This is the 2009 Statement on Genetic Defects released by the American Association of Equine Practitioners. It was approved in July 2009.
Congenital Defects

Congenital defects include all undesirable traits and pathologic conditions present at birth whether they are genetic or due to intra-uterine events that results from extra-uterine influences. Congenital defects do not necessarily indicate inheritance; they simply indicate that the defect was present at birth.

Inherited Tendencies

There are characteristics in horses that are influenced by a wide variety of genes, whose pattern of inheritance is complex and whose expression has strong environmental influences. Horses have been selectively bred for centuries to promote or discourage these characteristics. The selection for or against these inherited tendencies is the basis for our current breed registries. Size, power, color, speed, conformation, and many other characteristics that are genetically influenced are selected for or against by certain breed registries. Variations from ideal may be undesirable, but they are not deemed to be genetic defects.
Genetic Defects

Genetic defects are pathologic conditions of proven genetic origin. These may be the result of a mutation in a gene of major effect or mutations in multiple genes (polygenic) whose effects combine to produce a deleterious or undesirable result. The degree to which some traits are expressed in horses carrying particular mutations can be influenced by environmental factors. This is called incomplete penetrance.
Undesirable Traits

An undesirable trait, as designated by certain breed registries, is a condition or behavior which may or may not be present at birth, may develop over time, may or may not be a genetic defect, but precludes registration of that animal. A variation in color is an example of a characteristic that may be considered by a breed to be undesirable. Concealment of such undesirable traits by any means, including surgery, is prohibited by breed registry. It is therefore unethical for a veterinarian to perform such treatments, except when the treatment is intended to improve the health of the horse, and when the veterinarian reports the treatment to the breed registry.
Genetic Tests Available for Horses
Tests for mutations in single genes are currently (May 2009) available for 9 diseases.
Autosomal Dominant

1. Hyperkalemic periodic paralysis (HYPP) in the Quarter Horse.
2. Type 1 polysaccharide storage myopathy (PSSM) in numerous breeds.
3. Malignant hyperthermia in Quarter Horse-related breeds.
Autosomal Recessive

4. Overo lethal white syndrome in the Paint Horse
5. Combined immunodeficiency in Arabian Horses
6. Glycogen branching enzyme deficiency (GBED) in Quarter Horse-related breeds.
7. Junctional epidermolysis bullosa (JEB) in Belgians
8. JEB in Saddlebred horses
9. Hereditary equine regional dermal asthenia (HERDA) in Quarter Horse-related breeds.
There are numerous other conditions strongly suspected to be due to mutations in genes of major effect, but genetic tests for these conditions are not yet available. In some cases, such as Cerebellar Abiotrophy in Arabians, a marker that is linked to the genetic defect has been identified, but the gene and genetic mutation responsible for the disease are not yet known. New information in equine genetics is being generated very quickly, and any document of this type will require frequent updates, at least for the next few years.
AAEP Position
Surgical Correction of Undesirable Traits and Genetic Defects
According to the American Veterinary Medical Association, surgical correction of “genetic defects” for the purposes of concealing the defect is unethical. If surgical correction is undertaken for the purpose of improving the health of the individual, then it should be accompanied by sterilization to prevent the perpetuation of the genetic defect. The AAEP agrees with the intent of this position. Further, surgical correction of any characteristic specifically named by the breed organization as being prohibited, for the purpose of concealing the characteristic for obtaining registration, would be considered fraudulent and unethical. Such procedures offer no benefit to the horse and are intended only to deceive the breed organization. The AAEP does support surgical correction of conditions that are in the best interest of individual horses.
Identification of Genetic Traits
AAEP supports the use of genetic testing by veterinarians or breed associations to identify genetic mutations in animals so that owners can make informed decisions about breeding, purchase, and specific treatments. Breed associations should be contacted to determine if there are any restrictions on registration of horses with genetic defects. Licensed laboratories should be used for genetic testing.
More information on equine genetic diseases is available on these Web sites:

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