The mitochondrial tumor suppressor 1 (MTUS1) gene acts as a crucial tumor suppressor by inhibiting growth and proliferation of eukaryotic cells including tumor cell lines. Down regulation of MTUS1 gene has been implicated in a wide range of cancers as well as various human diseases. Alteration through nsSNPs can potentially damage the structure and/or function of the protein. As characterization of functional SNPs in such disease linked genes is a major challenge, it is feasible to analyze putative functional SNPs prior to performing larger population studies. Hence, in this in silico study we differentiated the potentially harmful nsSNPs of the MTUS1 gene from the neutral ones by using various sequence and structure based bioinformatic tools. In a total of 215 nsSNPs, 9 were found to be most likely to exert deleterious effect using 7 prediction tools. From which, 5nsSNPs (S1259L, E960K, P503T, L1084V and L1143Q) were selected as potentially damaging due to their presence in the highly conserved region and ability to decrease protein stability. In fact, 2 nsSNPs (S1259L and E960K) among these 5 were found to be individually associated with two distinctive cancers named Stomach adenocarcinoma and Uterine corpus endometrial carcinoma. As this is the first comprehensive study analyzing the functional nsSNPs of MTUS1, the results of the current study would certainly be helpful in future prospects concerning large population-based studies as well as drug discovery, especially developing individualized medicine.