Innate immunity plays a significant role in natural immune response. Complement system is a critical player in innate immunity and tightly regulated by various regulatory components. The present study was undertaken to predict deleterious/damaging SNPs using in silico analysis of CD 46 gene. Various tools like SIFT, PROVEAN, SNAP2, PredictSNP, I-mutant and Consurf were used for in silico analysis. CD46 study revealed 263 coding snSNPs. The SIFT sequence tool predicted a total of 85 variants, PROVEAN predicted 86 nsSNPs (out of 263) as deleterious and SNAP2 server predicted 115 variants to be effective in influencing the protein function. I mutant was used to calculate the free energy change value and reliability index to predict the functional deviations in proteins. The I-mutant revealed 37 deleterious mutations. Consurf results predicted conservation of residues in protein sites. While active site prediction analysis revealed 11 amino acid residues in chain B and 32 in D as active si

CD46, Complement system, In silico Analysis, nsSNPs