SYNGAP1-related encephalopathy is a rare neurodevelopmental disease characterized by diverse genetic mutations and phenotypic features. It is not known whether the blood-brain barrier (BBB) is affected in SYNGAP1 patients, therefore, this study aimed to establish a human induced pluripotent stem cell (hiPSC)-based BBB model of the SYNGAP1 disorder and identify relevant functional and molecular signatures. To establish the BBB models, SYNGAP1 knockout (KO), patient-derived hiPSC lines (Leu323Arg) and isogenic controls were differentiated into brain capillary endothelial-like cells and seeded on Transwell® inserts. Barrier properties were evaluated by transendothelial electrical resistance (TEER) and paracellular permeability assays. Functional studies were complemented by high-throughput qPCR gene expression analyses, RNA sequencing, DNA methylation analysis and immunofluorescence microscopy. Our data revealed that the KO and patient-derived cell lines exhibit a compromised barrier integrity (TEER reduction by ~27% and ~40%; permeability increase by ~55% and ~145% respectively) as compared to the control cell lines. Furthermore, significant differences were discovered in the DNA methylation and gene expression profiles, including downregulation of tight junction genes, and upregulation of vascular endothelial growth factor A in KO and patient-derived models as compared to control. In summary, our data indicates that loss or reduced levels of functional SYNGAP1 protein results in a weaker barrier formation of brain endothelial cells suggesting a significant change of the BBB in SYNGAP1 disorder, which could be relevant for new therapeutic approaches in the future. Acknowledgement: The EURAS project receives funding from the European Union’s Horizon Europe Research and Innovation Programme, Grant Agreement No. 101080580.