Purpose: The purpose of this study was to use targeted next-generation sequencing (NGS) to identify possible causative genes for isolated and sporadic human mesiodens. Methods: The targeted panel consisted of 101 target genes related to tooth development. NGS of this panel was initially performed on a discovery set (39 cases and 27 controls); association tests were performed after genotyping of nine selected variants in a validation set (57 cases and 56 controls). Results: Among these nine variants, a synonymous variant, ACVR2A (rs1128919) associated with mesiodens was identified. Moreover, in silico analysis was performed and demonstrated the instability of mRNA with the G allele. Conclusions: The formation of isolated and sporadic human mesiodens is associated with a synonymous variation in ACVR2A (rs1128919).