Background: The cytochrome c, somatic (CYCS) gene encodes a small haeme protein that functions as a central component of the electron transport chain in mitochondria. Most important health condition related to mutations in the coding region of this gene was Thrombocytopenia 4 and affect apoptosis. Aims: This study aimed to investigate the effect of non-synonymous SNPs (ns SNPs) of CYCS gene in protein function and structure using different computational software. Material and Methods: Different nsSNPs and protein related sequences were obtained from NCBI and ExPASY database (2020). Deleterious and damaging effect of SNPs were analyzed using SIFT, Provean, Polyphen-2 and SNPs & GO software. Protein stability was investigated using I-Mutant and MUpro software. The interaction of CYCS with other genes was studied using GeneMANIA software. The structural and functional impact of point mutations was predicted using Project Hope software. Results: A total of 100 Single Nucleotide Polymorphisms were retrieved from National Center of Biotechnology Information (NCBI). From these 68 were in the 3`UTR, 28 in the 5`UTR and 14 in the coding region (nsSNP). Only these 14 were selected for further investigations. Six nsSNPs were found to be deleterious while 8 were tolerated by SIFT. Using Provean 11 nsSNPs were found to be deleterious while 3 were Neutral. For PolyPhen-2, 5 nsSNPs were observed to be damaging while 9 were benign. Using PHD and SNPs&GO 9 and 6 nsSNPs were found to be disease related for the two software respectively. The change in the chemical nature of amino acid and how it affects the protein structure was analyzed using Project Hope. Conclusion: Six highly deleterious, damaging and disease related nsSNPs (rs17851278, rs11548796, rs121918552, rs11548820, rs11548818 and rs11548778) were detected at CYCS gene. These nsSNPs can be considered as candidate nsSNPs for diagnosis of Thrombocytopenia 4 and normal apoptosis.