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Pituitary dwarfism
Congenital hyposomatotropism, also known as pituitary dwarfism has been known to be an autosomal recessive disorder in the German Shepherd dog for a long time. The condition causes growth retardation after 2 months and by 3-4 months stunted growth is noticeable with most dogs being presented for growth retardation at 3-5 months of age. The puppy coat is retained into adulthood and guard hairs fail to fully develop outside of the distal extremities. Eventually full alopecia occurs. Progressive hyperpigmentation and scaling and wrinkly of the skin occur; papules, comedones and pyoderma become common. In male dogs cryptorchidism, testicular atrophy, and azoospermia typically occur due to the gonadotropin deficiency. In bitches continual anoestrus or irregular oestrus is common. At around 2-3 years of age these dwarves become lethargic and develop anorexia. The degree of growth retardation and other clinical symptoms varies between affected dogs.

Investigations into the genealogy in 1978 found the mutation evolved in 1940 or earlier. Multiple champions have been shown to be carriers of the mutation, explaining the spread and prevalence of the disorder. This condition has been observed in breeds that were crossed with German Shepherd dogs such as the Karelian Bear dog, Saarloos Wolfhound, and the Czechoslovakian Wolfdog. A case was described in a litter of Weimaraner dogs; however a mismating between a German Shepherd dog had occurred three generations prior. Pituitary dwarfism in other dog breeds (excluding those with German Shepherd ancestry) is extremely rare.

Unlike forms of pituitary dwarfism in other species and breeds where cysts are responsible, in German Shepherd dogs with pituitary dwarfism cysts are either very small or non-existent. Current evidence suggests the pituitary dwarfism in the breed is caused by the oropharyngeal ectoderm of the Rathke pouch's inability to differentiate into cells that secrete trophic hormones in the pars distalis. Build up of proteinaceous material may result in cyst formation, suggesting that cyst formation is a side effect but not a cause of the pituitary dwarfism.

A study comparing these German Shepherd dwarves to healthy dogs found a deficiency of growth hormone, thyroid-stimulating hormone, and prolactin, with an impaired release of gonadotropins. Adrenocorticotropic hormone secretion remained normal.

In humans mutations of the POU1F1 and PROP1 genes are most commonly associated with pituitary hormone deficiency. However research has excluded both of these genes as candidates for pituitary dwarfism in the German Shepherd dog. The LHX4 gene has also been excluded. In 2011 a study identified the LHX3 gene as being responsible for the defect. The University of Utrecht offers a genetic test for this defect.