Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing

Abstract

Roifman Syndrome is a rare congenital disorder characterized by growth retardation, cognitive delay, spondyloepiphyseal dysplasia and antibody deficiency. Here we utilize whole-genome sequencing of Roifman Syndrome patients to reveal compound heterozygous rare variants that disrupt highly conserved positions of the RNU4ATAC small nuclear RNA gene, a minor spliceosome component that is essential for minor intron splicing. Targeted sequencing confirms allele segregation in six cases from four unrelated families. RNU4ATAC rare variants have been recently reported to cause microcephalic osteodysplastic primordial dwarfism, type I (MOPD1), whose phenotype is distinct from Roifman Syndrome. Strikingly, all six of the Roifman Syndrome cases have one variant that overlaps MOPD1-implicated structural elements, while the other variant overlaps a highly conserved structural element not previously implicated in disease. RNA-seq analysis confirms extensive and specific defects of minor intron splicing. Available allele frequency data suggest that recessive genetic disorders caused by RNU4ATAC rare variants may be more prevalent than previously reported.

Extending the critical regions for mutations in the non‐coding gene RNU4ATAC in another patient with Roifman Syndrome

“…To our knowledge, twelve individuals affected with Roifman Syndrome have been described to date, of which ten cases are genetically confirmed 1, 2, 5, 6, 7, 8, 9, 10, 11. The case reported here is therefore the 13 th case of Roifman Syndrome.…”

“…The first four male individuals affected with this multisystem disorder were described as early as 1999 by Roifman, but it was Merico et al2 who described pathogenic variants in RNU4ATAC as the underlying cause for Roifman Syndrome. Whole‐genome sequencing in two affected siblings identified compound heterozygosity in RNU4ATAC as causative for Roifman Syndrome.…”

“…Both subregions are separated by the 5′stem‐loop, which functions as a binding platform for proteins required for tri‐snRNP formation of U4atac, U6atac, and U5. The 3′stem‐loop immediately precedes a binding site for Sm proteins, which are important for snRNP assembly and import into the nucleus2, 3, 12 (Figure 1). …”

“…Variants causing the more severe phenotype of MOPD1 both clusters in the 5′stem‐loop and a few are described at the Sm protein‐binding site and proximal portion of the 3′stem‐loop. For Lowry Wood Syndrome, no specific pattern of pathogenic variants could be identified in the three affected individuals described so far 2, 4, 5, 6…”

“…The syndrome was first reported by Roifman in 1999 1. Merico et al2 identified compound heterozygosity of pathogenic single‐nucleotide variants (SNVs) in RNU4ATAC to be causative for Roifman Syndrome in 2015. RNU4ATAC codes for the small nuclear RNA (snRNA) U4atac, which is part of the minor spliceosome complex that catalyzes the splicing of an atypical class of introns (U12‐ or “ATAC”‐type) from eukaryotic pre‐mRNA.…”