TAS2R38 I296V - GET-Evidence

Curation:
Currentness:

TAS2R38 I296V

(TAS2R38 Ile296Val)


Short summary

This variant is associated with “taster” status of PTC, along with 49P and 262A. Due to linkage disequilibrium, the independent effects of positions 296 and 262 is unclear. The presence of 49P confers taster status in a dominant fashion, but in the absence of 49P, the presence of 262A/296V is still positively associated with tasting PTC.

Variant evidence
Computational 2

Gene is associated with this trait, Polyphen2 predicts “probably damaging”, but amino acid change is not disruptive according to BLOSUM100.

See Kim UK et al. 2003 (12595690).

Functional -
Case/Control 2

p = 0.020

See Kim UK et al. 2003 (12595690), unpublished research (below).

Familial -
 
Clinical importance
Severity -
Treatability -
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

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • C @ chr7:141672604: 46.3% (4985/10758) in EVS
  • C @ chr7:141319072: 51.6% (66/128) in GET-Evidence
  • Frequency shown in summary reports: 46.3% (4985/10758)

Publications
 

Kim UK, Jorgenson E, Coon H, Leppert M, Risch N, Drayna D. Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide. Science. 2003 Feb 21;299(5610):1221-5. PubMed PMID: 12595690.

They studied the effect of three nonsynonymous variants in this gene on PTC taste sensitivity. They observed the 296V variant is in very strong linkage disequilibrium with 262A (the single exception was an African American subject). The “taster” haplotype for positions 49, 262, and 296 is “PAV”, the “nontaster” haplotype is “AVI” — thus, this variant is associated with the taster group. 81% of homozygotes for AVI were nontasters, as were 52% of AAV/AVI heterozygotes. Individuals carrying at least one copy of “PAV” were overwhelmingly likely to be “taster” (98%), but in the absence of 49P the 262/296 AV seems to be associated with “taster” as well.

The combined P-value of the NIH and Utah samples comparing AAV/AVI to AVI/AVI, using Fisher’s exact test, has p = 0.020.

Reed DR, Zhu G, Breslin PA, Duke FF, Henders AK, Campbell MJ, Montgomery GW, Medland SE, Martin NG, Wright MJ. The perception of quinine taste intensity is associated with common genetic variants in a bitter receptor cluster on chromosome 12. Hum Mol Genet. 2010 Nov 1;19(21):4278-85. Epub 2010 Jul 30. PubMed PMID: 20675712; PubMed Central PMCID: PMC2951861.

 

Genomes
 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het C @ chr7:141672604

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het C @ chr7:141672604

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het C @ chr7:141672604

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
hom C @ chr7:141672604

 

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom C @ chr7:141672604

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het C @ chr7:141672604

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het C @ chr7:141672604

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het C @ chr7:141672604

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het C @ chr7:141672604

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het C @ chr7:141672604

 

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
hom C @ chr7:141672604

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het C @ chr7:141672604

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het C @ chr7:141672604

 

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het C @ chr7:141672604

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
hom C @ chr7:141672604

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
hom C @ chr7:141672604

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het C @ chr7:141672604

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het C @ chr7:141672604

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het C @ chr7:141672604

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het C @ chr7:141672604

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom C @ chr7:141672604

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het C @ chr7:141672604

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het C @ chr7:141672604

 

GS06985 - var-GS06985-1100-36-ASM
het C @ chr7:141319073

 

GS06994 - var-GS06994-1100-36-ASM
het C @ chr7:141319073

 

GS07357 - var-GS07357-1100-36-ASM
het C @ chr7:141319073

 

GS10851 - var-GS10851-1100-36-ASM
hom C @ chr7:141319073

 

GS12004 - var-GS12004-1100-36-ASM
hom C @ chr7:141319073

 

GS18501 - var-GS18501-1100-36-ASM
het C @ chr7:141319073

 

GS18502 - var-GS18502-1100-36-ASM
het C @ chr7:141319073

 

GS18504 - var-GS18504-1100-36-ASM
hom C @ chr7:141319073

 

GS18505 - var-GS18505-1100-36-ASM
het C @ chr7:141319073

 

GS18508 - var-GS18508-1100-36-ASM
het C @ chr7:141319073

 

GS18526 - var-GS18526-1100-36-ASM
het C @ chr7:141319073

 

GS18537 - var-GS18537-1100-36-ASM
het C @ chr7:141319073

 

GS18555 - var-GS18555-1100-36-ASM
hom C @ chr7:141319073

 

GS18558 - var-GS18558-1100-36-ASM
het C @ chr7:141319073

 

GS18947 - var-GS18947-1100-36-ASM
hom C @ chr7:141319073

 

GS19017 - var-GS19017-1100-36-ASM
het C @ chr7:141319073

 

GS19020 - var-GS19020-1100-36-ASM
het C @ chr7:141319073

 

GS19025 - var-GS19025-1100-36-ASM
het C @ chr7:141319073

 

GS19026 - var-GS19026-1100-36-ASM
het C @ chr7:141319073

 

GS19238 - var-GS19238-1100-36-ASM
het C @ chr7:141319073

 

GS19239 - var-GS19239-1100-36-ASM
hom C @ chr7:141319073

 

GS19240 - var-GS19240-1100-36-ASM
hom C @ chr7:141319073

 

GS19648 - var-GS19648-1100-36-ASM
het C @ chr7:141319073

 

GS19669 - var-GS19669-1100-36-ASM
het C @ chr7:141319073

 

GS19670 - var-GS19670-1100-36-ASM
hom C @ chr7:141319073

 

GS19700 - var-GS19700-1100-36-ASM
het C @ chr7:141319073

 

GS19701 - var-GS19701-1100-36-ASM
hom C @ chr7:141319073

 

GS19703 - var-GS19703-1100-36-ASM
hom C @ chr7:141319073

 

GS19704 - var-GS19704-1100-36-ASM
hom C @ chr7:141319073

 

GS19735 - var-GS19735-1100-36-ASM
hom C @ chr7:141319073

 

GS19834 - var-GS19834-1100-36-ASM
het C @ chr7:141319073

 

GS20502 - var-GS20502-1100-36-ASM
het C @ chr7:141319073

 

GS20509 - var-GS20509-1100-36-ASM
het C @ chr7:141319073

 

GS21767 - var-GS21767-1100-36-ASM
het C @ chr7:141319073

 

Other external references
 

    dbSNP
  • rs10246939
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.984 (probably damaging)

Other in silico analyses
 

  • NBLOSUM100 score = –4
  • GET-Evidence autoscore = 5

Edit history
 

Gene search

"GENE" or "GENE A123C":

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