Abstract

Background Rauch-Steindl syndrome (RAUST) is a rare neurodevelopmental disorder caused by pathogenic variants in NSD2 , a histone methyltransferase gene at 4p16.3. Due to phenotypic overlap with Wolf-Hirschhorn syndrome (WHS), RAUST is often misdiagnosed. Missense variants in NSD2 are particularly challenging to interpret without functional validation. Methods Genomic DNA from the proband and her parents was extracted from peripheral blood. Trio-whole-exome sequencing (WES) was performed to identify candidate variants based on the clinical phenotype, followed by Sanger sequencing validation. RNA splicing impact was assessed via reverse transcription PCR and TA-cloning from peripheral blood mononuclear cells. Results A 7-year-8-month-old girl mainly presented with intrauterine and postnatal growth restriction, global developmental delay, intellectual disability, epilepsy, short stature, and facial dysmorphism was documented. Trio-WES identified a novel de novo missense variant in NSD2 (NM_001042424.3: c.2137G>C, p.Gly713Arg), which is located at the last base of exon 11 and was predicted to be highly likely to cause aberrant splicing. Functional analysis revealed this variant causes exon 11 skipping in 53% of transcripts, resulting in a frameshift (p.Leu672Glyfs*20) and premature truncation. Conclusion This is the first report of an NSD2 missense variant that functionally acts as a splicing mutation leading to protein truncation. Our findings highlight the necessity of RNA-level functional assays for accurate variant interpretation and reinforce genotype–phenotype distinctions between RAUST and WHS.