SPG7 T503A - 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:

SPG7 T503A

(SPG7 Thr503Ala)


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

  • G @ chr16:89613123: 14.2% (1530/10758) in EVS
  • G @ chr16:88140623: 14.8% (19/128) in GET-Evidence
  • Frequency shown in summary reports: 14.2% (1530/10758)

Publications
 

Deeken JF, Cormier T, Price DK, Sissung TM, Steinberg SM, Tran K, Liewehr DJ, Dahut WL, Miao X, Figg WD. A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform. Pharmacogenomics J. 2009 Dec 29. [Epub ahead of print] PubMed PMID: 20038957.

 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het G @ chr16:89613123

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het G @ chr16:89613123

 

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het G @ chr16:89613123

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom G @ chr16:89613123

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het G @ chr16:89613123

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het G @ chr16:89613123

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het G @ chr16:89613123

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het G @ chr16:89613123

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het G @ chr16:89613123

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom G @ chr16:89613123

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het G @ chr16:89613123

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het G @ chr16:89613123

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het G @ chr16:89613123

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het G @ chr16:89613123

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het G @ chr16:89613123

 

GS06994 - var-GS06994-1100-36-ASM
het G @ chr16:88140624

 

GS10851 - var-GS10851-1100-36-ASM
hom G @ chr16:88140624

 

GS18940 - var-GS18940-1100-36-ASM
het G @ chr16:88140624

 

GS18942 - var-GS18942-1100-36-ASM
het G @ chr16:88140624

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr16:88140624

 

GS19704 - var-GS19704-1100-36-ASM
het G @ chr16:88140624

 

GS20509 - var-GS20509-1100-36-ASM
het G @ chr16:88140624

 

NA12878

 

Other external references
 

    dbSNP
  • rs2292954
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PharmGKB
  • [Prostatic Neoplasms]
    [docetaxel; thalidomide]
    Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX
    www.ncbi.nlm.nih.gov/pubmed/20038957
    PolyPhen-2
  • Score: 0.001 (benign)
    Web search results (4 hits -- see all)
  • A clinical, genetic and biochemical study of SPG7 mutations ...
    Mutations in the SPG7 gene, encoding the mitochon- drial protein paraplegin, were the ® ... of the SPG7 gene were screened for mutations using a. combination of ...
    brain.oxfordjournals.org/cgi/reprint/awh125v1.pdf
  • Type II- 95%
    Gene name SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT ... CK2 (0.555) Polymorphism (dbSNP:rs17655) 8483504 OR5I1 Q13606 F76S 75 VAR_024101 ...
    nih.go.kr/phosphovariant/html/family_whole/TypeII-_95.txt
  • Type I- 95%
    ... GALC P54803 Y551S 551 VAR_003403 Src (0.816) GLD, belgian patient PLK4 O00444 ... (0.672) AT-III deficiency, type-I 9031473 9759613 SPG7 Q9UQ90 T503A ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_95.txt

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

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