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 (TYRP1) , 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 erroneously believed it to have been the dilute modifier gene (which turns eumelanin-based colours to caramel). However, the Barrington Brown homozygotes were different in colour to caramel cats. In the homozygous form, Barrington Brown had an additive effect on the other colours (some suggest cats with one copy of the gene and cats with two copies looked different, but a cat with only one copy of the gene shouldn't show any effect).

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) due to 2 mutations in the Tyrosinase (TYR) gene. 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 / white spotting gene which masks pigment.

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

Breakthrough Tabby Pattern in Colourpoints

Cats born of Siamese parents sometimes have a tabby/spotted pattern breaking through so strongly that the cat appears to be a tabby/spotted Oriental or a tabby/spotted sepia (Burmese) cat. Viewed closely, the pattern colour is heavily ticked on a paler ticked background. This breakthrough pattern is evident from kittenhood and not the same as age-related darkening in Colourpoint cats. It is inherited, possibly due to modifier genes that prevent the colourpoint gene from properly inhibiting the colour/pattern on the normally pale areas of the body.

Dense and Dilute colours are due to a simple gene pair (gene: Melanophilin or MLPH). 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.

Research has found that White Masking and White Spotting are dominant alleles of the same gene (called KIT) and the order of dominance is W >> Ws >> w >> wg.

W produces solid white and is the most dominant in the series. Ws is extremely variable in how it shows up; it is dominant over solid colour (non-white-spotted). A cat with a single copy of Ws might have a small amount of white or a large amount. Most often, though, cats with two copies of Ws have more white, and may even be solid white. Selective breeding can fix the amount of white because other genes, known as polygenes, can influence colour distribution e.g. Some breeds have been fixed for gloves or mitts. A separate recessive gene wg has been identified for Birman white gloving. There are hypothetical genes for other white mitted patterns and for the York Chocolate white pattern. There are other genes, as yet unidentified, for the white throat locket and white brisket spots.

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). Dominant white ( W ) 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). White spotting ( Ws ) is variable in expression from white locket through to solid white, and is rarely associated with deafness.

The Birman "White Gloving" pattern ( wg previously called G ) is the most recessive of the alleles identified. A cat with two copies of wg has gloved white feet and this trait has been fixed other white markings bred out - so that Birmans are homozygous for wg. Cats with the White Glove mutation are also found in the Ragdoll, Egyptian Mau, Exotic Shorthair, Maine Coon, Manx, Seychellois, Siamese, Siberian, Sphynx and Turkish Van. Testing has found that the Ragdoll "Mitted" pattern is different from wg. Because white feet can result from several different mutations, a genetic test has been developed for the White Gloving gene.

• Reference: B Gandolfi, LH Bach, et al. "Off with the gloves: Mutation in KIT for the unique white spotting phenotype of Birman cats".

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 (ASIP). 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) gene and the Wide Band gene will appear as shaded or tipped cats while those lacking Wide Band will be silver 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.

CHARCOAL (AGOUTI VARIANT)

The following information is courtesy Joshua Dabbs who is investigating charcoal Bengals with Terra Sinclair.

"Charcoal" is found in Bengals, especially in the early generations, and has also occurred in Savannahs due to Bengal outcrosses in breed development. Charcoal Bengals are "Aa" at the agouti locus. Charcoal is due to a variant in the agouti gene ("charcoal agouti" or A^Pb variant) inherited from the Asian Leopard Cat reacting with the domestic cat non-agouti gene (a). Non-agouti genes develop independently in different species and though the visual effect is similar, the gene mutations are different. In hybrids, they interact to produce novel effects. The genotype A^Pba results in an intermediate form between agouti and non-agouti. The intermediate form causes an increase in black pigmentation unevenly distributed throughout the coat. The distribution of pigmentation varies between cat, and often causes coloration and features to become more exaggerated to where they take on an entirely new appearance. The domestic cat version of the Agouti (A) gene is termed A^Fc in the table below.

Charcoal is now seen many generations down the line. Joshua Dabbs and Terra Sinclair investigated a number of pedigrees that supported that theory on inheritance of charcoal. These include a Bengal melanistic carrier that when paired with an F-Generation Bengal (F1 to F4 = 1 to 4 generations removed from a wild parent) produced charcoal colored brown spotted offspring. Early on in the breed history, charcoals were not properly identified as they they did not always pass their colouration to the next generation. They were misidentified as minks, smokes (from silver smoke Egyptian Mau outcrosses) or unrufoused browns. A high degree of rufism was sought in the original Bengals and the seemingly unrufoused browns were undesirable. A greater interest in the unrufoused Bengals (e.g. in silvers and melanistics (smokes)) has increased interest in, and acceptance of, the charcoal series.

Charcoal Bengals vary in appearance though there are identifying factors known as "Zorro" markings. Charcoals have pure white or off-white goggles around the eyes while smokes have ghost tabby markings. Accompanying the white goggles there is usually a dark "charcoal mask" from the forehead, down the nose-bridge and often underneath the eyes and extending into the mascara-lines; the mask resembles an upside-down "Y". Charcoals also have an unbroken "cape" or "sheet" down their backs (broad back-stripe), in some cats this extends into the patterns closest to the spine-line while others have a narrower "modified" cape running down the back. Charcoal Bengals, including the browns, tend to have silver glitter, rather than either gold glitter (on normal tawny colours) or crystal glitter (on the snows and silvers).

Charcoal Brown is the most common charcoal colour; some have a uniform charcoal colour, while others have lighter background on their sides and darker background towards the top and tail. Charcoal Browns may be born looking silver due to black markings on a light greyish, background. Others ("black charcoals") are born so dark they may appear melanistic, but the background lightens as the kittens grow. Charcoal silver, when paired with a regular silver Bengal, results in higher contrast in the kittens. Charcoal silvers may be born very dark, resembling a silver smoke except for the white facial markings, becoming black-on-silver as they grow; the darker ground colour also masks the appearance of tarnishing. Colourpoint variants show darker pigmentation in their pattern or the pointing (e.g. in lynx point) is more prominent due to the higher level of pigmentation. Charcoal Snows have a greater contrast with darker markings than regular snows. Charcoal Marbles have tended to carry a sheet of colour rather than having distinct marble patterning.

Charcoal Savannahs have white or off-white goggles around the eyes and a distinctive dark nose. Rather than a pronounced mask or cape (as in bengals), there appear to be dense tabby markings between the ears. The background colour is grey rather than golden/tawny. The colour seems to trace back to the Kirembo line and has turned up in the USA and UK.

The Extension gene (symbol E) or red factor controls the production of red and black pigment. The dominant allele E produces black pigment in the coat while the recessive allele e produces red pigment. The name comes from the effect of black or brown pigment not being extended throughout the whole coat, but being restricted to the skin of the extremities and to the eyes (for example in bay horses). Amber is due to a recessive mutation in the MC1R gene.

In Norwegian Forest Cats, 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 Extension Gene (also known as Black Modifier or Agouti Modifier) in those breeds. The extension locus (the melanocortin receptor) or its ligands (molecules that bind to that receptor), control melanocyte stimulating hormone and agouti signaling protein.

Similar to amber is russet, which turned up in a line of seal (brown) European-style Burmese in New Zealand in 2007. It has subsequently occurred found in the related Mandalay (similar to the Asian in Europe) and appears to be a mutation of the extension gene. The first known russet was a pure-bred Burmese called Molly in 2007. There is now an experimental programme in NZ to breed Russet Burmese and to investigate dilute russet, russet tabby and solid russet (as opposed to the Burmese sepia form of russet).

The first russet kitten Molly was born an "odd-coloured lilac (lavender)" which gradually lightened as she grew, progressing through lilac-caramel and chocolate ticked tabby and then dramatically changing to red. Chocolate ticked tabby and red were both impossible from her pedigree, and in any case, reds are not born as chocolate tabbies! Several more unusually coloured kittens were born in different litters and all went through the same colour/pattern changes. The ancestors of these kittens were seal Burmese and had no silver, tabby or Mandalay (Asian) blood. The pedigree had both dilute and chocolate, there were no reds, creams or torties until 4 generations back. DNA testing showed some kittens to be genetically seal and other genetically chocolate. Hence the new colour is due to a different mutation currently known as russet. Russet appears to be due to a recessive mutation that causes black pigment (eumelanin) to gradually fade to a minimal amount while leaving red pigment (phaeomelanin)unaffected.

Russet kittens resemble tabbies at birth, but have pink noses and paw-pads, pale fur around the pads and genitalia and a pale tail-tip - all of which would be dark in tabbies. The muzzle and fur around the eye is ivory. The back is solidly dark rather than ticked, becoming pale ivory halfway down the flanks. The back becomes more ticked appearance, almost a saddle, as kittens undergo the colour change and the face becomes reddish. By age two, they may resemble a red Burmese. It differs from amber as ambers have dark noses and paw-pads. Non-agouti (solid) amber kittens are very dark with a dark face that is last to go red while russet kittens have off-white faces (possible due to Burmese sepia gene in the mix), which are the first part to go red (rather than the last as in ambers), and pale undersides. The russet colour change appears to be slower than the amber colour change. Russet kittens to date have been larger at birth than their siblings and somewhat on the large side as adults.

In the Kurilian Bobtail, a dominant colour change gene has been identified. Copal (also known as Carnelian to breeders) causes brown tabby kittens to be born with reddish hues and turn into red tabbies with a dark tail-tip in adulthood. its effect on blue or non-tabbies has not been described yet.

"Golden" or "golden tabby" Siberians have a recessive Corin mutation which is a wide band gene. The name "zoloty" (Russian for golden) was suggested for this mutation because"golden" is already used for non-silver tipped, shaded and smoke cats. It is now called Sunshine.

A similar effect is seen in Bengals where different Corin mutations cause "Sorrel" Bengals where the pattern colour has faded from black to reddish brown. Bengal breeders also believe there is a rufousing gene that gives a very reddish background without fading the markings. The background colour of early Bengals has more highly rufoused than the golden colour preferred today. They refer to the posited gene as "rf).

Bengal rufousing (production of red pigment in place of black/brown) is distinct from tarnishing (where red pigment is not fully suppressed by the inhibitor (silver) gene). In Bengals, excepting silvers and melanistics, a high degree of rufousing is desirable.

Wideband is a recessive trait with different Corin alleles involved in different breeds.

Wideband "Sunshine" is only seen in agouti (tabby patterned) Siberian cats (and possibly also Kurilian cats) where it produces reddish areas in the black, blue etc coat. Because Sunshine is on a different locus to the Inhibitor (silver) gene, it is possible for both genes to occur in the same cat resulting in a "bi-metal" appearance where both silver and golden areas are present.

Wideband "Flaxen Gold" or "British Sunshine" is a very pale golden colour seen in British Shorthairs/Longhairs and Scottish Folds/Straights.

Bengal sorrel is also a Corin wideband gene and follows the same inheritance pattern, just substitute wb^BEN for wb^BSH in the tables above. 12 Corin variants causing wideband effect have been identified in the Bengal.