Abstract: Fibroblast growth factor receptor 2 (FGFR2) has important roles in embryonic development and tissue repair, especially bone and blood vessels. Many Single Nucleotide Polymorphism (SNPs) found in FGFR2 gene has been associated with various disorders such as crouzon, jackson-weiss syndromes, breast, ovarian and lung cancers. In this study, we performed a comprehensive analysis of the structural and functional impacts of all known SNPs in FGFR2 gene using publicly available computational prediction tools. Out of total 2255 SNPs retrieved from dbSNP, we found 58 non-synonymous SNP, 39 SNPs in the non-coding region which comprises 28 in 3’ UTR and 11 were found in 5’ UTR region. Among these SNPs, 10 non-synonymous SNPs were found to be damaging by both sequence homology based tool (SIFT) and structural homology based tool (PolyPhen). Untranslated region resource tools UTRscan and FastSNP were used to analyze the region which might change protein expression levels. Further, we modeled mutant protein and compared the energy minimization based on the native protein and identified major mutations from Tryptophan to Arginine and Tryptophan to Cysteine at position 290 of the native protein that caused the greatest impact on stability. From our results, we suggest two non-synonmous SNPs rs121918501 and rs121918499 could be a potential candidate for future studies on FGFR2 mutations.