Eiberg H, Troelsen J, Nielsen M, Mikkelsen A, Mengel-From J, Kjaer KW et al.Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Hum Genet 123:177-187

Article (PDF Available)inHuman Genetics 123(2):177-87 · April 2008with502 Reads
Impact Factor: 4.82 · DOI: 10.1007/s00439-007-0460-x · Source: PubMed
The human eye color is a quantitative trait displaying multifactorial inheritance. Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we finemapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. By association analyses, we identified two SNPs within this region that were perfectly associated with the blue and brown eye colors: rs12913832 and rs1129038. Of these, rs12913832 is located 21.152 bp upstream from the OCA2 promoter in a highly conserved sequence in intron 86 of HERC2. The brown eye color allele of rs12913832 is highly conserved throughout a number of species. As shown by a Luciferase assays in cell cultures, the element significantly reduces the activity of the OCA2 promoter and electrophoretic mobility shift assays demonstrate that the two alleles bind different subsets of nuclear extracts. One single haplotype, represented by six polymorphic SNPs covering half of the 3' end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.

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Available from: Jonas Mengel-From
Brown eyes, blue eyes. From a gene to its protein
The Cus-Mi-Bio staff, composed of both University Professors and High School teachers, are the
scientific editors and authors of this Handbook’s contents.
Workshop Leaders
Giovanna Viale
Professor of Biology and Genetics, Dept. of Biology and Genetics for Medical Sciences,
University of Milan, via Viotti 3/5, Milan, Italy
Cinzia Grazioli
High school teacher working full-time at Cus-Mi-Bio
Cus-Mi-Bio, University of Milan, via Viotti 3/5, Milan, Italy
Cristina Gritti
High school teacher working full-time at Cus-Mi-Bio
Cus-Mi-Bio, University of Milan, via Viotti 3/5, Milan, Italy
Page 1
Brown eyes, blue eyes. From a gene to its protein
There is a famous sequence in Quai des Brumes a very popular French film shot in the
1930s in which Jean Gabin, subdued by the sky blue of his interlocutor’s gaze, leans
over and breathes into Michèle Morgan’s ear, “T’as d’beaux yeux tu sais” meaning
literally: “You’ve got beautiful eyes you know” … though it means far more. The blue of
an eye is both fascinating and mysterious, and we are getting closer to an explanation for
it. It is common knowledge that the colour of our eyes is due to the accumulation of a
pigment in the iris melanin whose synthesis depends on the activity of a protein
known as P protein. Despite years of research, scientists had not been able to pin down a
modification in P protein, which could explain the azure of a look, until recently when
after a long sought a mutation was discovered – only not at all where they were expecting
P protein is essential to pigmentation. Although its precise function is unknown, it is a
key factor in the synthesis of melanin the pigment which gives our skin, our hair and
our eyes their colour. The motto goes: the more the melanin, the darker the eyes.
Albinism, on the other hand, which results from the discolouration of our skin, eyes and
hair occurs following a
serious defect in melanin
synthesis. To date,
approximately 40 mutations
have been identified on the P
protein gene, which are all
involved in one of the major
forms of albinism.
Note that there are several
other genes (and proteins)
whose loss of function is the
cause of different forms of
albinism. All of them are
involved in pigment
biosynthesis and/or
To find more info about the P protein, visit
From the database pull down menu on the left select the protein database and type “P
protein homo sapiens” in the search box.
You will find the record Q04671, Melanocyte-specific transporter protein.
From this site collect info about the P protein. It has 838aa.
Page 2
FUNCTION: Could be involved in the transport of tyrosine, the precursor to melanin
synthesis, within the melanocyte. Regulates the pH of melanosome and the melanosome
maturation. One of the components of the mammalian pigmentary system. Seems to
regulate the post-translational processing of tyrosinase, which catalyzes the limiting
reaction in melanin synthesis. May serve as a key control point at which ethnic skin color
variation is determined. Major determinant of brown and/or blue eye color.
section you will find
the name of the
corresponding gene
OCA2 (ocular
cutaneous albinism,
form 2).
In the list of
references (articles)
you’ll find a recent
paper by a group of
Danish scientists
which cast a new
light on the function
of P protein in
determining eye
Authors: Eiberg,H., Troelsen,J., Nielsen,M., Mikkelsen,A., Mengel-From,J., Kjaer,K.W.
and Hansen,L.
TITLE: Blue eye color in humans may be caused by a perfectly associated founder
mutation in a regulatory element located within the HERC2 gene inhibiting OCA2
JOURNAL: Hum. Genet. 123 (2), 177-187 (2008)
Blue eyes have poor melanin content. Convinced that this might have something to do
with P protein, researchers carried out a major study in the hope of discovering what it is
that makes the difference between brown eyes and blue eyes. To their surprise, they
found only one mutation and, what’s more, not on the P protein gene but on an adjacent
gene: HERC2. This particular mutation has the same effect as a switch and slows down
protein P synthesis, thus reducing its production. Without it, P protein is produced
normally and eyes are brown. In individuals carrying this mutation, P protein is produced
in smaller quantities and eyes turn out to be blue.
Check the chromosomal location of the two genes OCA2 and HERC2.
Return to NCBI home page and from the database pull down menu on the left select the
Gene database and type separately “OCA2” and “HERC2” in the search box.
Page 3
OCA2: Chromosome: 15; Location: 15q11.2-q12
HERC2: Chromosome: 15; Location: 15q13
In conclusions, HERC2 is adjacent to OCA2. The terminal part of the HERC2 gene
contains a switch which regulates OCA2 expression!
The authors have found that “One single haplotype, represented by six polymorphic
SNPs covering half of the 3' end of the HERC2 gene, was found in 155 blue-eyed
individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan,
What this implies, is that this mutation is a “founder mutation” i.e. it is shared by both
North European individuals and subjects from Turkey and Jordan. All blue-eyed
individuals indeed carry the same mutation which seems to have appeared about ten
thousand years ago. Before that, everyone had dark eyes. The first blue look appeared on
earth during the Neolithic period (about 6-10,000 years ago) when our ancestors left the
region of the Black Sea for a better future, and built settlements in Northern Europe. Ever
since, blue eyes have cleared millennia, gliding successfully through time.
Why are blue eyes still around? Why has evolution kept them?
The high frequency of blue eyed individuals in Scandinavia and Baltic regions indicates a
positive selection for this trait.
Several theories have been suggested to explain the evolutionary selection for
pigmentation traits which include UV radiations causing skin cancer, vitamin D
synthesis from precursors in diet food requiring UV radiations reaching the deep layers of
derma, and also sexual selection .
White skin which is a phenotype so typical to our Northern hemisphere is explained
as an adaptation to poor sunlight, thus favouring the synthesis of vitamin D. But blue
eyes? What are they for? A number of researchers suggest that it may simply have
something to do with sexual selection. Why not? How many of us have got hopelessly
lost in an ocean blue gawp? Jean Gabin seemed to know better…..
Structural features of the protein
For a complete card of the P protein go to
This protein is a transporter protein with at least one transmembrane domain
To view its main structural features copy it in FASTA format (click the yellow button on
the top right of the page).
Page 4
Go to:
and Paste the FASTA sequence in the search box. Click execute.
This software is dedicated to the prediction of transmembrane protein domains based on
R groups of aminoacid residues and gives a graphic representation of the disposition of
transmembrane domains in the membrane.
Look at the predicted transmembrane domains.
How many are they?
Which R groups are the most frequent in the aa predicted to be part of transmembrane
To answer this question visit also this listing of the different side groups for the various
amino acids:&http://www.elmhurst.edu/~chm/vchembook/562review.html&
3D structure of the protein
Return to http://uniprot.org/uniprot/Q04671
Scroll down the page to the section “3D structure databases” and click search.
Page 5
Your search hasn’t found any record for 3D structure of the human P protein; the first in
the list is
You can download the file with the blue arrow icon (PDB code 2a65A )and open it with
Deep$V i ew$$
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4,4+24;2"& (%':& $)"& EIB"%$& P%'$"+#& A#42.-+-& S.-$":& DJIFK0.G& 3'2"1724%& 5+'2'H.& 0"%,"%& +#&
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Page 6
    • "A certain combination of blue and brown colors in the eye may appear green or hazel from a distance even though no such pigment exists. The distinction between blue and brown eye colors can for the most part be explained genetically by one single-nucleotide polymorphim (SNP), rs12913832:A>G in the hect domain and RCC1-like domain 2 (HERC2; OMIM #605837) gene (Eiberg et al. 2008; Sturm et al. 2008). Although, rs12913832:A>G is located in intron 86 of HERC2, rs12913832:A>G is positioned in an enhancer element that regulates expression of the oculocutaneous albinism type II (OCA2; OMIM #611409) gene (Visser et al. 2012). "
    [Show description] [Hide description] DESCRIPTION: OCA2 sequencing of human in relation to human eye colours
    Full-text · Research · Jun 2016 · Pigment Cell & Melanoma Research
    • "For example, SNP rs12916300 at 15q13 (Figure S2) lies within intron 68 of HERC2, which encodes a ubiquitin-protein ligase recruited to sites of DNA damage from ionizing radiation, and which has been associated with BCC (Han et al., 2011) and pigmentation phenotypes (Han et al., 2011;Eiberg et al., 2008). This SNP is in high linkage disequilibrium (LD) (R 2 = 0.85) with rs12913832, another intronic SNP in HERC2 that M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 5 has been associated with pigmentation phenotypes (Sturm et al., 2008;Han et al., 2008;Eiberg et al., 2008;Branicki et al., 2009;Nan et al., 2009b) and that modifies expression of OCA2, a nearby gene encoding a melanosomal enzyme needed for melanin synthesis (Visser et al., 2012). However SNP rs12916300 remained associated with SCC risk with genome-wide significance after adjustment for rs12913832, suggesting that its effects are not merely due to its correlation with rs12913832. "
    [Show abstract] [Hide abstract] ABSTRACT: We report a genome-wide association study (GWAS) of cutaneous squamous cell carcinoma (SCC) conducted among non-Hispanic white (NHW) members of the Kaiser Permanente Northern California (KPNC) health care system. The study includes a genome-wide screen of 61,457 members (6,891 cases and 54,566 controls) genotyped on the Affymetrix Axiom European array and a replication phase involving an independent set of 6,410 additional members (810 cases and 5600 controls). Combined analysis of screening and replication phases identified ten loci containing single-nucleotide polymorphisms (SNPs) with P-values < 5x10-8. Six loci contain genes in the pigmentation pathway; SNPs at these loci appear to modulate SCC risk independently of the pigmentation phenotypes. Another locus contains HLA class II genes studied in relation to elevated SCC risk following immunosuppression. SNPs at the remaining three loci include an intronic SNP in FOXP1 at locus 3p13, an intergenic SNP at 3q28 near TP63, and an intergenic SNP at 9p22 near BNC2. These findings provide insights into the genetic factors accounting for inherited SCC susceptibility.
    Article · Jan 2016
    • "We selected fourteen markers for genotyping that have either previously been associated with iris colour in European populations or been associated with some other pigmentation phenotype (i.e. skin colour) in East or South Asia (Eaton et al., 2015; Edwards et al., 2012; Eiberg et al., 2008; Graf et al., 2005; Kayser et al., 2008; Liu et al., 2010; Rebbeck et al., 2002; Sturm et al., 2008; Walsh et al., 2011). These markers consisted of HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 rs16891982, SLC24A5 rs1426654, TYR rs1393350, IRF4 rs12203592, DSCR9 rs7277820, TYRP1 rs1408799, NPLOC4 rs9894429, LYST rs3768056, ASIP rs6058017, OCA2 rs1800414 and OCA2 rs74653330. "
    [Show abstract] [Hide abstract] ABSTRACT: In this study, we present a new quantitative method to measure iris colour based on high resolution photographs. We applied this method to analyze iris colour variation in a sample of individuals of East Asian, European and South Asian ancestry. We show that measuring iris colour using the coordinates of the CIELAB colour space uncovers a significant amount of variation that is not captured using conventional categorical classifications, such as "brown", "blue" or "green". We tested the association of a selected panel of polymorphisms with iris colour in each population group. Six markers showed significant associations with iris colour in the European sample, three in the South Asian sample and two in the East Asian sample. We also observed that the marker HERC2 rs12913832, which is the main determinant of "blue" vs. "brown" iris colour in European populations, is also significantly associated with central heterochromia in the European sample. This article is protected by copyright. All rights reserved.
    Full-text · Article · Nov 2015
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