Circulating Tumor Cells (CTCs) are important aspect for clinical prognosis and diagnosis from primary tumor to metastatic stage during transition of epithelial to mesenchymal stage. The transition of CTCs are characterized by genetic markers such as Sox4, CK-19 and EpCAM using RT-qPCR with the help of specific amplicons. Present cases study of Hepatocellular Carcinoma (HCC) tries to establish the possible link between KRAS oncogene mutation and methylene tetrahydrofolate reductase (MTHFR) C677T gene polymorphism using ARMS-PCR to determine the genetic heterogenicity. Findings reveals that in Tm values shift between case 85.00 and 88.00 GAPDH act as genomic control confirming the substitution of nucleotides from cytosine to thymidine followed by change of amino acids alanine to valine due to point mutation. Simultaneously, the KRAS oncogene showing lack of mutation after using two different sets of amplicons (280bp) to confirm the findings, and suggesting that heterozygous (CT genotype) conditions increase the “risk factor” independently in disease.