Integrated genetic and functional analyses reveal the pathogenic effects of a novel STXBP3 variant in very-early-onset inflammatory bowel disease with immunodeficiency

Abstract

Very early onset inflammatory bowel disease (VEOIBD) is frequently driven by monogenic defects. Pathogenic variants in the syntaxin-binding protein 3 ( STXBP3 ) gene have been implicated in VEOIBD; however, the relationship between specific variant types and clinical manifestations remains incompletely understood. This study aimed to identify the genetic cause in a patient with VEOIBD and explore the possible genotype-phenotype correlations of STXBP3 -related disorders. We performed trio-whole-exome sequencing (trio-WES) on a male infant presenting with VEOIBD, sensorineural hearing loss, and immunodeficiency. Functional consequences of the identified variant were investigated using RNA sequencing (RNA-seq), reverse transcription-polymerase chain reaction (RT-PCR), western blotting and co-immunoprecipitation (co-IP) assay. A systematic literature review was conducted to analyze clinical features and inheritance patterns across all reported STXBP3 cases. A novel heterozygous splice-site variant in STXBP3 (c.1022_1029 + 3del) was identified. RNA-seq and RT-PCR confirmed that this variant causes aberrant splicing, leading to the skipping of exon 12 and the production of a truncated protein. Co-IP showed that the aberrant protein reduced the ability to bind STX4. The comprehensive analysis of 13 patients revealed possible genotype-phenotype correlations: splice-site and frameshift variants were observed predominantly follow an autosomal dominant (AD) pattern associated with VEOIBD, sensorineural hearing loss, and immunodeficiency; conversely, missense variants generally follow an autosomal recessive (AR) pattern linked to VEOIBD, and congenital malformations. Given the small cohort, these comparisons were descriptive and were not intended to establish definitive genotype–phenotype associations. We identified a novel pathogenic STXBP3 variant and validated its impact on its function. The observed differences between AD and AR cases provided a preliminary, hypothesis-generating framework for understanding STXBP3-related disease, which require validation in larger cohorts.