By screening patients with undiagnosed multiple congenital anomalies and intellectual disability using array-comparative genomic hybridization, we identified an 884 kb heterozygous microdeletion at 14q13.3 in two siblings presenting with oligodontia, hypothyroidism and persistent pulmonary hypertension of the newborn, resulting from their parental gonosomal mosaicism. Among the six genes included in the deletion, haploinsufficiency of PAX9 and NKX2-1 was probably associated with their phenotypes. These results highlighted a possibility of recurrence of pathogenic copy-number variants associated with parental mosaicism, which requires careful genetic counseling.