Next-generation sequencing technologies enable comprehensive genetic analyses in monogenic and oligonenic diseases. Especially whole-exome sequencing(WES)targeting exonic regions of protein coding genes is mainly used for Mendelian diseases. Here we describe a case of Hand-foot-genital syndrome arising from a HOXA13 mutation[c.1102A>T(p.Ile368Phe)]as one of successful examples in our successful WES analyses.