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- Appaloosa blindness, Leopard complex spotting, LP (TRPM1 gene) Appaloosa
- Atlantoaxio-Occipital Malformation (HOXD3 gene) Arabian
- Auditory-pigmentary syndrome, PAX3 -related (PAX3 gene) American Paint Horse, Appaloosa, Noriker, Purebred Spanish, Quarter Horse
- Cerebellar Abiotrophy (MUTYH, TOE1 genes) Arabian, Eriskay, Gotland, Miniature Horse, Oldenbourg
- Dilute coat color with neurological defects (Lavender Foal Syndrome, LFS) (MYO5A gene) Arabian
- Dwarfism, chondrodysplasia (ACAN gene) Miniature Horse, Shetland Pony
- Familial neonatal hypoparathyroidism (RAPGEF5 gene)
- Fragile Foal Syndrome, FFS (PLOD1 gene) Morgan, Quarter Horse, Standardbred, Thoroughbred, Warmblood
- Glanzmann’s Thrombasthenia (ITGA2B gene) Oldenbourg, Peruvian Paro horse, Quarter Horse, Thoroughbred
- Glycogen branching enzyme deficiency, GBED (GBE1 gene) American Paint Horse, Quarter Horse
- Hereditary Equine Regional Dermal Asthenia, HERDA (PPIB gene) American Paint Horse, Appaloosa, Quarter Horse
- Hereditary Junctional Epidermolysis Bullosa, HJEB – American Saddlebred (LAMC3 gene) American Saddlebred
- Hereditary junctional epidermolysis bullosa, HJEB – Belgian (gene LAMC2)
- Hoof Wall Separation Syndrome (HWSS) (SERPINB11 gene) Connemara Pony
- Hydrocephalus, familial (B3GALNT2 gene) Frison
- Hyperkalemic Periodic Paralysis, HYPP (SCN4A gene) American Paint Horse, Quarter Horse
- Immune-mediated Myositis, IMM (MYH1 gene) Quarter Horse
- Immunodeficiency syndrome, SLC5A3-related (SLC5A3 gene) Dales Pony, Fell Pony
- Malignant hyperthermia, Quarter Horse (RYR1 gene) Quarter Horse
- Multiple congenital ocular anomalies (MCOA), PMEL-related (PMEL gene) American Miniature horse, Ardennes horse, Contois horse, Icelandic horse, Kentucky Mountain Saddle, Missouri Fox Trotter, Morgan… (plus)
- Myotonia, congenital, CLCN1-related (CLCN1 gene) New Forest Pony
- Naked Foal Syndrome (ST14 gene) Akhal-Teke horse
- Ocular Squamous Cell Carcinoma, SCC (DDB2 gene) American Paint Horse, Appaloosa, Belgian, Connemara Pony, Haflinger
- Overo lethal white foal syndrome, OLWFS (Megacolon) (EDNRB gene) American Paint Horse, Miniature Horse, Quarter Horse, Thoroughbred
- Polysaccharide Storage Myopathy 1, PSSM1 (GYS1 gene) American Paint Horse, Appaloosa, Draft horses, Quarter Horse, Warmblood
- Severe combined immunodeficiency disease, SCID (PRKDC gene) Arabian
- Skeletal Atavism (SHOX gene) Shetland Pony