Forkhead Box C2 gene plays an important role in the development of mesenchymal tissues. A mutation caused in FOXC2 gene leads to lymphedema-distichiasis. These variations occur mainly due to nsSNPs. Computational analysis of the SNPs occurring in this gene was done using SIFT, PolyPhen 2.0, I MUTANT 3.0, PANTHER, PhD SNP and SNPs & Go. The analysis unveils that out of 38 variants of this gene, 5 (I98V, I98M, P140L, R121H and S125L) were found deleterious by all the 6 servers. T147I was found damaging except by SNP&GO. Further the interaction between the different variants and protein was done using the STRING 9.05. The current study investigated the possible deleterious variations of the FOX C2 gene. Pre diagnosis of these variants would help predict the possible onset of a disease and further developing personalized drug to treat a particular disease.