Chondrodystrophy is a term used in veterinary medicine to indicate a dog with a combination of shorter legs and intervertebral disc disease. Prior to the discovery of the mutation that causes chondrodystrophy, many breeds were classified as chondrodystrophic just based on their short-legged phenotype. It turns out there are two major variants that cause short legs in dogs and only one affects the intervertebral discs. The genetic variant that causes chondrodystrophy is a special type of variant called a retrogene. It is an extra copy of the gene (FGF4) that is important in early development. This extra copy makes too much FGF4 in the wrong places. It only takes one extra copy to have an effect on development and thus the FGF4 retrogene, called FGF4L2 is dominantly inherited.

The intervertebral discs express FGF4 when the retrogene is present and this causes the inner portion of the disc to be replaced by cartilaginous tissue as early as 10 weeks of age. Later this inner portion can degrade further and mineralize. All of the changes to the intervertebral discs makes them prone to move or herniate from their normal location as shock absorbers in the vertebral column. Acute intervertebral disc herniation can result in severe pain and paralysis in its worse form. Even though FGF4L2 causes all the discs to be abnormal, they only occasionally herniate causing spinal cord compression.

FGF4L2 is found in many breeds of dogs, including the original chondrodystrophic breeds where it is very common. It also occurs less commonly in a long list of other breeds and has been identified as a region under selection across dog breeds due to its effects on leg length and other parts of the body. Many dogs with FGF4L2 never experience clinical problems associated with this variant and the other effects of FGF4L2 are desirable in some breeds. Since FGF4L2 is dominantly inherited and predisposes dogs to intervertebral disc herniation, it presents unusual challenges to breeders.