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Background  The purpose of this study was to analyze the association between the genetic polymorphism of genes ( PAX6 ,  SOSTDC1 and  FAM20B ) and the susceptibility to mesiodens.    Methods  This study was carried out on 50 patients with mesiodens and 50 controls. The family history of each patient with mesiodens were recorded. Genomic DNA was extracted from saliva samples, and single nucleotide polymorphisms were detected in all exons and exon/intron boundaries of  PAX6 ,  SOSTDC1  and  FAM20B  using Sanger sequencing. The data were analyzed using pearson chi-square test with theoretical frequency ≥ 5. For theoretical frequency less than 5 but at least 1 (≤20% cell), the data were analyzed by continuity correction. For the rest, Fisher’s Exact test was used. A  P -value< 0.05 was considered statistically significant. The Odds ratio (OR) and confidence intervals (CI) were recorded.    Results  Three polymorphisms were detected in  PAX6 . Two polymorphisms were detected in  SOSTDC1 . Twenty-nine polymorphisms were detected in  FAM20B . Although, the T allele of  FAM20B  (rs3766626) appears to be associated with mesiodens ( P  = 0.051), there were no significant differences of  PAX6 / SOSTDC1 / FAM20B  gene polymorphisms between the two groups. The T allele of  FAM20B  (rs3766626) was associated with susceptibility to two mesiodens ( P  < 0.001; OR = 8.333; CI = 2.516–27.600).    Conclusions  Lack of association between  PAX6 / SOSTDC1 / FAM20B  gene polymorphisms and mesiodens in the population studied was detected. Further studies with large samples on T allele of  FAM20B  (rs3766626) are needed.    Electronic supplementary material  The online version of this article (10.1186/s12903-019-0788-3) contains supplementary material, which is available to authorized users.

Lack of association between PAX6/SOSTDC1/FAM20B gene polymorphisms and mesiodens