TPCN2 M484L - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

TPCN2 M484L

(TPCN2 Met484Leu)


Short summary

 

Variant evidence
Computational -
Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated benign

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • T @ chr11:68846399: 12.9% (1383/10758) in EVS
  • T @ chr11:68602974: 7.1% (9/126) in GET-Evidence
  • Frequency shown in summary reports: 12.9% (1383/10758)

Publications
 

Genomes
 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het T @ chr11:68846399

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het T @ chr11:68846399

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het T @ chr11:68846399

 

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het T @ chr11:68846399

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het T @ chr11:68846399

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het T @ chr11:68846399

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het T @ chr11:68846399

 

GS10851 - var-GS10851-1100-36-ASM
het T @ chr11:68602975

 

GS12004 - var-GS12004-1100-36-ASM
het T @ chr11:68602975

 

GS19020 - var-GS19020-1100-36-ASM
het T @ chr11:68602975

 

GS19669 - var-GS19669-1100-36-ASM
het T @ chr11:68602975

 

GS19704 - var-GS19704-1100-36-ASM
het T @ chr11:68602975

 

GS20509 - var-GS20509-1100-36-ASM
het T @ chr11:68602975

 

Other external references
 

    dbSNP
  • rs35264875
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GWAS
  • Blond vs. brown hair color (rs35264875-T)
    Sulem 18-May-08 in Nat Genet
    OR or beta: 2.49 [1.96-3.15]
    Risk allele frequency: 0.22
    p-value: 4.00E-30
    Initial sample: 5,130 individuals
    Replication sample: 3,330 individuals
    www.ncbi.nlm.nih.gov/pubmed/18488028
    PolyPhen-2
  • Score: 0.333 (possibly damaging)
    Web search results (13 hits -- see all)
  • Appearance - SNPedia
    rs35264875 A>T. rs3829241 G>A [edit] Eye, Hair. rs1289399 G>T [edit] Genes. TYR. TYRP1. OCA2 ... This page was last modified on 24 March 2009, at 13:11. This page has ...
    www.snpedia.com/index.php?title=Appearance
  • TPCN2 [PharmGKB]
    rs35264875 at chr11:68602975 in TPCN2. GWAS Results: Two newly identified genetic ... TPCN2. Comparative Toxicogenomics Acc ID: 219931. ModBase: Q8NHX9. Common Searches ...
    www.pharmgkb.org/do/serve?objId=PA134937857&objCls=Gene
  • Table 1 : Shedding light on skin cancer : Nature Genetics
    Nature Genetics publishes the very highest quality research in genetics. It encompasses ... rs7495174. TPCN2. rs35264875. TPCN2. rs3829241. MC1R. RHC. MC1R. NRHC. Figures ...
    www.nature.com/ng/journal/v40/n7/fig_tab/ng0708-817_T1.html
  • SCAN results
    Below you'll find a table of reported GWAS (from NHGRI, February 2009), which includes ... TPCN2. rs35264875. 18488028. Blue vs. green eyes. 6.00E-17. Illumina [316, ...
    www.scandb.org/newinterface/gwas.php
  • GWAS Catalog 11-26-08
    http://www.ncbi.nlm.nih.gov/pubmed/18978792?ordinalpos=4&itool=EntrezSystem2. ... TPCN2. rs35264875-T. rs35264875. 0.22. 0.00E-01. 2.49 [1.96-3.15] Illumina ...
    genome.gov/Pages/About/OD/OPG/GWAS Catalog/...
  • Genetics of human pigmentation : Gene Expression
    Molecular Markers, Natural History, and Evolution. The Genetics of Human Populations ... KITLG and previously unknown SLC24A4, IRF4, TPCN2, candidate genes. ...
    scienceblogs.com/gnxp/.../genetics_of_human_pigmentation.php
  • Two pore calcium channel protein 2 - Homo sapiens (Human)
    TPCN2. Synonyms: TPC2. Organism. Homo sapiens (Human) [Complete proteome] Taxonomic ... Genetic variations in TPCN2 are associated with variation in skin/hair/eye ...
    www.uniprot.org/uniprot/Q8NHX9
  • Rs35264875 - SNPedia
    pharmgkb. rs35264875. hgvbaseg2p. rs35264875. medrefsnp. rs35264875 ... rs35264875. SNP Nexus. Gene. TPCN2. Chromosome. 11. Orientation. plus. Position. 68846399 ...
    www.snpedia.com/index.php/Rs35264875
  • genomemedicine.com - Table 1
    GWAS loci and the associated pigmentary and cancer phenotypes. Chromosomal region/locus ... TPCN2 (rs35264875 [T], rs3829241 [A]) [25] Blonde hair versus brown ...
    genomemedicine.com/content/1/10/95/table/T1

Other in silico analyses
 

  • NBLOSUM100 score = –3
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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