PPARG P12A - 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:

(See the latest version)

PPARG P12A

(PPARG Pro12Ala)


You are viewing an old version of this page that was saved on June 9, 2011 at 2:48pm by Han Luu.

Edited in this revision:

Short summary

 

Variant evidence
Computational 1

PolyPhen2: Possibly damaging 0.782
SIFT: Tolerated 0.09
GVGD: Class C25

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated pharmacogenetic

(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

  • G @ chr3:12393125: 8.9% (954/10758) in EVS
  • G @ chr3:12368124: 6.2% (8/128) in GET-Evidence
  • Frequency shown in summary reports: 8.9% (954/10758)

Publications
 

Butt C, Gladman D, Rahman P. PPAR-gamma gene polymorphisms and psoriatic arthritis. J Rheumatol. 2006 Aug;33(8):1631-3. PubMed PMID: 16783862.

 

301 Moved Permanently

Moved Permanently

The document has moved here.

PubMed PMID: 17463248

 

Genomes
 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het G @ chr3:12393125

 

 

GS06985 - var-GS06985-1100-36-ASM
het G @ chr3:12368125

 

GS07357 - var-GS07357-1100-36-ASM
het G @ chr3:12368125

 

GS18558 - var-GS18558-1100-36-ASM
het G @ chr3:12368125

 

snp-3

 

snp-5

 

Other external references
 

    dbSNP
  • rs1801282
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the PPARG gene
    Cardiovascular Disease Risk Factor (Carotid Intimal Medial Thick
    Diabetes Mellitus with Acanthosis Nigricans and Hypertension
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PPARG
    GWAS
  • Type 2 diabetes (rs1801282-C)
    Saxena 26-Apr-07 in Science
    OR or beta: 1.14 [1.08-1.20]
    Risk allele frequency: 0.86
    p-value: 0.000002 (DGI+FUSION+WTCCC)
    Initial sample: 1,464 cases, 1,467 controls
    Replication sample: 5,065 cases, 5,785 controls (also includes meta-analysis from DGI+FUSION+WTCCC)
    www.ncbi.nlm.nih.gov/pubmed/17463246
  • Type 2 diabetes (rs1801282-C)
    Scott 26-Apr-07 in Science
    OR or beta: 1.14 [1.08-1.20]
    Risk allele frequency: 0.82
    p-value: 0.000002 (DGI+FUSION+WTCCC)
    Initial sample: 1,161 cases, 1,174 controls
    Replication sample: 1,215 cases, 1,258 controls (also includes meta-analysis from DGI+FUSION+WTCCC)
    www.ncbi.nlm.nih.gov/pubmed/17463248
  • Type 2 diabetes (rs1801282-C)
    Zeggini 26-Apr-07 in Science
    OR or beta: 1.14 [1.08-1.20]
    p-value: 0.000002 (DGI+FUSION+WTCCC)
    Initial sample: 1,924 cases, 2,938 controls
    Replication sample: 3,757 cases, 5,346 controls (also includes meta-analysis from DGI+FUSION+WTCCC)
    www.ncbi.nlm.nih.gov/pubmed/17463249
    PharmGKB
  • [Arthritis, Psoriatic]
    Risk or phenotype-associated allele: G. Phenotype: For the Pro12Ala (rs1801282) SNP in the PPARG gene, an association was noted for the minor allele between psoriatic arthritis cases and controls (9.0% vs 13.8%, respectively; p = 0.017, OR 0.62, 95% CI 0.45-0.93). Study size: X. Study population/ethnicity: Caucasian
    www.ncbi.nlm.nih.gov/pubmed/16783862
  • [Diabetes Mellitus, Type 2]
    In a large Finnish case-control GWAS, rs1801282 was found to be associated with susceptibility to Type 2 Diabetes.
    www.ncbi.nlm.nih.gov/pubmed/17463248
    PolyPhen-2
  • Score: 0.979 (probably damaging)

Other in silico analyses
 

  • NBLOSUM100 score = 2
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

Log in