Abstract Background: Congenital cataract is one of the major causes of blindness and amblyopia in children. About one-third of the cases are inherited. Case presentation: We applied whole exome sequencing for a pediatric patient with congenital cataract, small penis, baldness and absence of eyebrows and detected a compound heterozygous mutation in the lanosterol synthase ( Conclusions: We concluded that the mutations affect the structural stability of the protein to some extent.