Association between brown eye colour in rs12913832:GG individuals and SNPs in TYR, TYRP1, and SLC24A4

• Published in: PloS one 2020-09, Vol.15 (9), p.e0239131-e0239131
• Main Authors: Meyer, Olivia S, Lunn, Maja M. B, Garcia, Sara L, Kjærbye, Anne B, Morling, Niels, Børsting, Claus, Andersen, Jeppe D
• Format: Article
• Language: English
• Subjects: Alleles; Binding sites; Biology and Life Sciences; Color; Deoxyribonucleic acid; DNA; Ethics; Eye color; Forensic medicine; Genetic aspects; Genomes; Genomics; Genotype & phenotype; Genotypes; Herc2 gene; Interferon regulatory factor 4; Medicine and Health Sciences; People and Places; Physiological aspects; Prediction models; Regulatory sequences; Single nucleotide polymorphisms; Single-nucleotide polymorphism
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0239131

The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809.