| Diagnosis | Omim Number | Sample Count |
| SALLA DISEASE | 604369 | 3 |
| SANDHOFF DISEASE | 268800 | 11 |
| SCHEIE SYNDROME | 607016 | 3 |
| SCHINZEL-GIEDION MIDFACE-RETRACTION SYNDROME | 269150 | 3 |
| SCHIZOPHRENIA; SCZD | 181500 | 17 |
| SCHUURS-HOEIJMAKERS SYNDROME; SHMS | | 13 |
| SCHWARTZ-JAMPEL SYNDROME; SJS | 255800 | 1 |
| SEA-BLUE HISTIOCYTE DISEASE | 269600 | 4 |
| SECKEL SYNDROME | 210600 | 3 |
| SEGMENTAL DYSTONIA | | 719 |
| SEIP SYNDROME | 269700 | 1 |
| SELENON-RELATED MYOPATHY;
RIGID SPINE MUSCULAR DYSTROPHY 1; RSMD1 | 602771 | 19 |
| SENSORY NEUROPATHY TYPE UNKNOWN | | 1 |
| SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-NEGATIVE, DUE TO ADENOSINE DEAMINASE DEFICIENCY | 102700 | 46 |
| SEX REVERSAL, AUTOSOMAL, 2; SRA2 | 154230 | 1 |
| SHORT/BRANCHED-CHAIN ACYL-COA DEHYDROGENASE DEFICIENCY; SBCADD | | 1 |
| SHPRINTZEN-GOLDBERG CRANIOSYNOSTOSIS SYNDROME | 182212 | 3 |
| SHWACHMAN-DIAMOND SYNDROME 1; SDS1 | 260400 | 2 |
| SIALIC ACID STORAGE DISEASE; SIASD | 269920 | 11 |
| SICKLE CELL ANEMIA | 603903 | 14 |
| SIMPSON-GOLABI-BEHMEL SYNDROME, TYPE 1; SGBS1 | 312870 | 2 |
| SITOSTEROLEMIA | 210250 | 5 |
| SJOGREN-LARSSON SYNDROME | 270200 | 3 |
| SMITH-LEMLI-OPITZ SYNDROME; SLOS | 270400 | 4 |
| SMITH-MAGENIS SYNDROME; SMS | 182290 | 88 |
| SOTOS SYNDROME | 117550 | 5 |
| SPASMODIC TORTICOLLIS-CERVICAL DYSTONIA | 602124 | 1 |
| SPASTIC PARAPLEGIA 4, AUTOSOMAL DOMINANT; SPG4 | 182601 | 3 |
| SPERMATOGENIC FAILURE, Y-LINKED, 2; SPGFY2 | 415000 | 12 |
| SPHEROCYTOSIS, HEREDITARY; HS | 182900 | 2 |
| SPINA BIFIDA | 182940 | 2 |
| SPINAL AND BULBAR MUSCULAR ATROPHY, X-LINKED 1; SMAX1 | 313200 | 3 |
| SPINAL MUSCULAR ATROPHY | | 20 |
| SPINAL MUSCULAR ATROPHY I; SMA1 | 253300 | 9 |
| SPINOCEREBELLAR ATAXIA | 183090 | 3 |
| SPINOCEREBELLAR ATAXIA 1; SCA1 | 164400 | 5 |
| SPONASTRIME DYSPLASIA | 271510 | 4 |
| SPONDYLOEPIMETAPHYSEAL DYSPLASIA WITH MULTIPLE DISLOCATIONS | 603546 | 1 |
| SPONDYLOPERIPHERAL DYSPLASIA | 271700 | 3 |
| STICKLER SYNDROME, TYPE I; STL1 | 108300 | 2 |
| STRIATAL NIGRAL DEGENERATION | | 1 |
| STROKE | | 6 |
| SUBARACHNOID HEMORRHAGE | | 1190 |
| SUN SENSITIVE HIGH CANCER SYNDROME | | 2 |
| SUPRANUCLEAR PALSY, PROGRESSIVE | 601104 | 1 |