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rs5770917

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) >1.4x increased risk for narcolepsy
(C;T) 1.4x increased risk for narcolepsy
(T;T) 0 normal
ReferenceGRCh38 38.1/141
Chromosome22
Position50578924
GeneCHKB, CPT1B
is asnp
is mentioned by
dbSNPrs5770917
ebirs5770917
HLIrs5770917
Exacrs5770917
Varsomers5770917
Maprs5770917
PheGenIrs5770917
hapmaprs5770917
1000 genomesrs5770917
hgdprs5770917
ensemblrs5770917
gopubmedrs5770917
geneviewrs5770917
scholarrs5770917
googlers5770917
pharmgkbrs5770917
gwascentralrs5770917
openSNPrs5770917
23andMers5770917
23andMe allrs5770917
SNP Nexus

SNPshotrs5770917
SNPdbers5770917
MSV3drs5770917
GWAS Ctlgrs5770917
GMAF0.1157
Max Magnitude0
? (C;C) (C;T) (T;T) 28
rs5770917, a SNP located between the CPT1B and CHKB genes, was associated with narcolepsy in study of 222 Japanese individuals with narcolepsy and 389 Japanese controls, with replication of top hits in 159 Japanese individuals with narcolepsy and 190 Japanese controls, followed by the testing of 424 Koreans, 785 individuals of European descent and 184 African Americans. The risk allele rs5770917(C) had an odds ratio of 1.79 (p = 4.4 x 10e-7) in Japanese subjects and an odds ratio of 1.40 (p = 0.02) in other ancestry groups.10.1038/ng.231

Note that rs5770917 is in tight linkage (r2 > 0.93) with several nearby SNPs: rs2269382 and rs2269381.10.1038/ng.231HLA-DQB1*0602 and relevance to Narcolepsy related to vaccination

GWAS
SNP rs5770917
PubMedID [PMID 18820697]
Condition Narcolepsy
Gene CPT1B
Risk Allele C
pValue 6.00E-008
OR 1.63
95% CI 1.37-1.95


[PMID 19404393OA-icon.png] Polymorphism located between CPT1B and CHKB, and HLA-DRB1*1501-DQB1*0602 haplotype confer susceptibility to CNS hypersomnias (essential hypersomnia)

OMIM612417
DescNARCOLEPSY 4; NRCLP4
Variant
Relatedalso
[PMID 19412176OA-icon.png] Narcolepsy is strongly associated with the T-cell receptor alpha locus.


[PMID 21358852OA-icon.png] Abnormally low serum acylcarnitine levels in narcolepsy patients.


[PMID 22177342OA-icon.png] TCRA, P2RY11, and CPT1B/CHKB associations in Chinese narcolepsy.


GET Evidence
rs5770917
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.0666667
summary