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Background Heterozygous PURA (Purine-rich element-binding protein A) variants cause PURA syndrome, a neurodevelopmental disorder characterised by hypotonia, seizures and intellectual disability. Previous studies have focused on the effect of the PURA variant in the cytoplasmic location, but nuclear mislocalisation remains to be explored.Methods We identified a de novo heterozygous frameshift variant (c.442del, p.L148Wfs*77) via trio whole-exome sequencing in one child suspected of PURA syndrome due to intellectual disability. Functional analyses included structural modelling, subcellular localisation assays, RNA-seq, CUT&Tag and DNA unwinding assays.Results The variant disrupts PURA repeats II–III, causing aberrant nuclear mislocalisation. RNA-seq revealed 688 differentially expressed genes enriched in neurodevelopmental pathways. CUT&Tag analysis revealed that PURA and Pol II exhibit enhanced binding at transcription start sites in cells expressing the variant, indicating dysregulated transcriptional engagement. Despite retained nucleic acid binding, the variant impaired DNA unwinding partly due to disrupted repeat III-mediated homodimerisation.Conclusions Nuclear mislocalisation of the PURA variant dysregulates transcriptional balance and impairs DNA unwinding, linking PURA’s structural integrity to neurodevelopmental deficits. This highlights PURA’s dual roles in cytoplasmic RNA regulation and nuclear transcription, providing mechanistic insights into PURA syndrome pathogenesis.