Splicing Interruption by Intron Variants in CSNK2B Causes Poirier-Bienvenu Neurodevelopmental Syndrome: A Focus on Genotype-Phenotype Correlations

Abstract

CSNK2B has recently been identified as the causative gene for Poirier-Bienvenu neurodevelopmental syndrome (POBINDS). POBINDS is a rare neurodevelopmental disorder characterized by early-onset epilepsy, developmental delay, hypotonia, and dysmorphism. Limited by the scarcity of patients, the genotype-phenotype correlations in POBINDS are still unclear. In the present study, we describe the clinical and genetic characteristics of eight individuals with POBINDS, most of whom suffered developmental delay, generalized epilepsy, and hypotonia. Minigene experiments confirmed that two intron variants (c.367+5G>A and c.367+6T>C) resulted in the skipping of exon 5, leading to a premature termination of mRNA transcription. Combining our data with the available literature, the types of POBINDS-causing variants included missense, nonsense, frameshift, and splicing, but the variant types do not reflect the clinical severity. Reduced casein kinase 2 holoenzyme activity may represent a unifying pathogenesis. We also found that individuals with missense variants in the zinc finger domain had manageable seizures (p = 0.009) and milder intellectual disability (p = 0.003) than those with missense variants in other domains of CSNK2B. This is the first study of genotype-phenotype correlations in POBINDS, drawing attention to the pathogenicity of intron variants and expanding the understanding of neurodevelopmental disorders.

Keywords: CSNK2B; Poirier–Bienvenu neurodevelopmental syndrome; genotype; intron variants; phenotype.

FIGURE 1

Minigene splicing assay for intron variants. (A) Schematic diagram of minigene plasmid construction. Red bases are targeted sites. (B) Minigene was transfected into HEK293 cells and Hela cells, respectively. A single band was detected by RT-PCR with a lower molecular weight than wild-type CSNK2B. (C,D) Sequencing of the above bands revealed that three splicing variants (c.367+2T>C, c.367+5G>A, and c.367+6T>C) all resulted in exon 5 skipping and early termination of the amino acids.

FIGURE 2

Information on POBINDS-causing CSNK2B mutations (n = 82). (A) Distribution of mutation types. (B) Schematic representation of the mutation distribution (top) and “MetaDome” tolerance level through whole gene (blew). Red vertical lines represent LOF mutations (including start loss, frameshift insertion/deletion, nonsense, and splicing site), and green vertical lines represent non-LOF mutations (including missense and in-frame insertion/deletion). The length of vertical lines represents the number of reported cases. The zinc finger domain is more tolerant than other regions, which is revealed by the “MetaDome” algorithm, this is also consistent with the clinical findings that missense mutation in the zinc finger domain leads to milder phenotypes. References and databases for all sources of mutation information are detailed in Supplementary Table 1.