CCMB Hyderabad scientists trace red hair in Indian girl to ultra-rare MC1R gene variant

Scientists at the CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, have traced a rare case of red hair in an Indian child to a previously unreported variant of the MC1R (melanocortin 1 receptor) gene. The study, reported in late May 2026, also offers fresh evidence on the genetic diversity that shapes skin and hair colour across India.

Indians typically have black or dark brown hair. Red hair, more often associated with European populations, is an extremely rare phenotype in India. The investigation began with a five-year-old Indian girl who had red hair on her scalp, eyebrows and body, even though her eyes were dark. Her parents had typical dark hair, suggesting that the trait was inherited in a recessive way.

The MC1R gene plays a key role in deciding which type of melanin the body produces. It can produce eumelanin, which gives a dark brown or black colour, or pheomelanin, which produces red or yellow shades. Using genome sequencing, the CCMB team identified a rare MC1R variant in the child, written as c.872C>A.

Senior scientist K. Thangaraj said the girl had inherited two copies of this variant, one from each parent, in line with an autosomal recessive pattern. The parents each carried only a single copy, which left their own hair colour unchanged. The double dose of the variant disrupted the function of the MC1R protein in the child and led to red hair.

To check how widespread such variation might be, the team analysed more than 11,000 individuals drawn from 91 populations across India, using data from the GenomeIndia Consortium along with samples from CCMB. They identified 21 new or ultra-rare MC1R variants, showing an unexpectedly deep level of diversity. Laboratory experiments and zebrafish models confirmed that some of these variants weaken gene function and affect pigmentation.

The researchers also studied a separate variant, c.-226A>T (rs3212363), which is linked to lighter skin in certain populations. It was found at high frequency in the Bodh community of Ladakh, but at much lower frequency in some Dravidian-speaking tribal groups of South India. Communities in northern and northeastern India, which generally have lighter complexions, also showed a higher share of this variant.

Scientists cautioned that skin colour is shaped by several genes, including SLC24A5 and SLC45A2, and cannot be explained by MC1R alone. India’s wide range of skin tones reflects its layered history of migration and admixture, environmental adaptation and social factors such as endogamy. The findings also have clinical importance because MC1R variants are associated with a higher risk of certain skin cancers, including melanoma.