Nephrotic syndrome (NS) contributes significantly to chronic kidney disease (CKD) -related mortality worldwide. Whole Exome Sequencing (WES) was used to identify pathogenic variants associated with NS in a Tamil Nadu patient cohort, with the long-term goal of developing a region-specific diagnostic strategy. The genomic DNA was extracted from 15 patients with proteinuria and 7 healthy controls and subjected to WES. Variants were systematically filtered and annotated against GRCh38 then prioritized using multiple prediction algorithms, including CADD, SIFT, FATHMM, PredictSNP2, and ClinVar annotations. Protein stability effects were evaluated using MUPro and PremPS. The functional consequences of the variant were assessed using PANTHER cSNP. Variant distribution patterns and pathogenicity scores were visualized using multi-parametric scatter plot and genotype heat maps. A total of 266 variants were identified across 59 nuclear genes previously reported to be associated with NS, including 114 non-synonymous substitutions. Integrated computational filtering based on CADD, ClinVar, PredictSNP2, PANTHER score and protein stability, prioritized 14 variants predicted to have deleterious effects. Functional annotation highlighted three variants of particular significance: CUBN (rs139724058), FAT1 (rs3733415), and TRPC6 (rs36111323). In the present pilot study, we identified genetic variants that may contribute to NS susceptibility in this South Indian cohort. This exploratory study findings provide preliminary candidate variants that may warrant investigation in larger cohorts and functional studies to establish clinical utility and address precision medicine strategies.
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