OCA2 R419Q - GET-Evidence

Curation:
Currentness:

OCA2 R419Q

(OCA2 Arg419Gln)


Short 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).

Variant evidence
Computational 1

Gene is associated with pigmentation.

Functional -
Case/Control 4

OR = 3, p < 0.001

See Rebbeck TR et al. 2002 (12163334).

Familial

No familial data

 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Low clinical importance, Likely benign

(The "low clinical importance, likely" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • T @ chr15:28230318: 5.7% (608/10758) in EVS
  • T @ chr15:25903912: 2.3% (3/128) in GET-Evidence
  • Frequency shown in summary reports: 5.7% (608/10758)

Publications
 

Rebbeck TR, Kanetsky PA, Walker AH, Holmes R, Halpern AC, Schuchter LM, Elder DE, Guerry D. P gene as an inherited biomarker of human eye color. Cancer Epidemiol Biomarkers Prev. 2002 Aug;11(8):782-4. PubMed PMID: 12163334.

This allele is associated with green/hazel eyes vs. blue/gray. 10.9% of individuals with blue/gray eyes have this variant and 27.1% of individuals with green/hazel have it. 16.2% of individuals with black/brown have it. P value < 0.001 and the highest odds ratio (blue/gray vs green/hazel) was 3.00. They also report an association with Arg305Trp and brown/black eyes vs. light eyes (blue/gray or green/hazel).

Genomes
 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het T @ chr15:28230318

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het T @ chr15:28230318

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het T @ chr15:28230318

 

 

GS07357 - var-GS07357-1100-36-ASM
het T @ chr15:25903913

 

GS20502 - var-GS20502-1100-36-ASM
het T @ chr15:25903913

 

Other external references
 

    dbSNP
  • rs1800407
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.998 (probably damaging)
    Web search results (70 hits -- see all)
  • ARTICLE
    We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP ... firmed that the common coding variant OCA2*R419Q. acts to modify the penetrance of this ...
    www.qimr.edu.au/davidD/Course/Papers/Sturm_EyeColour2008.pdf
  • AJHG - A Three–Single-Nucleotide Polymorphism Haplotype in ...
    We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this ... to clarify the role of the OCA2 locus in the inheritance of ...
    www.cell.com/AJHG/abstract/S0002-9297(07)62682-2
  • AJHG - Three Genome-wide Association Studies and a Linkage ...
    We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this ... trait locus linked to the OCA2 region of 15q accounts for 74 ...
    www.cell.com/AJHG/abstract/S0002-9297(08)00074-8
  • A single SNP in an evolutionary conserved region within ...
    We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat ...
    www.ncbi.nlm.nih.gov/pubmed/18252222
  • Pigmentation-related genes and their implication in malignant ...
    Pigmentation-related genes and their implication in malignant ... We found that the variant allele of OCA2 R419Q (rs1800407) was associated with increased risk of MM (OR 1.55, ...
    www.ncbi.nlm.nih.gov/pubmed/19320733
  • OCA2 - SNPedia
    OCA2, the oculocutaneous albinism gene (also known as the human P protein gene, or, DN10) ... OMIM 203200.0012 The R419Q variant of the OCA2 gene (AA at this ...
    www.snpedia.com/index.php?title=OCA2&redirect=no
  • Melanoma - SNPedia
    rs1800407 is one of several SNPs in the OCA2 gene that are associated with eye color. ... also found that the R419Q variant of the OCA2 gene (AA at this ...
    snpedia.com/index.php?title=Melanoma&oldid=129488
  • 1 SNP to rule them & in the darkness bind them? : Gene Expression
    ... OCA2, and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris ... the common coding variant OCA2*R419Q acts to modify the penetrance ...
    scienceblogs.com/gnxp/.../one_base_pair_to_rule_them_in.php
  • Eye for an Eye - Reference : Kosmix
    Reference related to Eye for an Eye from the best sources on the Web ... were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a ...
    www.kosmix.com/topic/Eye_for_an_eye/Reference
  • OMIM: 611409
    MIM Entry: 611409 Title: *611409 OCA2 GENE ;;PINK-EYED DILUTION; PED;; P GENE ... replicate the association of the R419Q variant of OCA2 with nonblue eye color in ...
    www.genome.jp/dbget-bin/www_bget?omim+611409

Other in silico analyses
 

  • NBLOSUM100 score = 0
  • GET-Evidence autoscore = 5

Edit history
 

Gene search

"GENE" or "GENE A123C":

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