OCA2 H615R - GET-Evidence

Curation:
Currentness:

(See the latest version)

OCA2 H615R

(OCA2 His615Arg)


You are viewing an old version of this page that was saved on November 12, 2012 at 4:57pm by Madeleine Ball.

Short summary

Associated with lighter skin pigmentation in East Asian populations.

Variant evidence
Computational 2

Polyphen 2 predicts disruptive effect, other variants in this gene cause albinism

Functional -
Case/Control 4

p = 0.002 for association with lighter pigmentation in east asians

See Edwards M et al. 2010 (20221248).

Familial -
 
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

other

Summary of published research, and additional commentary

 

Allele frequency

  • C @ chr15:28197037: 0.1% (7/10758) in EVS
  • C @ chr15:25870631: 8.6% (11/128) in GET-Evidence
  • Frequency shown in summary reports: 0.1% (7/10758)

Publications
 

Edited in this revision:

Yuasa I, Umetsu K, Harihara S, Kido A, Miyoshi A, Saitou N, Dashnyam B, Jin F, Lucotte G, Chattopadhyay PK, Henke L, Henke J. Distribution of two Asian-related coding SNPs in the MC1R and OCA2 genes. Biochem Genet. 2007 Aug;45(7-8):535-42. Epub 2007 Jun 15. PubMed PMID: 17570052.

 

Edwards M, Bigham A, Tan J, Li S, Gozdzik A, Ross K, Jin L, Parra EJ. Association of the OCA2 polymorphism His615Arg with melanin content in east Asian populations: further evidence of convergent evolution of skin pigmentation. PLoS Genet. 2010 Mar 5;6(3):e1000867. PubMed PMID: 20221248; PubMed Central PMCID: PMC2832666.

Show that His615Arg is “associated with lower melanin levels [and] is found at high frequencies in East Asian populations, but is absent or at very low frequencies in other population groups.”

Genomes
 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het C @ chr15:28197037

 

GS18526 - var-GS18526-1100-36-ASM
hom C @ chr15:25870632

 

GS18537 - var-GS18537-1100-36-ASM
het C @ chr15:25870632

 

GS18555 - var-GS18555-1100-36-ASM
hom C @ chr15:25870632

 

GS18558 - var-GS18558-1100-36-ASM
hom C @ chr15:25870632

 

GS18940 - var-GS18940-1100-36-ASM
hom C @ chr15:25870632

 

GS18956 - var-GS18956-1100-36-ASM
het C @ chr15:25870632

 

Other external references
 

    dbSNP
  • rs1800414
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.998 (probably damaging)
    Web search results (23 hits -- see all)
  • 123
    at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 ... frequencies for the MC1R and OCA2 genes in a total of 1809 unrelated individuals ...
    sayer.lab.nig.ac.jp/.../paper-pdf/Yuasa_Biochem.Genet07.pdf
  • Type 1 Melanocortin Receptor Summary Report | CureHunter
    Type 1 Melanocortin Receptor: A melanocortin receptor subtype found primarily in MELANOCYTES. It shows specificity for ALPHA-MSH and ADRENOCORTICOTROPIC HORMONE. ...
    curehunter.com/public/keywordSummaryD044102-Melanocortin-...
  • Oculocutaneous Albinism - Albinism, Yellow Mutant Summary ...
    Oculocutaneous Albinism: Heterogeneous group of autosomal recessive disorders comprising at least four recognized types, all having in common varying degrees of ...
    curehunter.com/public/keywordSummaryD016115-Tyrosinase-Ne...
  • The neighbor-joining method: a new method for reconstructing ...
    Distribution of Two Asian-Related Coding SNPs in the MC1R and OCA2 Genes. ... at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 ...
    lib.bioinfo.pl/pmid:3447015
  • Search Medical and Societal References - esrnexus
    ESRNexus is a publicly searchable online medical and societal ... gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, were investigated in a total of ...
    www.esrnexus.com/advsearch.aspx?txtAuthor=Henk
  • Document Title: Gene Polymorphism and Human Pigmentation
    SLC24A5, and OCA2 accounted for 77.3% of the variance in total amount of ... Population studies have shown that specific polymorphisms in the OCA2 and ...
    www.ncjrs.gov/pdffiles1/nij/grants/223980.pdf
  • Type III 97%
    ... sample, somatic mutation 16959974 OCA2 Q04671 H615R 618 VAR_006139 AGC (0.818) ... autosomal, dbSNP:rs6177) 7565946 10391209 OCA2 Q04671 S86R 89 VAR_006118 CAMK (0. ...
    www.nih.go.kr/phosphovariant/html/group_whole/TypeIII_97.txt
  • Distribution of two Asian-related coding SNPs in the MC1R and ...
    Distribution of two Asian-related coding SNPs in the MC1R and OCA2 genes. ... at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 ...
    www.ncbi.nlm.nih.gov/pubmed/17570052
  • Henke, L (L)
    Henke, L (L) :: Photodestruction of acetylcholinesterase. Recent ... MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, ...
    lib.bioinfo.pl/auid:954208
  • Biochemistry - Findings from Tottori University, Faculty of ...
    NewsRx is the leading source of news and information on Biochemistry ... receptor) gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, ...
    newsrx.com/library/topics/Oculocutaneous-Albinism/2726.html

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 5

Edit history
 

Gene search

"GENE" or "GENE A123C":

Log in