An Integrated Phenotypic and Genotypic Approach Reveals a High‐Risk Subtype Association for EBF3 Missense Variants Affecting the Zinc Finger Domain

Abstract

Objective: Collier/Olf/EBF (COE) transcription factors have distinct expression patterns in the developing and mature nervous system. To date, a neurological disease association has been conclusively established for only the Early B-cell Factor-3 (EBF3) COE family member through the identification of heterozygous loss-of-function variants in individuals with autism spectrum/neurodevelopmental disorders (NDD). Here, we identify a symptom severity risk association with missense variants primarily disrupting the zinc finger domain (ZNF) in EBF3-related NDD. Methods: A phenotypic assessment of 41 individuals was combined with a literature meta-analysis for a total of 83 individuals diagnosed with EBF3-related NDD. Quantitative diagnostic phenotypic and symptom severity scales were developed to compare EBF3 variant type and location to identify genotype-phenotype correlations. To stratify the effects of EBF3 variants disrupting either the DNA-binding domain (DBD) or the ZNF, we used in vivo fruit fly UAS-GAL4 expression and in vitro luciferase assays. Results: We show that patient symptom severity correlates with EBF3 missense variants perturbing the ZNF, which is a key protein domain required for stabilizing the interaction between EBF3 and the target DNA sequence. We found that ZNFassociated variants failed to restore viability in the fruit fly and impaired transcriptional activation. However, the recurrent variant EBF3 p.Arg209Trp in the DBD is capable of partially rescuing viability in the fly and preserved transcriptional activation. Interpretation: We describe a symptom severity risk association with ZNF perturbations and EBF3 loss-of-function in the largest reported cohort to date of EBF3-related NDD patients. This analysis should have potential predictive clinical value for newly identified patients with EBF3 gene variants.

A novel heterozygous variant of the SALL1 gene with atypical Townes‐Brocks syndrome phenotypes in Chinese family

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“…As stem cell-derived organoids are used to investigate the cellular phenotypes of genetic mutations associated with neuropsychiatric conditions 40,41 , we examined the expression of genes with coding variation associated with neurodevelopmental disorders (NDD) 42 , autism spectrum disorder (ASD) 42 , and schizophrenia (SCZ) 43 in cells generated in the organoid screen (Fig. S6A).…”

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

“…EBF3, which encodes the EBF transcription factor 3, is an example of both a CCDD gene and a multi-hit gene. Monoallelic EBF3 loss-of-function (LoF) coding mutations cause Hypotonia, Ataxia, and Delayed Development Syndrome (HADDS) 94 , and two individuals are reported with HADDS and DRS, one with a coding missense variant and one with a splice site variant 92,95 . We identified a series of coding and noncoding EBF3 variants ( Supplementary Table 11 ).…”