SLC30A8 R325W - GET-Evidence

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

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Curation:
Currentness:

SLC30A8 R325W

(SLC30A8 Arg325Trp)


Short summary

 

Variant evidence
Computational -
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

  • T @ chr8:118184783: 22.7% (2446/10758) in EVS
  • T @ chr8:118253963: 20.3% (24/118) in GET-Evidence
  • Frequency shown in summary reports: 22.7% (2446/10758)

Publications
 

Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU, Prokunina-Olsson L, Ding CJ, Swift AJ, Narisu N, Hu T, Pruim R, Xiao R, Li XY, Conneely KN, Riebow NL, Sprau AG, Tong M, White PP, Hetrick KN, Barnhart MW, Bark CW, Goldstein JL, Watkins L, Xiang F, Saramies J, Buchanan TA, Watanabe RM, Valle TT, Kinnunen L, Abecasis GR, Pugh EW, Doheny KF, Bergman RN, Tuomilehto J, Collins FS, Boehnke M. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science. 2007 Jun 1;316(5829):1341-5. Epub 2007 Apr 26. PubMed PMID: 17463248.

 

Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H, Timpson NJ, Perry JR, Rayner NW, Freathy RM, Barrett JC, Shields B, Morris AP, Ellard S, Groves CJ, Harries LW, Marchini JL, Owen KR, Knight B, Cardon LR, Walker M, Hitman GA, Morris AD, Doney AS; Wellcome Trust Case Control Consortium (WTCCC), McCarthy MI, Hattersley AT. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science. 2007 Jun 1;316(5829):1336-41. Epub 2007 Apr 26. Erratum in: Science. 2007 Aug 24;317(5841):1035-6. PubMed PMID: 17463249.

 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr8:118184783

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het T @ chr8:118184783

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het T @ chr8:118184783

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het T @ chr8:118184783

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het T @ chr8:118184783

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het T @ chr8:118184783

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het T @ chr8:118184783

 

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het T @ chr8:118184783

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het T @ chr8:118184783

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het T @ chr8:118184783

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom T @ chr8:118184783

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het T @ chr8:118184783

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het T @ chr8:118184783

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
hom T @ chr8:118184783

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
het T @ chr8:118184783

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het T @ chr8:118184783

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het T @ chr8:118184783

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het T @ chr8:118184783

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het T @ chr8:118184783

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het T @ chr8:118184783

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het T @ chr8:118184783

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het T @ chr8:118184783

 

GS10851 - var-GS10851-1100-36-ASM
het T @ chr8:118253964

 

GS12004 - var-GS12004-1100-36-ASM
het T @ chr8:118253964

 

GS18526 - var-GS18526-1100-36-ASM
het T @ chr8:118253964

 

GS18537 - var-GS18537-1100-36-ASM
het T @ chr8:118253964

 

GS18940 - var-GS18940-1100-36-ASM
het T @ chr8:118253964

 

GS18956 - var-GS18956-1100-36-ASM
het T @ chr8:118253964

 

GS19017 - var-GS19017-1100-36-ASM
het T @ chr8:118253964

 

GS19648 - var-GS19648-1100-36-ASM
het T @ chr8:118253964

 

GS19670 - var-GS19670-1100-36-ASM
het T @ chr8:118253964

 

GS20502 - var-GS20502-1100-36-ASM
het T @ chr8:118253964

 

GS20509 - var-GS20509-1100-36-ASM
hom T @ chr8:118253964

 

NA12878

 

Other external references
 

    dbSNP
  • rs13266634
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GWAS
  • Type 2 diabetes and other traits (rs13266634-C)
    Rung 6-Sep-09 in Nat Genet
    OR or beta: 1.16 [1.10-1.22]
    Risk allele frequency: 0.68
    p-value: 8.00E-08
    Initial sample: 679 French cases, 697 French controls
    Replication sample: 5,579 European cases, 7,096 European controls
    www.ncbi.nlm.nih.gov/pubmed/19734900
  • Type 2 diabetes (rs13266634-C)
    Takeuchi 29-Apr-09 in Diabetes
    OR or beta: 1.22 [1.16-1.28]
    Risk allele frequency: 0.57
    p-value: 2.00E-14
    Initial sample: 519 Japanese cases, 503 Japanese controls
    Replication sample: 5,629 Japanese cases, 7,370 Japanese controls
    www.ncbi.nlm.nih.gov/pubmed/19401414
  • Glycated hemoglobin levels (rs13266634-A)
    Pare 19-Dec-08 in PLoS Genet
    OR or beta: 0.02 [NR] % decrease
    Risk allele frequency: 0.30
    p-value: 5.00E-08
    Initial sample: 14,618 Caucasian women
    Replication sample: 455 Caucasian men and women
    www.ncbi.nlm.nih.gov/pubmed/19096518
  • Type 2 diabetes (rs13266634-?)
    Timpson 3-Dec-08 in Diabetes
    OR or beta: 1.18 [1.10-1.27]
    p-value: 0.000007 (non-obese)
    Initial sample: 1,924 cases, 2,938 controls
    Replication sample: 3,757 cases, 5,346 controls
    www.ncbi.nlm.nih.gov/pubmed/19056611
  • Type 2 diabetes (rs13266634-C)
    Saxena 26-Apr-07 in Science
    OR or beta: 1.12 [1.07-1.16]
    Risk allele frequency: 0.65
    p-value: 5.00E-08 (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 (rs13266634-C)
    Scott 26-Apr-07 in Science
    OR or beta: 1.12 [1.07-1.16]
    Risk allele frequency: 0.61
    p-value: 5.00E-08 (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 (rs13266634-C)
    Steinthorsdottir 26-Apr-07 in Nat Genet
    OR or beta: 1.15 [1.08-1.22]
    Risk allele frequency: 0.67
    p-value: 0.000003
    Initial sample: 1,399 EA cases, 5,275 EA controls
    Replication sample: 2,437 EA cases, 7,287 EA controls
    www.ncbi.nlm.nih.gov/pubmed/17460697
  • Type 2 diabetes (rs13266634-C)
    Zeggini 26-Apr-07 in Science
    OR or beta: 1.12 [1.07-1.16]
    Risk allele frequency: 0.69
    p-value: 5.00E-08 (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
  • Type 2 diabetes (rs13266634-C)
    Sladek 11-Feb-07 in Nature
    OR or beta: 1.18 [0.69-1.67]
    Risk allele frequency: 0.70
    p-value: 6.00E-08
    Initial sample: 661 cases, 614 controls
    Replication sample: 2,617 cases, 2,894 controls
    www.ncbi.nlm.nih.gov/pubmed/17293876
    PharmGKB
  • [Diabetes Mellitus, Type 2]
    This variant has been reported to be significantly associated with type 2 diabetes.
    www.ncbi.nlm.nih.gov/pubmed/17786204; PubMed ID:18162508; PubMed ID:18264689; PubM
  • [Diabetes Mellitus, Type 2]
    rs13266634 is associated with susceptibility to Type 2 Diabetes. The association has been noted in two case-control studies of UK subjects as well as in two other large case-control studies.
    www.ncbi.nlm.nih.gov/pubmed/17463249
  • [Diabetes Mellitus, Type 2]
    In a large Finnish case-control GWAS, rs13266634 was found to be associated with susceptibility to Type 2 Diabetes.
    www.ncbi.nlm.nih.gov/pubmed/17463248
  • [Diabetes Mellitus; Diabetes Mellitus, Type 2]
    GWAS Results: A genome-wide association study identifies novel risk loci for type 2 diabetes (Initial Sample Size: 1,380 cases, 1,323 controls; Replication Sample Size: 2,617 cases, 2,894 controls; Risk Allele: rs13266634-C).
    www.ncbi.nlm.nih.gov/pubmed/17293876; Web Resource:http://www.genome.gov/gwastudie
  • [Diabetes Mellitus; Diabetes Mellitus, Type 2]
    GWAS results: Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome wide association data. (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: 3,757 cases, 5,346 controls); (Region: 8q24.11; Reported Gene(s): SLC30A8; Risk Allele: rs13266634-?); (p-value= 0.000007).This variant is associated with Type 2 diabetes.
    www.ncbi.nlm.nih.gov/pubmed/19056611; Web Resource:http://www.genome.gov/gwastudie
    PolyPhen-2
  • Score: 0 (benign)

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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