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rs1800407

From SNPedia

Orientationminus
Stabilizedminus
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
ReferenceGRCh38 38.1/142
Chromosome15
Position27985172
GeneOCA2
is asnp
is mentioned by
dbSNPrs1800407
ebirs1800407
HLIrs1800407
Exacrs1800407
Varsomers1800407
Maprs1800407
PheGenIrs1800407
hapmaprs1800407
1000 genomesrs1800407
hgdprs1800407
ensemblrs1800407
gopubmedrs1800407
geneviewrs1800407
scholarrs1800407
googlers1800407
pharmgkbrs1800407
gwascentralrs1800407
openSNPrs1800407
23andMers1800407
23andMe allrs1800407
SNP Nexus

SNPshotrs1800407
SNPdbers1800407
MSV3drs1800407
GWAS Ctlgrs1800407
GMAF0.03489
Max Magnitude1
? (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 18252222OA-icon.png] 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.

Neighborrs28934272
Distance71


[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.

OMIM611409
DescOCA2 GENE
Variant
Relatedalso


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


[PMID 22065085OA-icon.png] 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
Variation info
Gene OCA2
CLNDBN Skin/hair/eye pigmentation, variation in, 1
Reversed 1
HGVS NC_000015.9:g.28230318C>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000001014.5,



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


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


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


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


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


GET Evidence
OCA2-R419Q
aa_change Arg419Gln
aa_change_short R419Q
impact benign
qualified_impact Low clinical importance, Likely benign
overall_frequency 0.0565161
summary This variant is associated with eye color, as is OCA2 R305W. Individuals with this variant are reported to be more likely to have green/hazel eyes as opposed to blue/gray eyes. Other variants in this gene are associated with oculocutaneous albinism (albinism which involves skin and eyes).



[PMID 23100201OA-icon.png] 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