ELAC2 S217L - 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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ELAC2 S217L

(ELAC2 Ser217Leu)


You are viewing an old version of this page that was saved on April 5, 2010 at 11:09am by Madeleine Ball.

Short summary

 

Variant evidence
Computational -
Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated pathogenic

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

recessive

Summary of published research, and additional commentary

Case/control numbers are used from cases referenced by Xu et al. (where they note that they only use numbers from the most recent publication when multiple publications used the same data source).

Allele frequency

  • A @ chr17:12915009: 27.3% (2942/10758) in EVS
  • A @ chr17:12855733: 24.6% (31/126) in GET-Evidence
  • Frequency shown in summary reports: 27.3% (2942/10758)

Publications
 

Added in this revision:

Robbins CM, Hernandez W, Ahaghotu C, Bennett J, Hoke G, Mason T, Pettaway CA, Vijayakumar S, Weinrich S, Furbert-Harris P, Dunston G, Powell IJ, Carpten JD, Kittles RA. Association of HPC2/ELAC2 and RNASEL non-synonymous variants with prostate cancer risk in African American familial and sporadic cases. Prostate. 2008 Dec 1;68(16):1790-7. PubMed PMID: 18767027.

 

Xu B, Tong N, Li JM, Zhang ZD, Wu HF. ELAC2 polymorphisms and prostate cancer risk: a meta-analysis based on 18 case-control studies. Prostate Cancer Prostatic Dis. 2010 Mar 16. [Epub ahead of print] PubMed PMID: 20231859.

The most recent meta-analysis of ELAC2 polymorphisms Ser217Leu and Ala541Thr, this concludes that these are associated with prostate cancer and may be “low-penetrance susceptibility markers of prostate cancer”. They note that there is publication bias for results supporting pathogenicity (p = 0.006) but that no single paper is necessary for their conclusion of pathogenicity (ie removal of any single paper doesn’t change this result).

Genomes
 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom A @ chr17:12915009

 

NA12156

 

NA12878

 

NA18507

 

NA19240

 

snp-27

 

snp-29

 

snp-6

 

Other external references
 

    dbSNP
  • rs4792311
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.025 (benign)
    Web search results (50 hits -- see all)
  • ELAC2 and prostate cancer risk in Afro-Caribbeans of Tobago.
    ELAC2 and prostate cancer risk in Afro-Caribbeans of Tobago. ... The frequency of the high-risk Leu allele at the S217L site was the same in cases and controls. ...
    www.ncbi.nlm.nih.gov/pubmed/12384782
  • Mendelian Inheritance in Man Document Reader
    ELAC2 is a member of an uncharacterized gene family predicted to encode a metal-dependent ... reported missense changes, S217L and A541T, were identified ...
    www.angis.org.au/bin/Databases/BIRX/birx_doc?phtomim+605367
  • ELAC2 (elaC homolog 2 (E. coli))
    ELAC2 (elaC homolog 2 (E. coli)), Authors: Yang Chen, Sean Tavtigian, Donna Shattuck. Published in: Atlas Genet Cytogenet Oncol Haematol.
    atlasgeneticsoncology.org/Genes/ELAC2ID40437ch17p11.html
  • Table 1
    dietary fats; may account for 20% of. Alzheimer disease. Age-related ... ELAC2. S217L. Prostate cancer. 0.30 and 0.04. Increased risk. Odds ratio 2.4-3.1. and A541T ...
    genomebiology.com/2001/2/8/COMMENT/2007/table/T1
  • AceView: Gene:ELAC2, a comprehensive annotation of human ...
    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=ELAC2
  • Characterization of TRZ1 , a yeast homolog of the human ...
    In humans, mutation of ELAC2 is associated with an increased risk of prostate cancer. ... ELAC2 (S217L) No. ELAC2 (A541T) No. ELAC2 (R781H) No. ELAC2 (1641insG) No. ELAC1. No. TRZ1 WT ...
    biomedcentral.com/content/download/xml/1471-2199-6-12.xml
  • Selected article
    Science, global weekly of science ... S217L. A541T. Japanese. 350 sporadic. 242 control. prostate cancer risk. 95. A541T. Japanese. 285 sporadic. 233 control. OR 4.02 (1.50, 10.8) ...
    bioscience.org/2007/v12/af/2375/fulltext.asp?...&doi=yes
  • Polymorphisms in the Prostate Cancer Susceptibility Gene HPC2 ...
    ... HPC2/ELAC2 that throws translation out of frame after amino acid 547 and that ... The S217L variation was detected as follows: 37 ng of genomic DNA was amplified ...
    www.drcatalona.com/journal/CancerResearch_article313.htm

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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