The genetic defect leading to the disease has been identified. By DNA testing the responsible mutation can be shown directly. This method provides a very high accuracy test and can be done at any age. It offers the possibility to distinguish not only between affected and clear horses, but also to identify clinically healthy carriers. This is an essential information for controlling the disease in the breed as carriers are able to spread the disease in the population, but can not be identified by means of common laboratory diagnostic.

A single autosomal dominant gene, leopard complex (LP), is responsible for different spotting patterns while modifier genes are thought to play a role in determining the amount of white patterning that is inherited. These patterns are called from lightest to darkest: „few spot leopard“, „leopard“, „snowcap blanket“, „blanket with spots“, „varnish roan (marble)“, „snowflake“, „frosted“, „speckled“ and „mottled“. Homozygosity for LP (LP/LP) is directly associated with congenital stationary night blindness (CSNB) in Appaloosa horses. Heterozygous carriers (LP/lp) are not affected. CSNB is characterized by impaired vision in dark conditions, and is present at birth.

Horses exhibiting the Tobiano spotting are characterised by white, depigmented areas with distinct borders that cross the dorsal midline and include at least one if not all four legs. The amount of white can vary from minimal areas on the lower legs to predominantly white over the entire body. The Tobiano white spotting pattern is a trait controlled by a dominant gene.

Splashed white is a variable white spotting pattern characterized primarily by extremely large blaze, extended white markings in legs, variable white spotting in belly, and often blue eyes. Some, but not all, splashed white horses are also deaf. Recent research has identified 3 mutations – SW-1, SW-2 and SW-3 - that cause splashed white phenotypes in horses. SW-1 has been found in several breeds - Quarter Horse, Paint, Trakehner, Miniature Horse, Shetland Pony and Icelandic Horse – and may be present in other breeds as well. Horses homozygous for SW-1 (SW1/SW1) have been identified, which suggests that this mutation is not homozygous lethal. SW-2 and the rare SW-3 occur exclusively in certain lines of Quarter Horses and Paints. Based on predictions from other species, SW-2 and SW-3 may be homozygous lethals and thus matings of two horses that carry SW-2 or SW-3 should be avoided.

Horses that carry combinations of the splashed white mutations, tobiano or lethal white overo can display extensive white patterning or be white.

Sabino

Sabino is a term used to describe a group of similar white spotting irregular patterns on the skin and hair of the legs, belly and face, often with roaning around the edges.

Sabino horses are described to have belly spots, irregular face markings that often extends past the eyes or onto the chin, white markings above the knees or hocks, and "splash" or "lacy" marks anywhere on the body, but in particular on the belly. Some Sabinos have patches of roan patterning on part of the body, particularly on the barrel and flanks. Some Sabinos may have a dark foot or two, but most have four white feet. Both blue and brown eyes are seen.

There is a number of mutations that produce the Sabino pattern, Sabino 1 (SB1) is one of these mutations that has been identified. Horses carrying this mutation are Sabinos, however not all Sabino horses carry this mutation, there are still unidentified mutations that produce the Sabino pattern.

The mode of inheritance is autosomal dominant, which means that only one copy of the Sabino 1 mutation is enough to produce a Sabino pattern. When  one copy of the Sabino 1 mutation is present (N / SB1) the horse is expected to have two or more white legs or feet, often with white marking on the front of the leg, an extensive blaze, white spotting on the midsection with roaned or jagged edges. Horses with two copies of the mutation (SB1/SB1) are almost completely white with pink or partially-pigmented skin, they are described as Sabino-White.