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rs16891982

From SNPedia

hair colour, melanoma
Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) 1.1 generally non-European, but if European, 7x more likely to have black hair
(C;G) 2 if European, 7x more likely to have black hair
(G;G) 1.1 Generally European; Light skin; Possibly an increased risk of melanoma
ReferenceGRCh38 38.1/141
Chromosome5
Position33951588
GeneSLC45A2
is asnp
is mentioned by
dbSNPrs16891982
ebirs16891982
HLIrs16891982
Exacrs16891982
Varsomers16891982
Maprs16891982
PheGenIrs16891982
hapmaprs16891982
1000 genomesrs16891982
hgdprs16891982
ensemblrs16891982
gopubmedrs16891982
geneviewrs16891982
scholarrs16891982
googlers16891982
pharmgkbrs16891982
gwascentralrs16891982
openSNPrs16891982
23andMers16891982
23andMe allrs16891982
SNP Nexus

SNPshotrs16891982
SNPdbers16891982
MSV3drs16891982
GWAS Ctlgrs16891982
Merged fromRs17855902
GMAF0.4408
Max Magnitude2
? (C;C) (C;G) (G;G) 28
Neighborrs28939380
Distance40

This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry [PMID 16847698]

[PMID 18563784] c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing)

An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7.[PMID 18806926]


Venter snp
Source plos
Gene SLC45A2
allele G
frequency 1
sift
HuRef 1103654071247
Disease Association Defects in SLC45A2 are the cause of oculocutaneous albinism type 4 (OCA4) (MIM:606574). OCA4 is an autosomal recessive disorder of pigmentation characterized by reduced biosynthesis of melanin in the skin, hair and eyes. It leads to reduced visual acuity.
GWAS
SNP rs16891982
PubMedID [PMID 17999355OA-icon.png]
Condition Skin pigmentation by reflectance spectroscopy
Gene SLC45A2
Risk Allele C
pValue 3.00E-011
OR 4.86
95% CI 2.88-8.21
Neighborrs17855902
Distance1
OMIM606202
DescSOLUTE CARRIER FAMILY 45, MEMBER 2; SLC45A2
Variant
Relatedalso
[PMID 19710684OA-icon.png] This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls), subjects with northern European ancestry (1,438 cases and 3,098 controls), northern European subjects adjusted for hair, eye, and skin colour, and northern European subjects adjusted for the MC1R genotype, respectively (p<0.001 for all).
GWAS snp
PMID [PMID 20585627OA-icon.png]
Trait Eye color
Title Web-based, participant-driven studies yield novel genetic associations for common traits
Risk Allele C
P-val 1E-12
Odds Ratio 0.84 [NR] unit increase


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

OMIM606202
Desc
Variant0008
Relatedalso


ClinVar
Risk rs16891982(G;G)
Alt rs16891982(G;G)
Reference rs16891982(C;C)
Significance Other
Disease Skin/hair/eye pigmentation Malignant melanoma of skin not specified
Variation info
Gene SLC45A2
CLNDBN Skin/hair/eye pigmentation, variation in, 5 Malignant melanoma of skin not specified
Reversed 0
HGVS NC_000005.9:g.33951693C\x3d; NC_000005.9:g.33951693C>G
CLNSRC OMIM Allelic Variant
CLNACC RCV000004763.4, RCV000022392.1, RCV000178963.1,



[PMID 18483556OA-icon.png] A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation.

[PMID 19340012OA-icon.png] Genome-wide association study of tanning phenotype in a population of European ancestry.

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

[PMID 19440451OA-icon.png] Haplotypes in SLC24A5 Gene as Ancestry Informative Markers in Different Populations.

[PMID 19668368OA-icon.png] Ancestry analysis in the 11-M Madrid bomb attack investigation.

[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 20806075OA-icon.png] Spectrum of candidate gene mutations associated with Indian familial oculocutaneous and ocular albinism.

[PMID 20850402] Genetic analysis of the SNPforID 34-plex ancestry informative SNP panel in Tunisian and Libyan populations.


[PMID 22912732OA-icon.png] Skin Color Variation in Orang Asli Tribes of Peninsular Malaysia


GET Evidence
SLC45A2-L374F
aa_change Leu374Phe
aa_change_short L374F
impact benign
qualified_impact Low clinical importance, Uncertain benign
overall_frequency 0.691764
summary Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma.



[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

Squamous Cell Carcinoma


[PMID 23393597OA-icon.png] Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study


[PMID 23786662OA-icon.png] Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS)


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


[PMID 25093503OA-icon.png] The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population


[PMID 25142205] Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework