CALHM1 L86P - 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:

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CALHM1 L86P

(CALHM1 Leu86Pro)


You are viewing an old version of this page that was saved on November 29, 2012 at 2:33am by Genome Importing Robot.

Short summary

 

Variant evidence
Computational 3

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 1.00
GVGD: GV 135.19; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.22);
PolyPhen=benign(0);
Condel=deleterious(0.778)
Mutation Tasting Prediction: Polymorphism, P value: 0.999976; no protein features affected.

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 @ chr10:105218252: 79.8% (8572/10744) in EVS
  • GGC,GGT @ chr10:105208241: 84.4% (81/96) in GET-Evidence
  • Frequency shown in summary reports: 79.8% (8572/10744)

Publications
 

Dreses-Werringloer U, Lambert JC, Vingtdeux V, Zhao H, Vais H, Siebert A, Jain A, Koppel J, Rovelet-Lecrux A, Hannequin D, Pasquier F, Galimberti D, Scarpini E, Mann D, Lendon C, Campion D, Amouyel P, Davies P, Foskett JK, Campagne F, Marambaud P. A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk. Cell. 2008 Jun 27;133(7):1149-61. PubMed PMID: 18585350; PubMed Central PMCID: PMC2577842.

 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het GGT @ chr10:105218252

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom GGT @ chr10:105218252

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het GGT @ chr10:105218252

 

 

 

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
hom G @ chr10:105218252

 

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het G @ chr10:105218252

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom G @ chr10:105218252

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het GGC @ chr10:105218252

 

Added in this revision:

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het GGC @ chr10:105218252

 

GS10851 - var-GS10851-1100-36-ASM
hom G @ chr10:105208242

 

GS12004 - var-GS12004-1100-36-ASM
hom G @ chr10:105208242

 

GS18502 - var-GS18502-1100-36-ASM
hom G @ chr10:105208242

 

GS18537 - var-GS18537-1100-36-ASM
hom G @ chr10:105208242

 

GS18558 - var-GS18558-1100-36-ASM
hom GGT @ chr10:105208242

 

GS18942 - var-GS18942-1100-36-ASM
hom G @ chr10:105208242

 

GS18947 - var-GS18947-1100-36-ASM
het GGT @ chr10:105208242

 

GS19129 - var-GS19129-1100-36-ASM
hom G @ chr10:105208242

 

GS19238 - var-GS19238-1100-36-ASM
hom G @ chr10:105208242

 

GS19239 - var-GS19239-1100-36-ASM
hom G @ chr10:105208242

 

GS19240 - var-GS19240-1100-36-ASM
hom G @ chr10:105208242

 

GS19669 - var-GS19669-1100-36-ASM
het G @ chr10:105208242

 

GS19703 - var-GS19703-1100-36-ASM
hom G @ chr10:105208242

 

GS19704 - var-GS19704-1100-36-ASM
hom G @ chr10:105208242

 

GS19735 - var-GS19735-1100-36-ASM
hom GGT @ chr10:105208242

 

GS19834 - var-GS19834-1100-36-ASM
hom G @ chr10:105208242

 

GS20502 - var-GS20502-1100-36-ASM
het GGT @ chr10:105208242

 

Other external references
 

    dbSNP
  • rs2986017
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PharmGKB
  • [Alzheimer Disease]
    This variant increases amyloid-beta levels by interfering with CALHM1-mediated Ca(2+) permeability. The SNP is significantly associated with Alzheimer's disease in independent case-control studies of 3404 participants.
    www.ncbi.nlm.nih.gov/pubmed/18585350
    PolyPhen-2
  • Score: 0 (benign)

Other in silico analyses
 

  • NBLOSUM100 score = 7
  • GET-Evidence autoscore = 1

Edit history
 

Gene search

"GENE" or "GENE A123C":

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