Functional analysis of a novel splice site variant of RAB3GAP2 in a fetus with congenital cataracts

BACKGROUND: Mutations in RAB3GAP2 are associated with Martsolf syndrome 1, characterized by postnatal microcephaly, congenital cataracts, and developmental delay. Two compound heterozygous variants of RAB3GAP2 were identified in a fetus with congenital cataract. This study aimed to assess the pathogenicity of the RAB3GAP2 variant c.304 + 5G > T. METHODS: Fetal lenses were evaluated using ultrasound. Whole exome sequencing (WES) was employed to identify splicing variants in RAB3GAP2, and Sanger sequencing confirmed the results. Pathogenicity was predicted using bioinformatics tools, including Mutation Taster, Combined Annotation Dependent Depletion, Splice AI, NetGene2, SpliceRover, and Alternative Splice Site Predictor. Reverse transcription PCR (RT-PCR) was conducted to detect RAB3GAP2 transcripts in peripheral blood leukocytes. A minigene assay was used to examine the variant's impact on splicing. RESULTS: Ultrasound examination revealed increased echogenicity in both fetal lenses, consistent with congenital cataracts. WES identified two compound heterozygous variants in RAB3GAP2: c.812-2 A > G (rs556159021) and c.304 + 5G > T. This study focused on the RAB3GAP2 variant c.304 + 5G > T. In silico analysis predicted that this variant disrupts the donor splice site in intron 3. RT-PCR analysis revealed an abnormal transcript with skipping of exon 3. The minigene assay showed that the RAB3GAP2 c.304 + 5G > T variant impaired mRNA splicing in HEK293T and HeLa cells. CONCLUSIONS: The RAB3GAP2 splicing variant (NM_012414.4:c.304 + 5G > T) is predicted to cause aberrant splicing and truncated proteins. These findings contribute valuable information for genetic counseling regarding congenital cataracts in future pregnancies within affected families.