A Family Affected By Autosomal Dominant Non-Syndromic Tooth Agenesis - A Genetic Study

Abstract

This study evaluated a family exhibiting the phenotype of non-syndromic tooth agenesis through whole exome sequencing to potentially identify pathogenic variants. Four family members, three with tooth agenesis and one without, were enrolled as on-site subjects for whole exome sequencing analysis using genomic DNA isolated from their blood samples. Variants found to segregate with the tooth agenesis phenotype were evaluated further. An additional three family members, all with tooth agenesis, were enrolled as off-site subjects. DNA isolated from these subjects were evaluated by means of polymerase chain reaction and restriction enzyme testing to confirm or exclude the potential candidate variants based on their segregation in the off-site subjects. Twenty-six variants were found to segregate with the tooth agenesis phenotype among the four on-site subjects. Potentially pathogenic mutants were identified through data filtering techniques such as DOMINO, CADD, and pLI. Of the twenty-six variants, seven heterozygous variants in novel candidate genes for tooth agenesis were identified: AHCYL1, WNT5B, HOXB2, VMP1, JUP, RNF43, and TP1. Only two variants created or destroyed a restriction enzyme site and thus, were able to be evaluated in the off-site subjects utilizing PCR/restriction enzyme testing, resulting in the elimination of JUP as a candidate variant. The six remaining novel candidate genes were then assessed through a literature review. It was determined that WNT5B, HOXB2, and RNF43 may have a role in early odontogenesis by potentially altering the key dental epithelium/mesenchyme interactions. RNF43 emerged as the most likely causal variant due to the significance of the altered interaction site between RNF43’s binding groove and RSPO1’s β-hairpin protrusion, ultimately leading to dysregulation of the Wnt signaling pathway. Also, it was revealed that three families, in a larger genetic study evaluating tooth agenesis, had mutations in RNF43. One of which, had an identical change at the 97th position from an aspartic acid to an asparagine, which further strengthened our belief in RNF43 being the causal variant. Analysis of the un-recruited family members and selective sequencing of the off-site subjects for the five candidate variants that did not alter restriction enzyme sites could help to rule out oligogenic inheritance.