Abstract
IN SILICO ANALYSIS FOR SPECULATING EFFECTS OF THE DELETERIOUS SNPs OF HUMAN CD2AP GENE ON ITS STRUCTURE AND FUNCTIONS ASSOCIATED WITH NEPHROTIC SYNDROME

Glory S. Parmar, Kinnari N. Mistry*, Sishir Gang, Dharamshibhai N. Rank and Chaitanya G. Joshi

ABSTRACT

Nephrotic syndrome is a kidney disorder that is clinically characterized by proteinuria, hyperlipidemia, hypoalbuminemia, and edema. This study aims to discover nsSNPs of the CD2AP gene through various in silico tools. A computational application helps us to reduce genotyping costs. CD2AP has a key role in the slit diaphragm assembly and function. Data of CD2AP was retrieved from NCBI dbSNP and Uniport KB and further used to explore adverse outcomes using SIFT, PolyPhen, SNP&GO, PHD SNP, PANTHER, PROVEAN SNAP2, I-Mutant, Mupro, and Strum. Out of 438 nsSNPs selected in this study, 11 SNPs: E287D, L156R, L288R, R111C, R500C, D16G, W309G, L127P, G23R, D125V, and W308S were having a damaging effect in all selected computational tools. Consurf, Hope, SOPMA, and GeneMANIA online tools were utilized to detect the evolutionary conservation of amino acids, structural impact of mutation, prediction of the secondary structure of the protein, and PPI network for functional annotation of a gene. The 3D structure was generated using I-TASSER and the stability of the built structure was confirmed through PROCHECK to get a Ramachandran plot. Post translation modification sites were checked by using Modpred software and ligand binding sites were detected using COACH.  Molecular Docking analysis showed that prednisolone has the highest binding affinity towards receptor molecules than that of cyclophosphamide and levamisole. Prednisolone might be a good treatment option. The present study demonstrates the harmful effect of Non-synonymous SNPs found in the CD2AP gene, which alters the amino acid interactions responsible for the change in its protein function.

Keywords: CD2AP gene; In-silico tools; Focal segmental glomerulosclerosis (FSGS); Nephrotic syndrome; Protein-Protein Interaction (PPI).


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