Congenital scoliosis (CS) is a congenital disease resulting in abnormal vertebral development. Several studies have indicated that both genetic and environmental factors during pregnancy increase the risk of CS development. However, the exact mechanisms underlying CS pathogenesis remain unknown. To address this issue, both genetic (by whole‑exome sequencing) and epigenetic (by methylated DNA immunoprecipitation sequencing) maps from CS disease‑discordant monozygotic twins were generated in the present study. The differences in the presence of common and rare single nucleotide polymorphisms and in methylation patterns between the twins were investigated. The results indicated that rare mutations were more likely to underlie CS development compared with common mutations. Furthermore, differences in the allele‑specific methylation pattern in the supervillin (SVIL) gene between the twins were identified. It has been reported that SVIL exerts a number of functions associated with CS, indicating its role as a novel mechanism promoting CS pathogenesis.