SH2B3 W262R - 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.

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Curation:
Currentness:

SH2B3 W262R

(SH2B3 Trp262Arg)


Short summary

 

Variant evidence
Computational 2

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 0.94
GVGD: GV 165.82; GD 0.00; Class C0 Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.96);
PolyPhen=benign(0)
Mutation Tasting Prediction: Polymorphism, P value: 0.999993; protein features (might be) affected (aa 194-307 DOMAIN PH gets lost)

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

  • C @ chr12:111884608: 63.4% (6818/10758) in EVS
  • C @ chr12:110368990: 77.3% (99/128) in GET-Evidence
  • Frequency shown in summary reports: 63.4% (6818/10758)

Publications
 

Gudbjartsson DF, Bjornsdottir US, Halapi E, Helgadottir A, Sulem P, Jonsdottir GM, Thorleifsson G, Helgadottir H, Steinthorsdottir V, Stefansson H, Williams C, Hui J, Beilby J, Warrington NM, James A, Palmer LJ, Koppelman GH, Heinzmann A, Krueger M, Boezen HM, Wheatley A, Altmuller J, Shin HD, Uh ST, Cheong HS, Jonsdottir B, Gislason D, Park CS, Rasmussen LM, Porsbjerg C, Hansen JW, Backer V, Werge T, Janson C, J├Ânsson UB, Ng MC, Chan J, So WY, Ma R, Shah SH, Granger CB, Quyyumi AA, Levey AI, Vaccarino V, Reilly MP, Rader DJ, Williams MJ, van Rij AM, Jones GT, Trabetti E, Malerba G, Pignatti PF, Boner A, Pescollderungg L, Girelli D, Olivieri O, Martinelli N, Ludviksson BR, Ludviksdottir D, Eyjolfsson GI, Arnar D, Thorgeirsson G, Deichmann K, Thompson PJ, Wjst M, Hall IP, Postma DS, Gislason T, Gulcher J, Kong A, Jonsdottir I, Thorsteinsdottir U, Stefansson K. Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet. 2009 Mar;41(3):342-7. Epub 2009 Feb 8. PubMed PMID: 19198610.

 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het C @ chr12:111884608

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het C @ chr12:111884608

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het C @ chr12:111884608

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het C @ chr12:111884608

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het C @ chr12:111884608

 

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het C @ chr12:111884608

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
hom C @ chr12:111884608

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het C @ chr12:111884608

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
hom C @ chr12:111884608

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom C @ chr12:111884608

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het C @ chr12:111884608

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het C @ chr12:111884608

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het C @ chr12:111884608

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
hom C @ chr12:111884608

 

 

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het C @ chr12:111884608

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom C @ chr12:111884608

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het C @ chr12:111884608

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom C @ chr12:111884608

 

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het C @ chr12:111884608

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het C @ chr12:111884608

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
hom C @ chr12:111884608

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
hom C @ chr12:111884608

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het C @ chr12:111884608

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
hom C @ chr12:111884608

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het C @ chr12:111884608

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het C @ chr12:111884608

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het C @ chr12:111884608

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom C @ chr12:111884608

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het C @ chr12:111884608

 

GS06985 - var-GS06985-1100-36-ASM
het C @ chr12:110368991

 

GS06994 - var-GS06994-1100-36-ASM
het C @ chr12:110368991

 

GS07357 - var-GS07357-1100-36-ASM
het C @ chr12:110368991

 

GS10851 - var-GS10851-1100-36-ASM
het C @ chr12:110368991

 

GS12004 - var-GS12004-1100-36-ASM
het C @ chr12:110368991

 

GS18501 - var-GS18501-1100-36-ASM
hom C @ chr12:110368991

 

GS18502 - var-GS18502-1100-36-ASM
hom C @ chr12:110368991

 

GS18504 - var-GS18504-1100-36-ASM
hom C @ chr12:110368991

 

GS18505 - var-GS18505-1100-36-ASM
hom C @ chr12:110368991

 

GS18508 - var-GS18508-1100-36-ASM
hom C @ chr12:110368991

 

GS18517 - var-GS18517-1100-36-ASM
hom C @ chr12:110368991

 

GS18526 - var-GS18526-1100-36-ASM
hom C @ chr12:110368991

 

GS18537 - var-GS18537-1100-36-ASM
hom C @ chr12:110368991

 

GS18555 - var-GS18555-1100-36-ASM
hom C @ chr12:110368991

 

GS18558 - var-GS18558-1100-36-ASM
hom C @ chr12:110368991

 

GS18940 - var-GS18940-1100-36-ASM
hom C @ chr12:110368991

 

GS18942 - var-GS18942-1100-36-ASM
hom C @ chr12:110368991

 

GS18947 - var-GS18947-1100-36-ASM
hom C @ chr12:110368991

 

GS18956 - var-GS18956-1100-36-ASM
hom C @ chr12:110368991

 

GS19017 - var-GS19017-1100-36-ASM
hom C @ chr12:110368991

 

GS19020 - var-GS19020-1100-36-ASM
hom C @ chr12:110368991

 

GS19025 - var-GS19025-1100-36-ASM
hom C @ chr12:110368991

 

GS19026 - var-GS19026-1100-36-ASM
hom C @ chr12:110368991

 

GS19129 - var-GS19129-1100-36-ASM
hom C @ chr12:110368991

 

GS19238 - var-GS19238-1100-36-ASM
hom C @ chr12:110368991

 

GS19239 - var-GS19239-1100-36-ASM
hom C @ chr12:110368991

 

GS19240 - var-GS19240-1100-36-ASM
hom C @ chr12:110368991

 

GS19649 - var-GS19649-1100-36-ASM
hom C @ chr12:110368991

 

GS19669 - var-GS19669-1100-36-ASM
hom C @ chr12:110368991

 

GS19670 - var-GS19670-1100-36-ASM
het C @ chr12:110368991

 

GS19700 - var-GS19700-1100-36-ASM
hom C @ chr12:110368991

 

GS19701 - var-GS19701-1100-36-ASM
hom C @ chr12:110368991

 

GS19703 - var-GS19703-1100-36-ASM
hom C @ chr12:110368991

 

GS19704 - var-GS19704-1100-36-ASM
hom C @ chr12:110368991

 

GS19735 - var-GS19735-1100-36-ASM
hom C @ chr12:110368991

 

GS19834 - var-GS19834-1100-36-ASM
het C @ chr12:110368991

 

GS20502 - var-GS20502-1100-36-ASM
het C @ chr12:110368991

 

GS20509 - var-GS20509-1100-36-ASM
het C @ chr12:110368991

 

GS21767 - var-GS21767-1100-36-ASM
hom C @ chr12:110368991

 

Other external references
 

    dbSNP
  • rs3184504
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GWAS
  • Type 1 diabetes (rs3184504-?)
    Barrett 10-May-09 in Nat Genet
    OR or beta: NR NR
    p-value: 3.00E-27
    Initial sample: 7,514 cases, 9,045 controls
    Replication sample: 4,267 cases, 4,670 controls, 4,342 trios
    www.ncbi.nlm.nih.gov/pubmed/19430480
  • Diastolic blood pressure (rs3184504-T)
    Levy 10-May-09 in Nat Genet
    OR or beta: 0.48 [0.36-0.60] mm Hg increase
    Risk allele frequency: 0.48
    p-value: 3.00E-14
    Initial sample: 29,136 individuals
    Replication sample: 34,433 individuals
    www.ncbi.nlm.nih.gov/pubmed/19430479
  • Systolic blood pressure (rs3184504-T)
    Levy 10-May-09 in Nat Genet
    OR or beta: 0.58 [0.38-0.78] mm Hg increase
    Risk allele frequency: 0.48
    p-value: 5.00E-09
    Initial sample: 29,136 individuals
    Replication sample: 34,433 individuals
    www.ncbi.nlm.nih.gov/pubmed/19430479
  • Plasma eosinophil count (rs3184504-T)
    Gudbjartsson 8-Feb-09 in Nat Genet
    OR or beta: 7.6 [5.9-9.3] % standard unit increa
    Risk allele frequency: 0.38
    p-value: 7.00E-19 (European)
    Initial sample: 9,392 individuals
    Replication sample: 12,118 individuals
    www.ncbi.nlm.nih.gov/pubmed/19198610
    PolyPhen-2
  • Score: 0 (benign)

Other in silico analyses
 

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

Edit history
 

Gene search

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