Clustered variants in the 5′ coding region of TRA2B cause a distinctive neurodevelopmental syndrome

• DOI: 10.1016/j.gim.2022.100003
• Publication Date: 2022-12-20T01:15:39Z
• Authors: Francis Ramond; Caroline Dalgliesh; Mona Grimmel; Oded Wechsberg; Annalisa Vetro; Renzo Guerrini; David FitzPatrick; Rebecca L. Poole; Marine Lebrun; Allan Bayat; Ute Grasshoff; Miriam Bertrand; Dennis Witt; Peter D. Turnpenny; Víctor Faundes; Lorena Santa María; Carolina Mendoza ...; Paulina Mabe; Shaun A. Hussain; Sureni V. Mullegama; Erin Torti; Barbara Oehl-Jasc...; Lina Basel Salmon; Naama Orenstein; Noa Ruhrman Shahar; Ofir Hagari; Lily Bazak; Sabine Hoffjan; Carlos E. Prada; Tobias Haack; David J. Elliott
• Keywords: Epilepsy; Infantile spasms; Serine-Arginine Splicing Factors; Autism Spectrum Disorder; Intellectual disability; 610; RNA-Binding Proteins; Nerve Tissue Proteins; Epilepsy Infantile; spasms Intellectual ;disability; Molecular genetics ;TRA2B; Alternative Splicing; HEK293 Cells; Neurodevelopmental Disorders; Intellectual Disability; 03 Salud y bienestar; authors declare no conflicts of interest; Humans; Protein Isoforms; 03 Good Health and Well-being; Molecular genetics; TRA2B

Transformer2 proteins (Tra2α and Tra2β) control splicing patterns in human cells, and no human phenotypes have been associated with germline variants in these genes. The aim of this work was to associate germline variants in the TRA2B gene to a novel neurodevelopmental disorder.A total of 12 individuals from 11 unrelated families who harbored predicted loss-of-function monoallelic variants, mostly de novo, were recruited. RNA sequencing and western blot analyses of Tra2β-1 and Tra2β-3 isoforms from patient-derived cells were performed. Tra2β1-GFP, Tra2β3-GFP and CHEK1 exon 3 plasmids were transfected into HEK-293 cells.All variants clustered in the 5' part of TRA2B, upstream of an alternative translation start site responsible for the expression of the noncanonical Tra2β-3 isoform. All affected individuals presented intellectual disability and/or developmental delay, frequently associated with infantile spasms, microcephaly, brain anomalies, autism spectrum disorder, feeding difficulties, and short stature. Experimental studies showed that these variants decreased the expression of the canonical Tra2β-1 isoform, whereas they increased the expression of the Tra2β-3 isoform, which is shorter and lacks the N-terminal RS1 domain. Increased expression of Tra2β-3-GFP were shown to interfere with the incorporation of CHEK1 exon 3 into its mature transcript, normally incorporated by Tra2β-1.Predicted loss-of-function variants clustered in the 5' portion of TRA2B cause a new neurodevelopmental syndrome through an apparently dominant negative disease mechanism involving the use of an alternative translation start site and the overexpression of a shorter, repressive Tra2β protein.