Rs1426654

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Orientationplus
Geno Mag Summary
(A;A) 2.7 probably light-skinned, European ancestry
(A;G) 2.5 mixed African/European ancestry possible
(G;G) 2.6 probably darker-skinned, Asian or African ancestry
ReferenceGRCh38 38.1/141
Chromosome15
Position48134287
GeneSLC24A5
is asnp
is mentioned by
dbSNPrs1426654
PheGenIrs1426654
nextbiors1426654
hapmaprs1426654
1000 genomesrs1426654
hgdprs1426654
ensemblrs1426654
gopubmedrs1426654
geneviewrs1426654
scholarrs1426654
googlers1426654
pharmgkbrs1426654
gwascentralrs1426654
openSNPrs1426654
23andMers1426654
23andMe allrs1426654
SNP Nexus

SNPshotrs1426654
SNPdbers1426654
MSV3drs1426654
GMAF0.4775
Max Magnitude2.7
? (A;A) (A;G) (G;G) 28
This SNP influences skin pigmentation. The allele, A111T, rs1426654(A), indicates light-skinned european ancestry. [PMID 16847698, PMID 16357253]

It appears as if this SNP is a relatively new one in human evolution; one estimate [PMID 17182896] is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, "European ancestors" were most likely relatively brown-skinned. Another study ([PMID 24048645OA-icon.png]) has concluded that almost individuals carrying the A111T variant can trace ancestry back to a single person who most likely lived at least 10,000 years ago.

This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study.[PMID 19440451OA-icon.png]

The 3 SNPs are:

OMIM113750
DescSKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 4; SHEP4
Variant
Relatedalso
OMIM609802
DescSOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER
Variant
Relatedalso
OMIM609802
Desc
Variant0001
Relatedalso


ClinVar
Risk rs1426654(G;G)
Alt rs1426654(G;G)
Reference rs1426654(A;A)
Significance Pathogenic
Disease Skin/hair/eye pigmentation
Variation info
Gene SLC24A5
CLNDBN Skin/hair/eye pigmentation, variation in, 4
Reversed 0
HGVS NC_000015.9:g.48426484A>G
CLNSRC OMIM Allelic Variant
CLNACC RCV000001552.2,



[PMID 16255080OA-icon.png] A haplotype map of the human genome.


[PMID 17557415OA-icon.png] A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping.


[PMID 17999355OA-icon.png] A genomewide association study of skin pigmentation in a South Asian population.


[PMID 18248681OA-icon.png] Prevalence of common disease-associated variants in Asian Indians.


[PMID 18282109OA-icon.png] Adaptations to climate in candidate genes for common metabolic disorders.


[PMID 18637132] A study of a single variant allele (rs1426654) of the pigmentation-related gene SLC24A5 in Greek subjects.


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


[PMID 19503611OA-icon.png] The role of geography in human adaptation.


[PMID 19737746OA-icon.png] Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation.


[PMID 19884608OA-icon.png] Interactive effect of stressful life events and the serotonin transporter 5-HTTLPR genotype on posttraumatic stress disorder diagnosis in 2 independent populations.


GET Evidence
SLC24A5-T111A
aa_change Thr111Ala
aa_change_short T111A
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.269753
summary



[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 23224873] NCKX5, a natural regulator of human skin colour variation, regulates the expression of key pigment genes MC1R and alpha-MSH and alters cholesterol homeostasis in normal human melanocytes.


[PMID 23771755OA-icon.png] Improved eye- and skin-color prediction based on 8 SNPs.