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The MC1R gene codes for a protein called melanocortin 1 receptor which is located on the receptors of melanocytes, the specialized cells that produce melanin. Melanin is produced as a defence against harmful UV rays and it comes in two forms - eumelanin and pheomelanin. People who primarily produce pheomelanin tend to have freckles. There is a strong genetic component to the development of freckles. It has been shown that identical twins have a similar number of freckles. This similarity is less common in fraternal twins. Variants of the MCR1 gene will lead to the presence of freckles.
When asking why people have freckles, one must understand that the spots will develop after being triggered by sunlight. UV-B radiation from the sun causes melanin production to increase due to the activation of melanocytes within the cells. Freckles are just a concentrated deposit of melanin in a particular location.
Freckles are most commonly found on the face, but can appear generally anywhere on the body as long as that location is exposed to the sun.
Although freckles are not a skin disorder, people with them are susceptible to a variety of skin problems. This is because a person with the pheomelanin type of melanin has a lower concentration of photoprotective melanin that guards against the harmful effects of UV-radiation. Sunscreen can be used to protect the skin of a freckled person.