The chocolate locus codes for a gene similar to tyrosinase. The gene product is known as tyrosinase related protein Type I (TYRPI). The function of this gene is to convert a brown intermediate of eumelanin into eumelanin a black colour. Animals with a SNP or other mutation leading to an inactive gene product can not produce eumelanin in its mature form. So the intermediate brown pigment is transported from the melanocytes to the fur producing a chocolate coloured animal.

The phenotype of rabbits with the chocolate mutation depends on the interaction of other genes involved with pigment production, pigment transport and fur type.

The mutation applied to a chestnut agouti will give rise to Cinnamon, when applied to a self black it will produce a chocolate or havana.

Many breeds of rabbit do not have well developed orange coloured rabbits. Typically they have excessive lacing on the ears and dark eumelanin pigments on the upper tail. Rex, Satin, Thrianta and New Zealand Red have some good examples of Orange/Red coated animals, however many Netherland dwarfs and various lop breeds still show dark pigments on the face ears and tail.

In these cases the chocolate mutation can help to hide these dark points with out loosing the intensity of the orange colour as is the case when the dilute gene is used.

The dilute gene will effect the intensity of the orange pigment pheomelanin along with eumelanin. The chocolate gene has no effect on pheomelanin, makining it the ideal choise for improved orange.