Pathogenicity of NUSAP1 Variants Is Defined by NMD-Escape: Evidence From Two Novel Cases and Systematic Population-Based Variant Analysis.
Protein-truncating variants in the 3' region of a transcript, evading mRNA degradation and giving rise to aberrant truncated proteins, are an underrecognized cause in Mendelian diseases. Here, we report two individuals with heterozygous de novo nonsense variants in the penultimate and last exon of NUSAP1, both presenting with early-onset refractory epilepsy, global developmental delay, congenital microcephaly, and a recognizable facial gestalt. RNA sequencing performed in one individual did not show a reduction in expression, compatible with escape of aberrant transcripts from nonsense mediated mRNA decay (NMD). We systematically analyzed gnomAD population data to delineate a critical region at the 3' region of NUSAP1, where nonsense variants introduce a premature termination codon and escape NMD. Such variants are absent from healthy controls, while frameshift variants producing C-terminal elongations appear tolerated. This position-dependent model provides guidance for diagnostic variant interpretation.