The mystery of India's red-haired child unlocks hidden colour genes
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Tracking a gene responsible for red hair in an Indian girl led scientists to a treasure trove of pigment genes. Credit: CSIR-CCMB<br>When scientists at the CSIR-Centre for Cellular and Molecular Biology (CCMB) in Hyderabad heard about a red-haired girl in a south Indian village, they got curious. In India most people have dark hair, and red hair is extremely rare.<br>They began by studying a specific gene responsible for hair and skin colour — the melanocortin 1 receptor (MCR1) gene — in the five-year-old girl. Her red hair, they found, stemmed from an ultra-rare mutation of the MCR1 gene1. She inherited two copies of this mutation, one from each parent. Her parents have black hair as they carry single copies of the mutation.<br>Kumarasamy Thangaraj, a geneticist at CCMB, told Nature India that this mutation p.Ala291Asp is different from the versions of the MC1R gene that give red hair to Europeans, among whom natural red hair is much more common.<br>The scientists confirmed with laboratory experiments and zebrafish studies that the mutation disrupts normal function of the MC1R gene, reducing pigmentation. In these experiments, they also found a second rare mutation, p.Gly248Cys, that impairs the gene's activity.<br>Encouraged by the findings, Thangaraj and team turned the study into one of the largest examinations of the MC1R variation in India. They screened 11,021 individuals from 91 Indian communities to find 21 novel or extremely rare variants, nine of which appear only in Indians.<br>The girl's mutation turned out to be just one piece of a much larger puzzle. Of the nine variants exclusively detected in Indians, two carried the mutation p.Ala57Thr, associated with malignant skin cancer risk. Another mutation -- p.Ile40Thr -- was found to carry the risk of skin cancer as well as reduced photoprotection and altered sensitivity to certain anaesthetics.<br>The scientists also looked at a common non-coding variant called rs3212363, previously thought to be responsible for lighter skin pigmentation in South Asians but never confirmed. The variant was found in high frequencies among the Bodh population of Ladakh, a high-altitude Himalayan region where lighter complexions are common.<br>Analysing 277 members of the Bodh community, the team found that people carrying two copies of the T version of this variant had melanin levels of around 8.5 units lower, on average, compared to those carrying two copies of the A version.<br>The variant's frequency varied widely across the country, ranging from 89% in the Bodh population to roughly 38% in a South Indian tribal group. The researchers say this distribution reflects the country's complex population history and genetic diversity.<br>South Asia’s pigment diversity<br>Pigmentation in South Asia is shaped by a richer genetic architecture than previously recognised, the findings suggest. They reflect the subcontinent's long history of migration, isolation and adaptation.<br>Across India's diverse ethnic groups, skin tones vary widely — from pale to wheatish, brown and dark brown. In South Asia, pigmentation genetics has largely focused on variants in SLC24A5, TYR and SLC45A2. The new findings place MC1R more firmly on that map, expanding the list of genes that contribute to visible differences in skin and hair colour across the region.<br>Manjari Jonnalagadda, who studies skin-pigmentation genetics at Symbiosis International University, Pune, says the discovery of functionally significant MC1R alleles, including variants linked to cancer susceptibility, challenges assumptions about how populations adapt to environmental pressures such as ultraviolet radiation. It also opens up new avenues for understanding rare disease mechanisms.<br>The study highlights that discoveries made in European populations do not always capture the full spectrum of biological diversity elsewhere in the world. Although MC1R is famous for its role in producing red hair in Europeans, the Indian variants uncovered here appear to have arisen independently, revealing alternative genetic routes to similar trait.
doi: https://doi.org/10.1038/d44151-026-00124-7
References<br>Kashyap, D.K. et al. Hum Genomics Genet. Adv. 7 , 100603 (2026).<br>Article<br>PubMed
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