ITGB3 L59P - GET-Evidence

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

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Curation:
Currentness:

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ITGB3 L59P

(ITGB3 Leu59Pro)


You are viewing an old version of this page that was saved on November 29, 2012 at 2:53am by Genome Importing Robot.

Short summary

 

Variant evidence
Computational 1

PolyPhen2: Benign, score 0.039
SIFT: Affect protein function 0.01
GVGD: Class C25

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

Impact

Insufficiently evaluated not reviewed

(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

  • C @ chr17:45360730: 13.5% (1452/10758) in EVS
  • C @ chr17:42715728: 8.7% (11/126) in GET-Evidence
  • Frequency shown in summary reports: 13.5% (1452/10758)

Publications
 

Genomes
 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het C @ chr17:42715729

 

Added in this revision:

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het C @ chr17:45360730

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het C @ chr17:45360730

 

hu6E4515 - PGP15 (hu6E4515) build 37, from CGI var (software ver 1.12.0.47), CGI sample GS000005532
het C @ chr17:45360730

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het C @ chr17:42715729

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het C @ chr17:45360730

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom C @ chr17:45360730

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het C @ chr17:45360730

 

GS06994 - var-GS06994-1100-36-ASM
het C @ chr17:42715729

 

GS18502 - var-GS18502-1100-36-ASM
hom C @ chr17:42715729

 

GS19026 - var-GS19026-1100-36-ASM
het C @ chr17:42715729

 

GS19239 - var-GS19239-1100-36-ASM
het C @ chr17:42715729

 

GS19240 - var-GS19240-1100-36-ASM
het C @ chr17:42715729

 

GS19670 - var-GS19670-1100-36-ASM
het C @ chr17:42715729

 

Other external references
 

    dbSNP
  • rs5918
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.02 (benign)
    Web search results (50 hits -- see all)
  • Non-Hodgkin Lymphoma - SNPedia
    Variations of the following genes were implicated in risk for one or more types ... most significant (p<0.01) findings were for: rs5918, ITGB3 L59P (OR = 0.66, CI: 0.52-0.85) ...
    www.snpedia.com/index.php?title=Non-Hodgkin_Lymphoma
  • Genetic variation in 1253 immune and inflammation genes and ...
    Genetic variation in 1253 immune and inflammation genes and risk of non-Hodgkin lymphoma. ... coagulation pathways (FGG and ITGB3) may be important in the etiology ...
    www.ncbi.nlm.nih.gov/pubmed/17827388
  • Blood -- Genetic variation in 1253 immune and inflammation ...
    In nsSNP analyses, the strongest findings (p0.01) were for ITGB3 L59P (OR=0.66, 0.52-0.85), TLR6 V427A (OR=5.20, 1.77-15.3), SELPLG M264V (OR=3.20, ...
    bloodjournal.hematologylibrary.org/cgi/content/short/...
  • Blood -- Genetic variation in 1253 immune and inflammation ...
    In nsSNP analyses, the strongest findings (P .01) were for ITGB3 L59P (odds ratio [OR] = 0.66; 95% confidence interval [CI] 0.52-0.85), TLR6 V427A ...
    bloodjournal.hematologylibrary.org/cgi/content/.../13/4455
  • Neoplasia: Genetic variation in 1253 immune and inflammation ...
    In nsSNP analyses, the strongest findings (P .01) were for ITGB3 L59P (odds ratio [OR] = 0.66; 95% confidence interval [CI] 0.52-0.85), TLR6 V427A ...
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2234796
  • Rs5918 - SNPedia
    The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918 ... Lymphoma, both for the SNP (which is also known as L59P) and for its gene, ITGB3. ...
    www.snpedia.com/index.php?title=Rs5918
  • Cunningham, JM (Julie M)
    Cunningham, JM (Julie M) :: Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Mutations in CHEK2 associated with prostate cancer ...
    lib.bioinfo.pl/auid:36077
  • Prevalence in the United States of Selected Candidate Gene ...
    Discussion: Learn how these nationally representative data on allele frequency and genotype prevalence may provide a valuable resource for future epidemiologic ...
    www.medscape.com/viewarticle/586942_4

Other in silico analyses
 

  • NBLOSUM100 score = 7
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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