TPCN2 G734E - GET-Evidence

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Curation:
Currentness:

TPCN2 G734E

(TPCN2 Gly734Glu)


Short summary

Pigmentation allele.

Variant evidence
Computational 1

NBLOSUM = 4

See unpublished research (below).

Functional -
Case/Control 2

OR = 1.55, significance = 6.2 * 10^-16.

See unpublished research (below).

Familial

See unpublished research (below).

 
Clinical importance
Severity -
Treatability

See unpublished research (below).

Penetrance -
 

Impact

Low clinical importance, Uncertain benign

(The "low clinical importance, uncertain" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

undefined

Summary of published research, and additional commentary

 

Allele frequency

  • A @ chr11:68855363: 28.6% (3078/10756) in EVS
  • A @ chr11:68611938: 20.5% (25/122) in GET-Evidence
  • Frequency shown in summary reports: 28.6% (3078/10756)

Publications
 

301 Moved Permanently

Moved Permanently

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PubMed PMID: 18488028

In this paper, this variant — identified as SNP rs3829241— was associated with blond hair (vs. brown hair) with an OR of 1.55 (weighted average from table 1) and a significance of 6.2 * 10^-16. The authors hypothesize that this non-synonymous change to the protein is causal (ie, they do not believe the SNP is associated with a different, nearby causal gene).

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het A @ chr11:68855363

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het A @ chr11:68855363

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
hom A @ chr11:68855363

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
het A @ chr11:68611939

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het A @ chr11:68855363

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het A @ chr11:68611939

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het A @ chr11:68855363

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
hom A @ chr11:68855363

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom A @ chr11:68855363

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
hom A @ chr11:68855363

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
hom A @ chr11:68855363

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het A @ chr11:68855363

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom A @ chr11:68855363

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het A @ chr11:68611939

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom A @ chr11:68855363

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het A @ chr11:68855363

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het A @ chr11:68855363

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het A @ chr11:68855363

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr11:68855363

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het A @ chr11:68855363

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het A @ chr11:68855363

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het A @ chr11:68855363

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het A @ chr11:68855363

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het A @ chr11:68855363

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
hom A @ chr11:68855363

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het A @ chr11:68855363

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
hom A @ chr11:68855363

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het A @ chr11:68855363

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het A @ chr11:68855363

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het A @ chr11:68855363

 

GS06985 - var-GS06985-1100-36-ASM
het A @ chr11:68611939

 

GS06994 - var-GS06994-1100-36-ASM
het A @ chr11:68611939

 

GS10851 - var-GS10851-1100-36-ASM
het A @ chr11:68611939

 

GS12004 - var-GS12004-1100-36-ASM
het A @ chr11:68611939

 

GS18526 - var-GS18526-1100-36-ASM
het A @ chr11:68611939

 

GS18537 - var-GS18537-1100-36-ASM
het A @ chr11:68611939

 

GS18940 - var-GS18940-1100-36-ASM
het A @ chr11:68611939

 

GS18947 - var-GS18947-1100-36-ASM
het A @ chr11:68611939

 

GS19649 - var-GS19649-1100-36-ASM
het A @ chr11:68611939

 

GS19669 - var-GS19669-1100-36-ASM
het A @ chr11:68611939

 

GS19704 - var-GS19704-1100-36-ASM
het A @ chr11:68611939

 

GS20502 - var-GS20502-1100-36-ASM
hom A @ chr11:68611939

 

GS20509 - var-GS20509-1100-36-ASM
het A @ chr11:68611939

 

Other external references
 

    dbSNP
  • rs3829241
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0 (benign)

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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