NM_139075.4(TPCN2):c.1450A>T (p.Met484Leu) AND Skin/hair/eye pigmentation, variation in, 10

Germline classification:: association (1 submission)
Last evaluated:: May 18, 2015
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000000763.2

Allele description [Variation Report for NM_139075.4(TPCN2):c.1450A>T (p.Met484Leu)]

NM_139075.4(TPCN2):c.1450A>T (p.Met484Leu)

Gene:

TPCN2:two pore segment channel 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.3

Genomic location:

Preferred name:

NM_139075.4(TPCN2):c.1450A>T (p.Met484Leu)

HGVS:

NC_000011.10:g.69078931A>T
NG_016153.1:g.35050A>T
NM_139075.4:c.1450A>TMANE SELECT
NP_620714.2:p.Met484Leu
NC_000011.9:g.68846399A>T
Q8NHX9:p.Met484Leu

Protein change:

M484L; MET484LEU

Links:

UniProtKB: Q8NHX9#VAR_047956; OMIM: 612163.0001; dbSNP: rs35264875

NCBI 1000 Genomes Browser:

rs35264875

Molecular consequence:

NM_139075.4:c.1450A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Skin/hair/eye pigmentation, variation in, 10 (SHEP10)
Synonyms:: SKIN/HAIR/EYE PIGMENTATION 10, BLOND/BROWN HAIR
Identifiers:: MedGen: C2677088; OMIM: 612267

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000020913	OMIM	no assertion criteria provided	association (May 18, 2015)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000020913

OMIM

no assertion criteria provided

association
(May 18, 2015)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Two newly identified genetic determinants of pigmentation in Europeans.

Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, Jakobsdottir M, Steinberg S, Gudjonsson SA, Palsson A, Thorleifsson G, Pálsson S, Sigurgeirsson B, Thorisdottir K, Ragnarsson R, Benediktsdottir KR, Aben KK, Vermeulen SH, Goldstein AM, Tucker MA, Kiemeney LA, Olafsson JH, Gulcher J, et al.

Nat Genet. 2008 Jul;40(7):835-7. doi: 10.1038/ng.160. Epub 2008 May 18.

PubMed [citation]

PMID:: 18488028

Details of each submission

From OMIM, SCV000020913.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a genomewide association study for variants associated with human pigmentation characteristics (SHEP10; 612267) among 5,130 Icelanders, with follow-up analyses in 2,116 Icelanders and 1,214 Dutch individuals, Sulem et al. (2008) found that an A-to-T transversion in the TPCN2 gene (rs35264875), resulting in a met484-to-leu amino acid change (M484L), was significantly associated with blond rather than brown hair (P = 3.6 x 10(-30)). The rs35264875T allele was found at a frequency of 22%.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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