a range of abnormal phenotypes associated with Joubert syndrome (JS) in humans. However, the phenotypic spectrum and genetic evidence linking FAM149B1 to ciliopathies remain limited, with no prenatal cases previously described. Here, we report the first prenatal case from a non-consanguineous Chinese family presenting with isolated right pelvicalyceal and ureteral dilation at 24 weeks of gestation. Notably, the fetus lacked cerebellar malformations or hallmark neuroimaging features such as molar tooth sign (MTS). Trio-whole-exome sequencing (Trio-WES) identified novel compound heterozygous loss-of-function variants in FAM149B1: paternal c.279T>A (p.Tyr93*) and maternal c.574dup (p.Ser192Phefs*7). Both variants are predicted to trigger nonsense-mediated mRNA decay (NMD), consistent with a loss-of-function mechanism, and parental segregation confirmed asymptomatic heterozygous carrier status, supporting autosomal recessive inheritance. Gene-disease validity assessment assigned a "Strong" classification to FAM149B1-related ciliopathy under ClinGen guidelines, enabling definitive classification of the variants as pathogenic or likely pathogenic. This case expands the phenotypic spectrum of FAM149B1-related disorders to include isolated urinary tract malformations in the prenatal period, where neurological manifestations may be absent or subtle. Our findings highlight the utility of prenatal exome sequencing in atypical cases and contribute to the understanding of the expanding genetic and phenotypic landscape of ciliopathies.
Jinyu Liu, Yi Wu, Shixuan Xu et al.· Intractable & Rare Diseases...· 0 citations
Findings support a dose-dependent SLC20A2 disease spectrum and expand the phenotype associated with biallelic loss of function from primary brain calcification toward severe early-onset neurodevelopmental disorder with prominent vascular and leptomeningeal calcification.
Mehmet Burak Mutlu, Abdullah Sezer, Elif Özdemir et al.· Journal of Human Genetics· 0 citations
The data establish BHLHE22 as a previously unrecognized neurodevelopmental disease gene that results in a distinct syndrome characterised by abnormalities in brain development, cognition, tone and movement.
Carolyn Le, T. Kalaycı, Z. Uyguner et al.· Journal of Medical Genetics· 0 citations
Introduction: Arrhythmogenic cardiomyopathy (ACM) is a myocardial disorder characterized by fibrofatty replacement of the myocardium and is associated with heart failure and sudden cardiac death. It can involve either ventricle, including left-dominant forms defined partly by genetic findings. Methods: We investigated a consanguineous family with four affected daughters presenting with ACM, epidermolytic palmoplantar keratoderma, and woolly hair. The two eldest siblings died suddenly during childhood. The remaining two affected siblings underwent genetic analysis using autozygosity mapping and whole-exome sequencing, followed by segregation analysis. Results: Autozygosity mapping identified a shared identity-by-descent (IBD) interval at the DSP locus on chromosome 6. Exome sequencing revealed a novel homozygous nonsense variant (c.4297C>T; p.Gln1433*; rs1554108283) in exon 23 of DSP. This variant introduces a premature termination codon within the region specific to transcript variant 1, sparing transcript variant 2. Both parents were heterozygous carriers. Cardiac imaging in the affected siblings demonstrated biventricular involvement, including left ventricular systolic dysfunction and right ventricular dilatation. Skin biopsy in one patient confirmed epidermolytic palmoplantar keratoderma. Conclusions: We describe a novel homozygous nonsense variant in the transcript 1-specific region of DSP causing Carvajal syndrome, characterized by severe biventricular ACM, epidermolytic palmoplantar keratoderma, and woolly hair, in a consanguineous Arabian family with four affected sisters.
Dalal A. Al-Mutairi, Mustafa Alqbandi, A. AlTurki et al.· Journal of Clinical Medicine· 0 citations
Neurodevelopmental disorder, speech impairment, and dysmorphic facies (NEDSID) is an autosomal dominant condition primarily driven by SETD1A haploinsufficiency. While most documented cases are sporadic, genomic mechanisms underlying intrafamilial phenotypic heterogeneity remain poorly understood. This study presents a comprehensive clinical, neurophysiological, and molecular characterization of a two-generation Mexican family segregating a novel heterozygous missense SETD1A variant. Whole-exome sequencing (WES) identified a c.1604G>A (p.Gly535Glu) substitution localized within the critical Functional Location on SETD1A (FLOS) domain, which was validated via automated Sanger sequencing across all family members and 100 ethnically matched controls. The proband exhibited a moderate NEDSID phenotype, including global developmental delay, macrocephaly, borderline IQ (79) with pronounced information-processing deficits, and abnormal EEG sharp waves. Conversely, first-degree relatives carrying the identical variant presented with mild, non-intellectually disabling phenotypes characterized primarily by isolated psychiatric disorders (bipolar disorder, depression) and minimal dysmorphism. Structural 3D modeling and multi-algorithmic in silico profiling confirmed high evolutionary conservation and a deleterious impact (CADD: 22.2, SIFT: 0.00, GERP: 2.924), classifying the variant as a Variant of Uncertain Significance (VUS)/Likely Pathogenic according to ACMG/AMP criteria (PM2, PP1, PP3, PP4). Furthermore, epigenetic dysregulation and chromatin remodeling defects increasingly link these histone-modifier variants to broader psychiatric landscapes. Emerging transcriptomic profiling confirms that dosage-sensitive COMPASS complex disruptions alter downstream neurodevelopmental gene cascades. Our findings present observational evidence of intrafamilial clinical variability in a single pedigree with a SETD1A missense alteration, supporting the hypothesis that non-catalytic domain substitutions may contribute to diverse neurodevelopmental outcomes.
L. M. G. Huerta, Miguel Ángel Fonseca Sánchez, Marcela Esquivel Velázquez et al.· Diseases· 0 citations