rs1800407

minus

Geno	Mag	Summary
(A;A)	1	green/hazel/brown/black eyes more likely
(A;G)	1	green/hazel/brown/black eyes more likely
(G;G)	1	blue/gray eyes more possible

Reference

GRCh38 38.1/142

Chromosome

15

Position

27985172

Gene

OCA2

is a	snp
is	mentioned by
dbSNP	rs1800407
dbSNP (classic)	rs1800407
ClinGen	rs1800407
ebi	rs1800407
HLI	rs1800407
Exac	rs1800407
Gnomad	rs1800407
Varsome	rs1800407
LitVar	rs1800407
Map	rs1800407
PheGenI	rs1800407
Biobank	rs1800407
1000 genomes	rs1800407
hgdp	rs1800407
ensembl	rs1800407
geneview	rs1800407
scholar	rs1800407
google	rs1800407
pharmgkb	rs1800407
gwascentral	rs1800407
openSNP	rs1800407
23andMe	rs1800407
SNPshot	rs1800407
SNPdbe	rs1800407
MSV3d	rs1800407
GWAS Ctlg	rs1800407

GMAF

0.03489

Max Magnitude

1

?

(A;A) (A;G) (G;G)

28

rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012]

[PMID 18093281] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour.

[PMID 18252222 ] Among rs12913832(A;A) individuals, the penetrance for green/hazel eyes was 50%, 21%, and 6%, respectively, for rs1800407(A;A), (A;G), and (G;G) genotypes, respectively. R419Q is also a significant risk factor (odd ratio 1.27, p=0.0006) for cutaneous malignant melanoma.

[PMID 19208107] Interactions between HERC2, OCA2 and MC1R may influence human pigmentation phenotype.

[PMID 19320733] Pigmentation-related genes and their implication in malignant melanoma susceptibility.

OMIM	611409
Desc	OCA2 GENE
Variant
Related	also

[PMID 20457063] Human eye colour and HERC2, OCA2 and MATP

[PMID 22065085 ] A global view of the OCA2-HERC2 region and pigmentation

ClinVar
Risk	Rs1800407(A;A)
Alt	Rs1800407(A;A)
Reference	Rs1800407(G;G)
Significance	Other
Disease	Skin/hair/eye pigmentation not specified Oculocutaneous albinism
Variation	info
Gene	OCA2
CLNDBN	Skin/hair/eye pigmentation, variation in, 1 not specified Oculocutaneous albinism
Reversed	1
HGVS	NC_000015.9:g.28230318C>T
CLNSRC	OMIM Allelic Variant UniProtKB (protein)
CLNACC	RCV000001014.6, RCV000252408.2, RCV000397427.1,

[PMID 17236130 ] A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation.

[PMID 19384953 ] Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians.

[PMID 20042077 ] Genetic determinants of hair and eye colours in the Scottish and Danish populations.

[PMID 20463881 ] Digital quantification of human eye color highlights genetic association of three new loci.

[PMID 20585627 ] Web-based, participant-driven studies yield novel genetic associations for common traits.

[PMID 23100201 ] A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model

[PMID 25142205] Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework