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rs9652490

From SNPedia

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Geno Mag Summary
(A;A) 2 ~2x increased risk for Parkinson's disease, and, essential tremor
(A;G) 1.5 Slightly increased risk of developing Parkinson's Disease
(G;G) 1 Normal risk of developing Parkinson's Disease
ReferenceGRCh38 38.1/141
Chromosome15
Position77671545
GeneLINGO1
is asnp
is mentioned by
dbSNPrs9652490
ebirs9652490
HLIrs9652490
Exacrs9652490
Varsomers9652490
Maprs9652490
PheGenIrs9652490
hapmaprs9652490
1000 genomesrs9652490
hgdprs9652490
ensemblrs9652490
gopubmedrs9652490
geneviewrs9652490
scholarrs9652490
googlers9652490
pharmgkbrs9652490
gwascentralrs9652490
openSNPrs9652490
23andMers9652490
23andMe allrs9652490
SNP Nexus

SNPshotrs9652490
SNPdbers9652490
MSV3drs9652490
GWAS Ctlgrs9652490
GMAF0.2759
Max Magnitude2
? (A;A) (A;G) (G;G) 28
rs9652490 is a SNP in the LINGO1 gene. Note: it is unclear why one set of authors report the risk allele for essential tremors to be (G), while the others just as clearly report the risk allele to be (A).

A follow-up case-control study replicated the original association of rs9652490(A;A) to an ~2x increased risk for Parkinson's disease, but also found the same risk for essential tremor (ET), thus linking the two diseases. The ET study was based on ~300 patients.[PMID 19720553OA-icon.png]

23andMe blog "In a combined analysis of 752 subjects with essential tremor from Iceland, Austria, Germany and the United States and 15,797 controls, Stefansson et al found that the G version of rs9652490 in the LINGO1 gene is associated with increased odds of the condition. Carrying one G increases the odds of essential tremor by 1.55 times compared to two As. The approximately 5% of the population with European ancestry with two Gs has 2.40 times increased odds."

[PMID 20957646] Finds no evidence that rs9652490 is associated with Parkinson's disease in a Chinese population, or, based on a meta-analysis.

GWAS snp
PMID [PMID 19182806OA-icon.png]
Trait Essential tremor
Title Variant in the sequence of the LINGO1 gene confers risk of essential tremor
Risk Allele G
P-val 1E-9
Odds Ratio 1.55 [1.35-1.79]
OMIM190300
DescTREMOR, HEREDITARY ESSENTIAL, 1; ETM1
Variant
Relatedalso
[PMID 19720553OA-icon.png] LINGO1 rs9652490 is associated with essential tremor and Parkinson disease

[PMID 19908305OA-icon.png] Role of LINGO1 polymorphisms in Parkinson's disease



[PMID 20117178] Analysis of LINGO1 (rs9652490) polymorphism in sporadic Parkinson's disease in a Polish population, and a meta-analysis


[PMID 20310002] LINGO1 polymorphisms are associated with essential tremor in Europeans

[PMID 20951767] LINGO1 rs9652490 variant in Parkinson disease patients


[PMID 21264305OA-icon.png] LINGO1 Variants in the French-Canadian Population


[PMID 22166413] Genetics of essential tremor


[PMID 22710005] Genetic variation in LINGO-1 (rs9652490) and risk of Parkinson's disease: twelve studies and a meta-analysis


[PMID 20369022OA-icon.png] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.


[PMID 20369371OA-icon.png] LINGO1 and LINGO2 variants are associated with essential tremor and Parkinson disease.


[PMID 20372186OA-icon.png] Replication of the LINGO1 gene association with essential tremor in a North American population.


[PMID 20600614] Screening for two SNPs of LINGO1 gene in patients with essential tremor or sporadic Parkinson's disease in Chinese population.


[PMID 21158743] Analysis of Lingo1 variant in sporadic and familial essential tremor among Asians.


[PMID 21207446] LINGO1 gene analysis in Parkinson's disease phenotypes.


[PMID 21219542] Lack of association of LINGO1 rs9652490 and rs11856808 SNPs with familial essential tremor.


[PMID 21955595] LINGO1 rs9652490 and rs11856808 are not associated with the risk of Parkinson's disease: results of a meta-analysis.


[PMID 22425540] LINGO1 and risk for essential tremor: results of a meta-analysis of rs9652490 and rs11856808.


GET Evidence
rs9652490
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.373016
summary



[PMID 23574883OA-icon.png] LINGO1 rs9652490 and rs11856808 polymorphisms are not associated with risk for multiple sclerosis