Branchio-oculo-facial syndrome is difficult to diagnose because it has incomplete penetrance. It is often misdiagnosed as branchio-oto-renal syndrome because of their similarities in symptoms.

Branchio-oculo-facial syndrome (BOFS) is a disease that arises from a mutation in the TFAP2A gene. It is a rare autosomal dominant disorder that starts to affect a child's development before birth. Symptoms of this condition include skin abnormalities on the neck, deformities of the ears and eyes, and other distinctive facial features such a cleft lip along with slow growth, mental retardation and premature graying of hair.