Functional analysis of a de novo variant in the neurodevelopment and generalized epilepsy disease gene NBEA

Thomas Boulin,Omar Itani,Sonia El Mouridi,Alice Leclercq-Blondel,Marie Gendrel,Ellen Macnamara,Ariane Soldatos,Jennifer L Murphy,Mark P Gorman,Anika Lindsey,Shino Shimada,Darian Turner,Gary A Silverman,Dustin Baldridge,May C Malicdan,Tim Schedl,Stephen C Pak

doi:10.1016/j.ymgme.2021.07.013

Abstract

Neurobeachin (NBEA) was initially identified as a candidate gene for autism. Recently, variants in NBEA have been associated with neurodevelopmental delay and childhood epilepsy. Here, we report on a novel NBEA missense variant (c.5899G > A, p.Gly1967Arg) in the Domain of Unknown Function 1088 (DUF1088) identified in a child enrolled in the Undiagnosed Diseases Network (UDN), who presented with neurodevelopmental delay and seizures. Modeling of this variant in the Caenorhabditis elegans NBEA ortholog, sel-2, indicated that the variant was damaging to in vivo function as evidenced by altered cell fate determination and trafficking of potassium channels in neurons. The variant effect was indistinguishable from that of the reference null mutation suggesting that the variant is a strong hypomorph or a complete loss-of-function. Our experimental data provide strong support for the molecular diagnosis and pathogenicity of the NBEA p.Gly1967Arg variant and the importance of the DUF1088 for NBEA function.

Highlights

Neurobeachin, encoded by the NBEA gene, is a large (327 kDa), brain-enriched, multi-domain protein, that has been widely conserved during evolution
We introduced the patient missense change into sel-2, the ortholog of Neurobeachin in C. elegans, using CRISPR/Cas9 gene editing and assessed the impact of sel-2 Gly1514Arg, corresponding to NBEA p.Gly1967Arg, using two in vivo assays that test the functionality of SEL-2
Our proband is a six-year-old female who presented with epilepsy, global developmental delay, and ataxia. She was enrolled in the Undiagnosed Diseases Network protocol, 15-HG-0130, which is approved by the NIH National Human Genome Research Institute Institutional Review Board (IRB), and was seen at the NIH Clinical Center

Summary

Introduction

Neurobeachin, encoded by the NBEA gene, is a large (327 kDa), brain-enriched, multi-domain protein, that has been widely conserved during evolution. In Drosophila, mutants in the NBEA ortholog, rugose, have associative odor learning defects and abnormal synaptic architecture and physiology at larval neuromuscular junctions [1,2]. Neurobeachin is required for both electrical and chemical synapse formation, and to maintain dendritic complexity [3]. Neurobeachin has been implicated in vesicle trafficking and synaptic structure and function [3,4,5,6,7]. Nbea knockout neurons in vitro fail to develop a normal number of dendritic spines [5]. Neurobeachin contributes to the trafficking of membrane proteins to pre- and postsynaptic sites [8].

Methods

Results

Conclusion