A novel de novo multi-exon deletion of SYT1 in a child with Baker-Gordon syndrome.

BACKGROUND: Baker-Gordon syndrome (BGS) is a rare autosomal dominant neurodevelopmental disorder caused by heterozygous pathogenic variants in SYT1, which encodes synaptotagmin-1, a key Ca2⁺ sensor for synaptic vesicle exocytosis. CASE PRESENTATION: We describe a 13-month-old Chinese boy who presented with global developmental delay, axial hypotonia, stereotypic hand-flapping movements, limited vocalization, and mild facial dysmorphism. Brain magnetic resonance imaging revealed a simplified gyral pattern involving the frontal and parietal lobes. Trio-based whole-exome sequencing with read-depth copy-number variant (CNV) analysis identified a novel de novo heterozygous deletion spanning exons 6-8 of SYT1, which was subsequently confirmed by quantitative PCR. CONCLUSION: This study broadens the mutational spectrum of BGS and provides further evidence that intragenic multi-exon deletions affecting key functional domains may represent an alternative pathogenic mechanism in addition to the predominantly reported missense variants. Our findings also highlight the value of exon-level CNV analysis in the genetic diagnosis of neurodevelopmental disorders.