FUT2 G258S - GET-Evidence

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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:

FUT2 G258S

(FUT2 Gly258Ser)


Short summary

 

Variant evidence
Computational 1

PolyPhen2: Probably damaging 0.997
SIFT: Tolerated 0.14
GVGD: GV 55.27; GD 0.00; Class C0
Variant Effect Predictor (Ensembl): SIFT=deleterious(0.03);
PolyPhen=probably_damaging(0.997);
Condel=deleterious(0.985)
Mutation Tasting Prediction: Polymorphism, P value: 0.133696; protein features (might be) affected (aa 29-343 TOPO_DOM Lumenal (Potential) 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

  • A @ chr19:49206985: 50.9% (5472/10758) in EVS
  • A @ chr19:53898796: 42.2% (54/128) in GET-Evidence
  • Frequency shown in summary reports: 50.9% (5472/10758)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
hom A @ chr19:49206985

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het A @ chr19:49206985

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het A @ chr19:49206985

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom A @ chr19:49206985

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
hom A @ chr19:49206985

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het A @ chr19:49206985

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het A @ chr19:49206985

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het A @ chr19:49206985

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het A @ chr19:49206985

 

hu3A8D13 - PGP13 (hu3A8D13) build 37, from CGI var (software ver 1.11.0.16), CGI sample GS000003289
hom A @ chr19:49206985

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom A @ chr19:49206985

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het A @ chr19:49206985

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
hom A @ chr19:49206985

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het A @ chr19:49206985

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het A @ chr19:49206985

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom A @ chr19:49206985

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het A @ chr19:49206985

 

hu6E4515 - PGP15 (hu6E4515) build 37, from CGI var (software ver 1.12.0.47), CGI sample GS000005532
het A @ chr19:49206985

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het A @ chr19:53898797

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het A @ chr19:49206985

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr19:49206985

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
hom A @ chr19:49206985

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het A @ chr19:49206985

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het A @ chr19:49206985

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het A @ chr19:49206985

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het A @ chr19:49206985

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom A @ chr19:49206985

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het A @ chr19:49206985

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom A @ chr19:49206985

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het A @ chr19:49206985

 

GS06985 - var-GS06985-1100-36-ASM
hom A @ chr19:53898797

 

GS06994 - var-GS06994-1100-36-ASM
het A @ chr19:53898797

 

GS10851 - var-GS10851-1100-36-ASM
het A @ chr19:53898797

 

GS12004 - var-GS12004-1100-36-ASM
het A @ chr19:53898797

 

GS18501 - var-GS18501-1100-36-ASM
hom A @ chr19:53898797

 

GS18502 - var-GS18502-1100-36-ASM
het A @ chr19:53898797

 

GS18504 - var-GS18504-1100-36-ASM
het A @ chr19:53898797

 

GS18505 - var-GS18505-1100-36-ASM
het A @ chr19:53898797

 

GS18508 - var-GS18508-1100-36-ASM
het A @ chr19:53898797

 

GS18517 - var-GS18517-1100-36-ASM
het A @ chr19:53898797

 

GS19017 - var-GS19017-1100-36-ASM
het A @ chr19:53898797

 

GS19020 - var-GS19020-1100-36-ASM
het A @ chr19:53898797

 

GS19025 - var-GS19025-1100-36-ASM
hom A @ chr19:53898797

 

GS19129 - var-GS19129-1100-36-ASM
het A @ chr19:53898797

 

GS19238 - var-GS19238-1100-36-ASM
het A @ chr19:53898797

 

GS19239 - var-GS19239-1100-36-ASM
hom A @ chr19:53898797

 

GS19240 - var-GS19240-1100-36-ASM
het A @ chr19:53898797

 

GS19649 - var-GS19649-1100-36-ASM
het A @ chr19:53898797

 

GS19669 - var-GS19669-1100-36-ASM
het A @ chr19:53898797

 

GS19670 - var-GS19670-1100-36-ASM
het A @ chr19:53898797

 

GS19701 - var-GS19701-1100-36-ASM
hom A @ chr19:53898797

 

GS19703 - var-GS19703-1100-36-ASM
het A @ chr19:53898797

 

GS19834 - var-GS19834-1100-36-ASM
hom A @ chr19:53898797

 

GS20502 - var-GS20502-1100-36-ASM
het A @ chr19:53898797

 

GS21767 - var-GS21767-1100-36-ASM
het A @ chr19:53898797

 

Other external references
 

    dbSNP
  • rs602662
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GWAS
  • Folate pathway vitamin levels (rs602662-A)
    Tanaka 18-Mar-09 in Am J Hum Genet
    OR or beta: 49.77 [37.09-62.45] pg/ml increase
    Risk allele frequency: 0.53
    p-value: 3.00E-20 (vitamin B12)
    Initial sample: 2,934 individuals
    Replication sample: 686 individuals
    www.ncbi.nlm.nih.gov/pubmed/19303062
    PolyPhen-2
  • Score: 0.954 (probably damaging)

Other in silico analyses
 

  • NBLOSUM100 score = 2
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

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