| | Disease name | Disease category |
| CLN6A/CLN6B | H00149 | Neuronal ceroid lipofuscinosis | Inherited metabolic disorder, Lysosomal disease |
| H02276 | Kufs disease | Inherited metabolic disorder, Lysosomal disease |
| CLN8 | H00149 | Neuronal ceroid lipofuscinosis | Inherited metabolic disorder, Lysosomal disease |
| CLSD | H01105 | Cranio-lenticulo-sutural dysplasia | Congenital malformation |
| CDAN2/CWS7 | H00917 | Congenital dyserythropoietic anemia | Hematologic disease |
| H01222 | Cowden syndrome | Congenital malformation |
| CLCRP2 | H01572 | Cole-Carpenter syndrome | Congenital malformation |
| HPBKS | H03035 | Halperin-Birk syndrome | Congenital malformation |
| AIAISD1 | H03012 | Autoinflammation and autoimmunity, systemic, with immune dysregulation | Immune system disease |
| MCPH19/OPDD | H00269 | Primary microcephaly | Congenital malformation |
| H03036 | Childhood- or juvenile-onset osteoporosis with developmental delay | Musculoskeletal disease |
| BARMACS | H02708 | Baralle-Macken syndrome | Congenital malformation |
| SSMG | H03039 | Short stature-micrognathia syndrome | Congenital malformation |
| IMD128 | H00093 | Combined immunodeficiency | Primary immunodeficiency |
| SCN12 | H00100 | Neutropenic disorders | Primary immunodeficiency |
| PVNH8 | H00270 | Periventricular nodular heterotopia | Congenital malformation |
| ML II/III | H00143 | Mucolipidosis II | Inherited metabolic disorder, Lysosomal disease |
| H02130 | Mucolipidosis III | Inherited metabolic disorder, Lysosomal disease |
| MLIIIC | H02130 | Mucolipidosis III | Inherited metabolic disorder, Lysosomal disease |
| DMAN | H02729 | Ain-Naz type of dysostosis multiplex | Congenital malformation |
| HCC | H00048 | Hepatocellular carcinoma | Cancer |
| USRIS | H02692 | Usmani-Riazuddin syndrome | Nervous system disease |
| KIDAR | H00712 | KID/HID syndrome | Congenital malformation |
| MEDNIK | H02220 | MEDNIK syndrome | Congenital malformation |
| PGS | H03038 | Pettigrew syndrome | Congenital malformation |
| PSORS15 | H01656 | Psoriasis | Immune system disease |
| MRD56 | H00773 | Autosomal dominant intellectual developmental disorder | Mental and behavioural disorder |
| CMT2B | H00264 | Charcot-Marie-Tooth disease | Neurodegenerative disease |
| CLN3 | H02275 | Batten disease | Inherited metabolic disorder, Lysosomal disease |
| CLN5 | H00149 | Neuronal ceroid lipofuscinosis | Inherited metabolic disorder, Lysosomal disease |
| PARK17 | H00057 | Parkinson disease | Neurodegenerative disease |
| SPG48 | H00266 | Hereditary spastic paraplegia | Nervous system disease |
| ALS5/CMT2X/SPG11 | H00058 | Amyotrophic lateral sclerosis (ALS) | Neurodegenerative disease |
| H00264 | Charcot-Marie-Tooth disease | Neurodegenerative disease |
| H00266 | Hereditary spastic paraplegia | Nervous system disease |
| SPG15 | H00266 | Hereditary spastic paraplegia | Nervous system disease |
| HPS10 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| HPS2 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| DEE48 | H00606 | Early infantile epileptic encephalopathy | Nervous system disease |
| HPS8 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| HPS11 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| HPS9 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| NEDBAC | H03044 | Neurodevelopmental disorder with structural brain abnormalities and craniofacial abnormalities | Congenital malformation |
| HPS7 | H00166 | Hermansky-Pudlak syndrome | Inherited metabolic disorder |
| OCA3 | H00168 | Oculocutaneous albinism | Inherited metabolic disorder |
| OCA2 | H00168 | Oculocutaneous albinism | Inherited metabolic disorder |
| EPM4 | H00810 | Progressive myoclonic epilepsy | Nervous system disease |
| OPTA3/B6 | H00436 | Osteopetrosis | Congenital malformation |
| SCAR29 | H01891 | Autosomal recessive spinocerebellar ataxias | Neurodegenerative disease |
| HLD12/DYT32 | H00679 | Hypomyelinating leukodystrophy | Inherited metabolic disorder |
| H00831 | Primary dystonia | Nervous system disease |
| DYT30 | H00831 | Primary dystonia | Nervous system disease |
| MPSPS | H02205 | Mucopolysaccharidosis-plus syndrome | Inherited metabolic disorder |
| VICIS/NEDPAM | H02133 | Vici syndrome | Immune system disease |
| H03045 | Neurodevelopmental disorder with parkinsonism or other movement abnormalities | Congenital malformation |
| CEDNIK | H00799 | CEDNIK syndrome | Congenital malformation |