It appears that variation in the gene, known as MC1R, is also related to differences in how old people look to other people - their perceived age, researchers said.
People carrying particular MC1R variants in their DNA look, on average, almost two years older than they are, researchers said.
"For the first time, a gene has been found that explains in part why some people look older and others younger for their age," said Manfred Kayser from Erasmus MC University Medical Centre Rotterdam in the Netherlands.
Perceived age has also been shown to predict a person's health and mortality, suggesting that the age we perceive a person to be from the appearance of their face might also be related in important ways to a person's biological age and health, they said.
Researchers searched the genomes of more than 2,600 elderly Dutch Europeans for DNA variants associated with differences in perceived facial age and wrinkling as estimated from digital facial images.
The strongest hits for perceived facial age were for DNA variants in the MC1R gene. This finding was confirmed in two other large European studies, researchers said.
In addition to its role in skin colour, MC1R is also known to play a role in other biological processes, such as inflammation and DNA damage repair, researchers said.
The gene's influence on these processes might be the reason it links to youthful looks, they said.
The findings were published in the journal Current Biology.
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