Methionine synthase reductase (MTRR) is the locus of the cblE class of inborn errors of cobalamin metabolism that is characterized by megaloblastic anemia and homocystinuria. Two highly prevalent SNPs, c.66A>G (p.Ile22Met) and c.524C>T (p.Ser175Leu), are found in the MTRR gene. On the basis of the allele frequency of these amino acids and sequence comparison with members of the same family of proteins, the p.Ile22/p.Ser175 sequence is designated as wild type. While characterizing a pathogenic methionine synthase reductase (MSR) mutation, c.166G>A (p.Val56Met), we discovered an interaction between the mutation and one of the polymorphic sites. Thus, when the p.Val56Met mutant was initially expressed in the p.Ile22/p.Ser175 background, we were surprised to find that kinetically, it was virtually indistinguishable from wild-type protein. To determine if the polymorphisms interacted with the p.Val56Met mutation, it was expressed in all four possible genetic backgrounds. We found that in the p.Ile22Met background, the p.Val56Met mutation impacted the kinetics of MSR and an approximately three- to 10-fold higher concentration of the p.Ile22Met/p.Val56Met mutant was required for maximal activation of methionine synthase vs. the range seen with wild-type MSR variants. A comparable (three- to seven-fold) diminution in MSR activity was observed in extracts of fibroblast cells from patients carrying the p.Val56Met mutation on one MSR allele and a null mutation on the other. These results predicted that the patient allele encodes the p.Val56Met mutation and the p.Ile22Met variation, which was confirmed by sequence analysis. This study reveals how a genetic variation can modulate phenotypic expression of a disease-causing mutation.