Background Leber’s inherited optic neuropathy (LHON) is well known for incomplete penetrance. A pair of monozygotic twins carrying 14484T > C LHON mutation: one displayed LHON characteristics (affected LHON) and the other twin was an unaffected LHON carrier, were studied to identify possible modifier(s) for LHON manifestation. Methods Primary fibroblasts from affected and unaffected monozygotic twins with 14484T > C LHON mutation were treated with different insults to differentiate cellular phenotype between the two fibroblasts. RNA sequencing of the fibroblasts indicated differentially expressed genes and whole genome sequencing was used to identify candidates for disease modifier. Results Our results suggested that fibroblast from unaffected carrier was able to adapt to galactose and hydrogen peroxide insult, while affected fibroblasts were not. We found reduced expression of total SOD2 with high proportion of inactive SOD2 (acetylated SOD2) in affected LHON fibroblast, while decreased expression of SIRT3 was detected in affected LHON fibroblasts treated with combination of insults. Differential expression indicated enrichment of a pathway relating to negative regulator of cell death pathway in unaffected carrier fibroblast. Expression of receptor for prostaglandin E receptor (PTGER3) was found to be affected by two SNPs. Unaffected LHON fibroblast possessed rs75523942 that indicates a positive effect on PTGER3 expression, while affected LHON fibroblast possessed rs496483 that indicates a negative effect on PTGER3 expression. Discordant SNPs on prostaglandin E receptor 3 (PTGER3) were identified as eQTL. Conclusions This study indicates that prostanoid receptor could be a possible modifier for LHON manifestation of these twins.