CTSD A58V - GET-Evidence

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

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Curation:
Currentness:

CTSD A58V

(CTSD Ala58Val)


Short summary

 

Variant evidence
Computational -
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

  • A @ chr11:1782594: 6.5% (694/10758) in EVS
  • A @ chr11:1739169: 6.3% (8/126) in GET-Evidence
  • Frequency shown in summary reports: 6.5% (694/10758)

Publications
 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het A @ chr11:1782594

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het A @ chr11:1782594

 

 

 

 

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het A @ chr11:1782594

 

GS10851 - var-GS10851-1100-36-ASM
het A @ chr11:1739170

 

GS18558 - var-GS18558-1100-36-ASM
het A @ chr11:1739170

 

GS19669 - var-GS19669-1100-36-ASM
het A @ chr11:1739170

 

NA12878

 

Other external references
 

    dbSNP
  • rs17571
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.003 (benign)
    Web search results (11 hits -- see all)
  • BiomedExperts: Cathepsin D: screening for new polymorphisms ...
    Previous findings revealed a significant association between the T allele of the 224 C/T (A58V) polymorphism in exon 2 of the CTSD gene and late onset AD. ...
    biomedexperts.com/Abstract.bme/11786931/...
  • AceView: Gene:CTSD, 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=CTSD
  • Genetics | BRAINnet - Brain Research And Integrative ...
    MolecularNeuro – Collection via cheek swab or saliva method (and in some cases bloods) of DNA for extraction of SNPs and other variants of interest which
    www.brainnet.net/the-brainnet-advantage/genetics
  • NCI CANCERLIT® Search: Genetic Counseling and Screening ...
    Cathepsin D (CTSD) is a lysosomal protease involved in the ... between the T allele of the 224 C/T (A58V) polymorphism in exon 2 of the CTSD gene and late onset AD. ...
    es.oncolink.org/types/article.cfm?c=1&s=2&ss=11&id=8013
  • SNP Name
    CTSD. 11. rs17571. nonsynonymous associated with AD[3] and general intelligence [4]. A58V. 0.71. CTSD. 11. rs13345. synonymous. 0.81. CTSH. 15. rs12148472. intron/splice site. 0.85 ...
    biomedcentral.com/.../supplementary/1471-2156-8-43-s1.doc
  • Table 3 Text
    ... total chromosomes genotyped MAF mean MAF stdev chromosomes genotyped ... criterion prediction score number sequences aligned prediction score divergence ...
    icr.ac.uk/research/research_sections/.../2842.txt
  • Type II- 97%
    ... Reference(s) for phosphorylation site ENPEP Q07075 R213Q 216 VAR_030359 AGC (0. ... sample, somatic mutation 17344846 CTSD P07339 A58V 56 VAR_011621 gCK1 (0.561) ...
    www.nih.go.kr/phosphovariant/html/group_whole/TypeII-_97.txt
  • Cathepsin D: screening for new polymorphisms using single ...
    Cathepsin D (CTSD) is a lysosomal protease involved in the pathogenesis of several diseases such as breast cancer and possibly Alzheimer's disease (AD)
    www.medscape.com/medline/abstract/11786931?prt=true
  • Parkinson Disease Knowledgebase
    The findings suggest interference of CTSD and APOE polymorphisms in the ... Variation Impact. Negative Result. Variation. p.A58V. c.306C>T. RefSeq ID. rs17571. suisheng ...
    datam.i2r.a-star.edu.sg/mdpd/detail.php?symbol=CTSD&sec=1
  • How to... | BRAINnet - Brain Research And Integrative ...
    .. Acknowledge the BRAINnet Database? Refer to the Data? Acknowledging the BRAINnet Database BRAINnet Acknowledgments to use
    www.brainnet.net/how-to

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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