This lists the different loci and combinations of alleles, including a few hypothetical or unconfirmed genes. In the case of the posited genes listed, there has been sufficient breeding data or study of cats with the trait(s) for the genes to be statistically likely.

This is a gene series with the order of dominance: Black/Brown > Chocolate > Cinnamon. Browning genes code for tyrosinase related protein-1, an enzyme involved in the metabolic pathway for eumelanin pigment production. The dominant form, B, produces black color. Recessive variants are b (chocolate) and bl (cinnamon/light brown).

Don Shaw's "Barrington Brown" may be a further recessive brown colour. It was observed in a colony of laboratory cats, none of which left the laboratory. Some breeders consider it to have been the dilute modifier (caramel) gene. However, the Barrington Brown homozygotes and heterozygotes were different in colour i.e. the two alleles had an additive effect on each other.

This is a sex-linked trait carried on the X chromosome. It causes phaeomelanin (orange pigment) to completely replace eumelanin (black or brown pigment). Red can also be modified in the following fashion:
O + d/d (homozygous for dilute colour) = Cream
O + d/d + Dm (dilute modifier) = Apricot

Colourpoint is a series of alleles (also known as temperature-sensitive albino). The order of dominance is C > cb/cs >  ca > c. The alleles cs and cb are co-dominant to each other and expression of these is temperature sensitive with the pigmentation being restricted to the cooler extremities of the body: muzzle, ears, tail and legs. Colourpoint cats in colder regions generally have darker body colour and more extensive points while those in warmer regions generally have paler bodies and smaller coloured areas. This can also be demonstrated by bandaging a cat's limb while it is moulting - the newly grown fur will be paler because the bandaged area is relatively warm. Colourpoint expression is also age-related, with older cats tending to be darker than younger cats.

True albino cats (absence of pigment) are rare because the more dominant alleles must be absent in order for albino to show up. Almost all blue-eyed white cats are due to the epistatic white gene or the white spotting gene which mask pigment.

The C gene codes for the enzyme tyrosinase, the first step in pigment production.

Dense and Dilute colours are due to a simple gene pair. When two dilute alleles are present, it changes the basic (dense) colour to its dilute form e.g. black dilutes to blue, chocolate dilutes to lilac, cinnamon dilutes to fawn, red dilutes to cream. The dominant Dilute Modifier gene only affects dilute colours. Dilute modifier has no effect on Dense colours, but may be carried by dense-colour cats and passed on to offspring and may therefore show up in later generations that also have the two dilute alleles.

D/d, codes for melanophilin, a protein involved in the transportation and deposition of pigment into a growing hair. The dominant form allows denser deposition of pigment.

This brightens black areas of the coat, modifying Black and Blue to Amber and Light Amber respectively. It has not yet been found in combination with other genes recessive to black. So far, it has only been observed in Norwegian Forest Cats where cinnamon and fawn alleles are known to be absent. It has also been called "fox". It may be present in other breeds, but its similarity to fawn and cinnamon means it may not have been identified as the Black Modifier in those breeds.

The black/agouti modifier may be related to the extension locus (the melanocortin receptor) or its ligands (molecules that bind to that receptor), melanocyte stimulating hormone and agouti signaling protein.

Epistatic white masks other colour and pattern alleles hence solid white cats may genetically be solid or patterned cats in any colour. The underlying colour will show up in any offspring that don't inherit the dominant epistatic white allele. The white spotting gene creates white markings on a solid or patterned cat. There are hypothetical genes for the white mitted pattern and for the York Chocolate white pattern. There are believed to be genes, as yet unidentified, for the white throat locket and white brisket spots.

The epistatic white gene is associated with developmental defects where melanocytes fail to migrate properly. This can result in one or both blue eyes and in degenerative changes in the succule and cochlea of the ear (resulting in partial or total deafness). The white spotting gene is variable in expression from white locket through to solid white and high grade white spotting can resemble epistatic white, however it is rarely associated with deafness.

Epistatic white prevents migration of pigment-producing cells to the skin during embryologic development. The number of melanocytes are greatly reduced, but not always absent (hence temporary smudges of colour on the heads of some kittens). It is sometimes called dominant white.

The agouti gene (A/a) determines whether the background colour is agouti or solid i.e. whether the tabby genes present are expressed or not. It codes for agouti signalling protein. The dominant, wild-type A causes the agouti shift phenomenon which causes hairs to be black pigmented at the tips and orange pigmented at the roots, allowing any underlying tabby pattern to be revealed. The recessive non-agouti (or hypermelanism) allele, prevents this shift in the pigmentation pathway and hides the tabby pattern (apart from ghost striping). The sex-linked O (orange) gene is epistatic (dominant) over non-agouti, hence red cats still have tabby markings (particularly visible in tortie cats where solid black patches and red-tabby are interspersed).

The secondary tabby locus is also called patterned/unpatterned tabby and determines whether an underlying blotched or striped pattern is manifested or not (in essence, it givesor denies permission for the tabby pattern to be expressed). The primary tabby locus determines the tabby type - classic or mackerel. The spotted pattern modifier changes these two patterns into spotted tabbies.

There are other hypothetical modifier genes affecting the overall pattern: Chaos (intermixes dark and light areas, disrupting the normal striped pattern), Confusion (adjacent hairs have different numbers and widths of colour bands) , Unconfused (adjacent hairs have consistent numbers and widths of colour bands), Erase (erases residual markings on limbs), and Roan (intermixes solid white hairs with coloured hairs). Tabby cats with both a colour inhibitor (silver/golden) gene and the Wide Band gene will appear as shaded or tipped cats while those lacking Wide Band will be silver/golden tabbies.

An unidentified "grizzled" gene in Chausie cats, that may be related to agouti gene, produces silver-tipped black fur and appears to have been inherited from the breed's wild Jungle Cat ancestors in which this trait is found.

Mackerel and Classic tabbies are modified by the ticked tabby allele and the spotted tabby allele. They must have non ticked (a/a) and non-spotted (sp/sp) alleles both present for the Mackerel or Classic tabby pattern to show up.

Spotted Tabby is a dominant modifier of both Mackerel and Classic Tabby, but is hypostatic to Ticked Tabby (is masked by epistatic ticked tabby gene). It modifies both tabby patterns into spotted patterns.

Breeder observations and analysis of pedigrees have resulted in several posited tabby modifiers. The Tabby Pattern Size modifier modifies the Classic Tabby Pattern by creating pale areas within the blotched markings and may be the same as the hypothetical Chaos modifier.

The Tabby Pattern Spot Modifier converts the 2 basic tabby patterns into spotted patterns. Spotted mackerel tabby will have smaller, more numerous, more vertically aligned spots while spotted classic tabby will have larger spots with less evident vertical alignment.

The Bengal Glitter Gene causes the golden glittered effect on Bengal cats and is inherited either from the wild ancestors (both Asian Leopard Cats and the Margay have been used in foundation cats) or from a domestic cat used in the foundation stock. Initially there was thought to be a single recessive glitter gene termed "gl".

Further study of hair types suggest there are 2 different types of glitter which are currently termed "Mica" and "Satin".

Mica glitter affects the tips of hairs. Homozygous recessive mi results in reflective hair-tips with what appear to be small flecks of mica (a highly reflective silicate crystal) embedded in the tip and visible under a microscope. Unlike the satin mutation, mica only affects the hair-tip. It was present in a domestic cat used in Jean Mill's original hybrids between Asian Leopard Cats and domestics.