rs35264875

This is a variant in the TPCN2 gene that changes a methionine to an leucine.

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GWAS Catalog Trait Associations (1)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

hair color

Sulem P et al. “Two newly identified genetic determinants of pigmentation in Europeans.” Nature Genetics 40(7):835-837 (2008)

Allele T

OR 2.49

p 4.0e-30

N 5,130

Large GWAS

European

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ClinVar annotation

Association

1 submitter1 publication

SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 10 (SHEP10)

View on ClinVar →

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Research that mentions this SNP (2)

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Association of TGFβ1 and clinical factors with scar outcome following melanoma excision

AssociationN=202Ward SV et al.(2012)· Archives of Dermatological Research

Genetic association study of 202 melanoma patients examining SNPs in 24 candidate genes related to pigmentation and wound healing in relation to scar outcome. SNP rs8110090 in TGFβ1 was significantly associated with poorer scar outcomes (p=0.0002). Clinical factors including younger age, shorter time since surgery, and presence of infection or eczema were also associated with worse scarring.

Traits studied:Scar heightScar outcome following melanoma excisionScar vascularityWound healing

PubMed DOI Metascience Observatory

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Model-based prediction of human hair color using DNA variants

AssociationN=385Wojciech Branicki et al.(2011)· Human Genetics

This study demonstrates that human hair color can be predicted from DNA variants with high accuracy using a multinomial logistic regression model. A subset of 13 genetic markers from 11 genes (MC1R, HERC2, IRF4, TYR, EXOC2, SLC45A2, TYRP1, OCA2, SLC24A4, KITLG, ASIP) predicted hair color categories in Polish Europeans with AUC values of 0.93 for red hair, 0.87 for black hair, 0.82 for brown hair, and 0.81 for blond hair. MC1R variants showed the strongest association with red hair (OR=12.64 for R variants, P=2.5×10⁻¹⁷), while rs12913832 in HERC2 was significantly associated with darker hair colors (OR=3.33 for black, P=4.3×10⁻⁶).

Traits studied:Auburn hairBlack hairBlond hairBlond-red hairBrown hairDark-blond hairHair colorRed hair

PubMed DOI Metascience Observatory

About TPCN2

This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]