Functional impact of a novel splice-site variant in ASXL3: Bainbridge-Ropers syndrome
Novel mutations in the coding regions of ASXL3 (MIM 615115) have been associated with Bainbridge-Ropers syndrome (BRS; OMIM #615485). This syndrome was first described in 2013 by Bainbridge et al. as being caused by a mutation on ASXL3, a gene located on chromosome 18q12.1. BRS is characterized by a non-specific clinical phenotype that includes feeding disorders, hypotonia, intellectual disability, and developmental delay. The phenotypic spectrum of BRS often overlaps with Bohring–Opitz syndrome. However, identification of a mutation in ASXL3 confirms the BRS diagnosis. Reported ASXL3 mutations have been expanding the scope of understanding of BRS and of its diagnosis. Srivastava et al. reported that, together with BRCA1-Associated Protein-1 (BAP1), ASXL3 acts in the PR-DUB complex, known to remove monoubiquitin from the histone protein H2A. Thus, loss-of-function variants in ASXL3 affect the function of the PR-DUB complex, resulting in high levels of ubiquitinated H2A. Here, we report the case of a child with developmental delay, hypotonia, feeding disorder, and alternating exotropia. Conventional testing failed to yield a genetic diagnosis. Whole exome sequencing revealed a heterozygous, novel de novo splice site mutation in ASXL3 intron 11 (c. 3039 + 1 G > T, IVS 11 + 1 G > T). This single nucleotide variant affects the canonical splice donor site at the beginning of intron 11. The objective of our study is to define the functional impact of this splice-site mutation on RNA processing and protein signaling pathways, to confirm the diagnosis of BRS in our patient. We first confirmed (by RT-PCR) that ASXL3 is indeed expressed in patient-derived fibroblasts. Next, we performed Western blot analysis which showed an increase in ubiquitination of the H2A protein. We await the results of RNA sequencing studies from patient and control fibroblasts, to define precisely the effect of the mutation on RNA splicing. We expect that this will confirm that the mutant allele results in an abnormal, truncated protein that causes a gain-of-function cellular phenotype through epigenetic mechanisms. These findings will confirm this novel splice-site variant as a cause of BRS.