17q12 recurrent deletion syndrome is characterized by variable combinations of the three following findings: structural or functional abnormalities of the kidney and urinary tract, maturity-onset diabetes of the young type 5 (MODY5), and neurodevelopmental or neuropsychiatric disorders (e.g., developmental delay, intellectual disability, autism spectrum disorder [ASD], attention-deficit/hyperactivity disorder [ADHD], schizophrenia, anxiety, and bipolar disorder). Using a method of data analysis that avoids ascertainment bias, the authors determined that multicystic kidneys and other structural and functional kidney anomalies occur in 85%-90% of affected individuals, MODY5 in approximately 40%, and some degree of developmental delay or learning disability in approximately 50%. MODY5 is most often diagnosed before age 25 years (range: age 10-50 years).

Any renal-hepatic-pancreatic dysplasia in which the cause of the disease is a mutation in the NPHP3 gene.

Congenital NAD deficiency disorder (CNDD) is a multisystem condition in which cardiac, renal, vertebral, and limb anomalies are common, mimicking the clinical features described in VACTERL association. Congenital heart defects can include left-sided heart lesions, right-sided heart lesions, or both. Almost all surviving individuals have short stature, many with disproportionately shortened limbs. Vertebral anomalies, including hemivertebrae and vertebral fusion, occur frequently, often with rib anomalies. Renal anomalies may be severe, including dysplasia/hypoplasia and renal agenesis. Developmental delay / intellectual disability has been reported in more than half of affected individuals, although some affected individuals have had normal development, and some individuals succumbed to their congenital anomalies before developmental assessment could be performed. Other less common features may include cleft palate, eye anomalies, sensorineural hearing loss, tracheoesophageal fistula, polysplenia, anteriorly displaced anus, tethered spinal cord, cystic hygroma, epilepsy, hypothyroidism, and hypoparathyroidism.