KAT6B mutations are responsible for Say-Barber-Biesecker-Young-Simpson syndrome or Genitopatellar syndrome, with most mutations occurring in its exon 18. A pregnancy with normal early antenatal examination revealed the presence of hypospadias in the fetus but with no abnormal amniotic fluid volume in ultrasonography at 29th+ 4d weeks’ gestation. After amniocentesis, the trios’ whole exome sequencing was performed and a novel frameshift mutation (KAT6B: exon10: c.2153_2159del, p. R718Lfs*3) was identified for her fetus, then verified by the parents as a de novo mutation. Following this couple’s decision to induce labor, the appearance of the fetus had hypospadias but with a normal face and was able to be palpated for the patella. KAT6B mutations often occur with a variety of symptoms. To our acknowledgment, this is the first report of a novel de novo KAT6B mutation causing only hypospadias for the fetus, which further expands the spectrum of KAT6B variants and the genotype-phenotype relationship for this disease.