In this work, we have analyzed the genetic variation that can alter the expression and the function in BRCA2 gene using computational methods. Out of the total 534 SNPs, 101 were found to be non synonymous (nsSNPs). Among the 7 SNPs in the untranslated region, 3 SNPs were found in 5′ and 4 SNPs were found in 3′ un-translated regions (UTR). 20.7% nsSNPs were found to be damaging by both SIFT and PolyPhen server among the 101 nsSNPs investigated. UTR resource tool suggested that 2 SNPs in the 5′ UTR region and 4 SNPs in the 3′ UTR regions might change the protein expression levels. It was found that mutation from asparagine to isoleucine at the position 3124 of the native protein of BRCA2 gene was most deleterious by both SIFT and PolyPhen servers. A structural analysis of this mutated protein and the native protein was made which had a RMSD value of 3.01 Å. Based on this work, we proposed that this most deleterious nsSNP with a SNPid rs28897759 is an important candidate for the cause of breast cancer by BRCA2 gene. © 2008 Institute of Microbiology, Chinese Academy of Sciences and Chinese Society for Microbiology.