- Saethre-Chotzen syndrome
- Schinzel-Giedion syndrome
- Schizophrenia
- Schwartz-Jampel syndrome
- Scleroderma
- Scoliosis
- Sebastian syndrome
- Seckel syndrome
- Severe combined immunodeficiency
- Short-rib polydactyly
- Shprintzen-Goldberg craniosynostosis syndrome
- Sickle cell disease
- Simpson-Golabi-Behmel syndrome
- Sirenomelia
- Sjögren-Larsson syndrome
- Smith-Fineman-Myers syndrome
- Smith-Lemli-Opitz syndrome
- Smith-Magenis syndrome
- Sotos syndrome
- Spastic cerebral palsy
- Spherocytosis, hereditary
- Spina bifida
- Spinal muscular atrophy
- Spinocerebellar ataxia
- Spondyloepiphyseal dysplasia
- SRY (sex determining region Y)
- Stickler syndrome
- Stomach cancer
- Sturge-Weber syndrome
- Sutherland-Haan syndrome
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