The genetic disorders listed are either connected to colors found in the Chincoteague Pony or are found in breeds that have been crossbred into the Chincoteague Pony. This is a not a comprehensive list. Chincoteagues have been found with a couple of the listed disorders and there is a very real possibly others may be found.
Cerebellar Abiotrophy (CA)
Cerebellar Abiotrophy, also called Cerebellar Cortical Abiotrophy, is a neurological condition primarily found in Arabians. It has also been found in Partbred Arabians and breeds with Arabian ancestors. CA causes neurons in the brain to die off shortly after the affected horse is born. Noticeable symptoms are a palsy like head shaking, lack of a normal blinking response, and an awkward movement of the forelimbs called hyper-metric action. The symptoms can start appearing 6 weeks after birth, or they may be gradual and not obvious until the horse is much older. CA is recessive; heterozygous is an unaffected carrier, homozygous will suffer from the disease. There is a test available for CA.
Degenerative Suspensory Ligament Disease (DSLD)
Degenerative Suspensory Ligament Disease, also known as Equine Systemic Proteoglycan Accumulation (ESPA), is a disease of the connecting tissues. Dropped fetlocks, also known as coon-footed, is a typical sign of a horse suffering from DSLD although the condition affects all of the connecting tissue of the body. Other symptoms of DSLD are persistent lameness, pasterns shifting towards horizontal, and the straightening of hocks and stifles. There is no cure for DSLD and treatments manage the pain but do not slow down the progression. Horses with DSLD are usually euthanized when the pain can no longer be managed. DSLD is genetic, but the gene has not been identified and there is not a test available.
DSLD is present in the Chincoteague population as multiple Chincoteague Ponies with the characteristic dropped pasterns and chronic lameness have been identified.
Lavender Foal Syndrome (LFS)
Lavender Foal Syndrome occurs in Egyptian Arabians, part-Egyptian Arabian horses, part-bred Arabians, and has also been found in some Crabbet Arabian lines. It is also called Coat Color Dilution Lethal. Foals are unable to stand or nurse, have neurological problems, and often have seizures. The name lavender comes from foals with the syndrome have a diluted lavender, pink, or a pale chestnut coat color. There is no cure and the foals are usually euthanized shortly after birth. LFS is recessive; heterozygous is an unaffected carrier, homozygous will suffer from the disease. There is a test available for LFS.
Hereditary Equine Regional Dermal Asthenia (HERDA)
HERDA is found mainly from horses descended from the Quarter Horse stallion Poco Bueno. While it originated in Quarter Horses, HERDA has spread to other breeds due to crossbreeding. Horses affected with HERDA lack an adhesion within the dermis of their skin. When a HERDA horse is ridden or suffers trauma to the skin the outer layer of skin separates and can tear off. The average lifespan of a HERDA affected horse is 2 to 4 years. HERDA is recessive; is recessive; heterozygous is an unaffected carrier, homozygous will suffer from the disease. There is a test available for HERDA.
Hyperkalemic Periodic Paralysis (HYPP)
HYPP is found in horses descended from the Quarter Horse stallion Impressive. While it originated in Quarter Horses, HYPP has spread to other breeds due to crossbreeding. HYPP overloads the system with high potassium levels that cause episodes of varying degrees affecting the horse's muscles. The episodes can range from visually undetectable mild muscle twitching, crawling skin, hind quarter paralysis, or paralysis of muscles surrounding the heart and lungs which lead to death via heart attack or suffocation. HYPP is dominant and thus only requires one parent to have and pass the disorder. A horse homozygous for HYPPP will always pass it to their foals (H/H) and a horse with one copy will pass it to approximately half of their foals (N/H). H/H horses are barred from registration by the AQHA and the ApHC, but not the APHA. There is a test available for HYPP.
Incontinentia Pigmenti (IP)
IP creates a heritable form of brindle as a symptom of this genetic disorder. IP is dominant and results in partial hairlessness with abnormalities of the teeth, hooves, and eyes. IP is also only found in females as the males die in utero.
Lordosis is more commonly known as swayback. Horses with lordosis have a loss of muscle tone in the back and abdominal muscles as well as a stretching or weakening of the ligaments resulting in a dropping of the back. Lordosis is often seen in aged horses and/or in mares that have had multiple foals. Horses with long backs are more prone to lordosis. It can also occur due to overwork or in horses that were put to work too young. Horses with lordosis do not appear to suffer any ill effects. It was discovered in a study in Saddlebreds, where lordosis is common, that it is genetic and is recessive.
Multiple Chincoteagues have been found with lordosis. It is often found in older feral mares that have had many foals. A well-known swayback is the feral mare Unci and it is reportedly a lifelong condition. She has three non-swayback offspring in the feral herd, including one stallion, so it will remain to be seen if any of her descendants inherit the recessive condition. Lordosis is also in Misty descendants, Starry Night and Mistral's Stormy Weather are two known individuals.
Multiple Congenital Ocular Anomalies (MCOA)
MCOA is a genetic disorder linked to the silver dilution. Heterozygous horses are not affected by homozygous silver horses are. MOCA affected horses can have multiple abnormalities of the eye including cysts, cloudy eyes, abnormal lens positions, and pop eyes. Horses with MOCA often have impaired vision and difficulties in adapting to changing light conditions. Silver to silver breedings are not recommended. The Wild Horse Dilemma by Bonnie Gruenberg stated that a silver stallion from Shackleford Banks herd of feral horses tested positive for MOCA.
Overo Lethal White Syndrome (OLWS)
Overo Lethal White Syndrome is linked to the frame pinto pattern. All frame pinto horses are positive for OLWS. Heterozygous horses are carriers but not affected, lethal whites are homozygous for frame. Thus two frames should never be bred together. Lethal whites are born completely white with blue eyes and have an incomplete digestive system. Signs of colic appear within the first few hours after birth. Lethal white foals that are not euthanized die painfully within days. There is a test for OLWS, which is also the test to determine if a horse is a frame. Frame can be very minimal so it is strongly suggested that any horses with frame relatives or are suspected of having frame be tested.
Severe Combined Immunodeficiency (SCID)
Severe Combined Immunodeficiency is found in Arabians. SCID has also been found in partbred Arabians and breeds with Arabian ancestors. SCID causes a foal to be born with virtually no immune system. SCID foals usually die by the time they are five months old of an infection their body cannot fight. There is no visible defect in SCID foals. SCID is recessive; heterozygous is an unaffected carrier, homozygous will suffer from the disease. There is a test available for SCID. Known carriers of SCID should not be bred together.
There is a genetic link between the splash pinto pattern and deafness. Most splashes are not deaf, but there are many that are. The cause and correlation between splash and deafness is not known at this time. It is theorized that splash inhibits the production of pigment in the inner ear which results in deafness. The theory is similar to the deafness found in other species.
Splash is common in the Chincoteague population, however no deaf Chincoteagues have been found to date.
Feral mare Whisper of Living Legend has a high foal mortality rate. The majority of her foals die before weaning. One daughter, Trinity, was kept in the feral herd and died at age 4. A son, Wild Wings of Assateague, died at age 2 after exhibiting signs of colic. The majority of her foals were sired by Courtney's Boy with whom she shares a common ancestor.