rs1426654

plus

Geno	Mag	Summary
(A;A)	2.7	probably light-skinned, European ancestry
(A;G)	2.5	mixed European + (African or Asian) ancestry possible
(G;G)	2.6	probably darker-skinned, Asian or African ancestry

Reference

GRCh38 38.1/141

Chromosome

15

Position

48134287

Gene	MYEF2, SLC24A5

is a	snp
is	mentioned by
dbSNP	rs1426654
dbSNP (classic)	rs1426654
ClinGen	rs1426654
ebi	rs1426654
HLI	rs1426654
Exac	rs1426654
Gnomad	rs1426654
Varsome	rs1426654
LitVar	rs1426654
Map	rs1426654
PheGenI	rs1426654
Biobank	rs1426654
1000 genomes	rs1426654
hgdp	rs1426654
ensembl	rs1426654
geneview	rs1426654
scholar	rs1426654
google	rs1426654
pharmgkb	rs1426654
gwascentral	rs1426654
openSNP	rs1426654
23andMe	rs1426654
SNPshot	rs1426654
SNPdbe	rs1426654
MSV3d	rs1426654
GWAS Ctlg	rs1426654

GMAF

0.4775

Max Magnitude

2.7

?

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

28

This SNP influences skin pigmentation. The allele, A111T, rs1426654(A), indicates light-skinned West Eurasian 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 24048645 ]) 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 West Eurasian (Middle Eastern, Caucasian, European, etc.), African, or East Eurasian, based on a 2009 study.[PMID 19440451 ]

The 3 SNPs are:

10.1038/ncomms10815 A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

OMIM	113750
Desc	SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 4; SHEP4
Variant
Related	also

OMIM	609802
Desc	SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER
Variant
Related	also

OMIM	609802
Desc
Variant	0001
Related	also

ClinVar
Risk	Rs1426654(G;G) rs1426654(T;T)
Alt	Rs1426654(G;G) rs1426654(T;T)
Reference	Rs1426654(A;A)
Significance	Other
Disease	Skin/hair/eye pigmentation not specified
Variation	info
Gene	SLC24A5
CLNDBN	Skin/hair/eye pigmentation, variation in, 4 not specified
Reversed	0
HGVS	NC_000015.9:g.48426484A\x3d; NC_000015.9:g.48426484A>G
CLNSRC	OMIM Allelic Variant
CLNACC	RCV000001552.3, RCV000250857.1,

[PMID 16255080 ] A haplotype map of the human genome.

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

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

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

[PMID 18282109 ] 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 19384953 ] Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians.

[PMID 19503611 ] The role of geography in human adaptation.

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

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

[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 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 23771755 ] Improved eye- and skin-color prediction based on 8 SNPs.

[PMID 33167923 ] Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil.