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.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

CALHM1 L86P

(CALHM1 Leu86Pro)


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
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het GGC @ chr10:105218252

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het GGC @ chr10:105218252

 

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

 

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom G @ chr10:105218252

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom G @ chr10:105218252

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het G @ chr10:105218252

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het GGT @ chr10:105218252

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
hom GGT @ chr10:105218252

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het G @ chr10:105218252

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het GGT @ chr10:105218252

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het GGC @ chr10:105218252

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het GGC @ chr10:105218252

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
het GGC @ chr10:105218252

 

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

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het G @ chr10:105218252

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het G @ chr10:105218252

 

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

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het G @ chr10:105218252

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom G @ chr10:105218252

 

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

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom G @ chr10:105218252

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het GGC @ chr10:105218252

 

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

 

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

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het GGT @ chr10:105218252

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het GGT @ chr10:105218252

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het GGT @ chr10:105218252

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het GGC @ chr10:105218252

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het GGT @ chr10:105218252

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom GGT @ chr10:105218252

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
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":

Log in