By screening through the candidate genes of tooth agenesis with exome data, we identified no potential disease-causing sequence variants in MSX1,PAX9,AXIN2,LTBP3,EDA,EDAR, and EDARADD, but did identify two missense mutations in WNT10A (g.6825C>T, c.310C>T, p.Arg104Cys; g.14712T>A, c.637T>A, p.Gly213Ser). Here, LTBP3 is linked to tooth agenesis.