F5 K858R - GET-Evidence

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

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Curation:
Currentness:

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F5 K858R

(F5 Lys858Arg)


You are viewing an old version of this page that was saved on November 29, 2012 at 3:23am by Genome Importing Robot.

Short summary

 

Variant evidence
Computational 3

PolyPhen2: Benign, score 0.001
SIFT: Tolerated 0.50
GVGD: GV 133.77; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.68);
PolyPhen=benign(0);
Condel=neutral(0.286)
Mutation Tasting Prediction: Polymorphism, P value: 0.999945
protein features (might be) affected (aa 692-1573 REGION B gets lost; aa 738-1573 PROPEP Activation peptide (connecting region) /FTId=PRO_0000002980 gets lost)

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 @ chr1:169511755: 24.4% (2624/10758) in EVS
  • C @ chr1:167778378: 30.5% (39/128) in GET-Evidence
  • Frequency shown in summary reports: 24.4% (2624/10758)

Publications
 

Genomes
 

Added in this revision:

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het C @ chr1:169511755

 

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het C @ chr1:169511755

 

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het C @ chr1:169511755

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het C @ chr1:169511755

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het C @ chr1:169511755

 

GS07357 - var-GS07357-1100-36-ASM
hom C @ chr1:167778379

 

GS10851 - var-GS10851-1100-36-ASM
het C @ chr1:167778379

 

GS18501 - var-GS18501-1100-36-ASM
het C @ chr1:167778379

 

GS18502 - var-GS18502-1100-36-ASM
het C @ chr1:167778379

 

GS18505 - var-GS18505-1100-36-ASM
het C @ chr1:167778379

 

GS18537 - var-GS18537-1100-36-ASM
het C @ chr1:167778379

 

GS18940 - var-GS18940-1100-36-ASM
het C @ chr1:167778379

 

GS18947 - var-GS18947-1100-36-ASM
het C @ chr1:167778379

 

GS18956 - var-GS18956-1100-36-ASM
het C @ chr1:167778379

 

GS19026 - var-GS19026-1100-36-ASM
het C @ chr1:167778379

 

GS19129 - var-GS19129-1100-36-ASM
het C @ chr1:167778379

 

GS19649 - var-GS19649-1100-36-ASM
het C @ chr1:167778379

 

GS19669 - var-GS19669-1100-36-ASM
hom C @ chr1:167778379

 

GS19670 - var-GS19670-1100-36-ASM
hom C @ chr1:167778379

 

GS19700 - var-GS19700-1100-36-ASM
het C @ chr1:167778379

 

GS19704 - var-GS19704-1100-36-ASM
het C @ chr1:167778379

 

GS19735 - var-GS19735-1100-36-ASM
hom C @ chr1:167778379

 

GS19834 - var-GS19834-1100-36-ASM
het C @ chr1:167778379

 

GS20502 - var-GS20502-1100-36-ASM
het C @ chr1:167778379

 

Other external references
 

    dbSNP
  • rs4524
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the F5 gene
    Budd-Chiari Syndrome
    Factor V Cambridge Thrombophilia
    Factor V Deficiency
    Factor V Leiden Thrombophilia
    Factor V R2 Mutation Thrombophilia
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/F5
    Web search results (5 hits -- see all)
  • AceView: Gene:F5, a comprehensive annotation of human, mouse ...
    AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on ...
    ncbi.nlm.nih.gov/IEB/Research/Acembly/...&a=clones&l=F5
  • telnet.23_sithqx
    <!DOCTYPE xhtml PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http: ... 6!N33)N*!V#Q64m`ET#E4A,hX%F5+N58VUfDGGkp-QNY&quot;'-EFB(8H1'()Z!!&quot;`NK ...
    iubio.bio.indiana.edu/.../util/mac/telnet/telnet.23_sithqx
  • <!DOCTYPE xhtml PUBLIC "-/W3C/DTD XHTML 1.0 Transitional/EN ...
    ... h9%9B9%e69d3&quot;!+$K,L@Ji6&quot;b!*!'8Cd!N!B TQ`!!D6m!N!ENL`dD#+Pc&quot;J560 ... 5 jbL'6!N33)N*!V#Q64m`ET#E4A,hX%F5+N58VUfDGGkp-QNY&quot;'-EFB(8H1'()Z! ...
    iubio.bio.indiana.edu/soft/util/mac/telnet/...
  • Thrombosis in Postmenopausal Women Association of Genetic ...
    Factor V (F5) Lower half. 71.3.‡ 5. 7. 91.7 .24 .39. Upper half. 71.3.‡ 9. 10 ... K858R. 27.0. 0.74 (0.60-0.90) .003 .14. 8.7 0.75 (0.58-0.97) 0.52 (0.30 ...
    jama.ama-assn.org/cgi/reprint/297/5/489.pdf
  • Table 1 Text
    ... 213 rs4524 F5 2153 1 166243413 NM_000130 NP_000121 A/G K858R minus 3195262 738 ... 216 rs4524 F5 2153 1 166243413 NM_000130 NP_000121 A/G K858R minus 12674294 1303 ...
    icr.ac.uk/research/research_sections/.../2841.txt

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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