Rs2228603

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Associated with Nonalcoholic Fatty Liver Disease.
Orientationplus
Geno Mag Summary
(C;C) 0 common in complete genomics
Make rs2228603(C;T)
Make rs2228603(T;T)
ReferenceGRCh38 38.1/141
Chromosome19
Position19219115
GeneNCAN
is asnp
is mentioned by
dbSNPrs2228603
Exacrs2228603
PheGenIrs2228603
nextbiors2228603
hapmaprs2228603
1000 genomesrs2228603
hgdprs2228603
ensemblrs2228603
gopubmedrs2228603
geneviewrs2228603
scholarrs2228603
googlers2228603
pharmgkbrs2228603
gwascentralrs2228603
openSNPrs2228603
23andMers2228603
23andMe allrs2228603
SNP Nexus

SNPshotrs2228603
SNPdbers2228603
MSV3drs2228603
GMAF0.04683
? (C;C) (C;T) (T;T) 28
rs2228603 is a SNP in the NCAN gene (also known as CSPG3), coding for the neurocan core protein. The T risk allele results in a proline to serine missense mutation at position 92 of the protein.

In a large GWAS of individuals of European descent published in March, 2011, rs2228603 was found to be associated with nonalcoholic fatty liver disease (NAFLD), as evidenced by hepatic steatosis found by CT scanning and confirmed by histology. The investigators confirmed their initial findings with using the same case cohort and two separate control groups and found genome-wide significant odds ratios of 1.65 (95% CI = 1.15-2.87; p=5.29E-5; p=6.82E-10) and 1.9 (95% CI not reported) NAFLD is associated with higher LDL-C and lower LDL-C levels as well as impaired fasting glucose and increased risk of insulin resistance and diabetes. However, rs2228603 was found to be associated with lower triglycerides and plasma LDL-Cholesterol in this study [PMID 21423719OA-icon.png].

GWAS
SNP rs2228603
PubMedID [PMID 21423719OA-icon.png]
Condition Nonalcoholic fatty liver disease
Gene NCAN
Risk Allele T
pValue 5.29E-5
OR 1.65
95% CI (1.15-2.87)
GWAS
SNP rs2228603
PubMedID [PMID 21423719OA-icon.png]
Condition Nonalcoholic fatty liver disease
Gene NCAN
Risk Allele T
pValue 6.82E-10
OR 1.90
95% CI NR


[PMID 22719876OA-icon.png] Genetic Polymorphisms of the Human PNPLA3 Gene Are Strongly Associated with Severity of Non-Alcoholic Fatty Liver Disease in Japanese


[PMID 18193044OA-icon.png] Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.


[PMID 18852197OA-icon.png] Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants.


[PMID 19802338OA-icon.png] Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication.


GET Evidence
NCAN-P92S
aa_change Pro92Ser
aa_change_short P92S
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.0532627
summary



[PMID 24477042] Genetic variants in GCKR and PNPLA3 confer susceptibility to nonalcoholic fatty liver disease in obese individuals


[PMID 24946282] A common polymorphism in the NCAN gene is associated with hepatocellular carcinoma in alcoholic liver disease