chr2:27730940:T>C Detail (hg19) (GCKR)

Information

Genome

Assembly Position
hg19 chr2:27,730,940-27,730,940
hg38 chr2:27,508,073-27,508,073 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001486.3:c.1337T>C NP_001477.2:p.Leu446Pro
Ensemble ENST00000264717.7:c.1337T>C ENST00000264717.7:p.Leu446Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.450
ToMMo:0.438
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.506

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600842 OMIM
HGNC 4196 HGNC
Ensembl ENSG00000084734 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6251819 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2010-02-01 no assertion criteria provided Fasting plasma glucose level quantitative trait locus 5 germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.162 Diabetes Mellitus, Non-Insulin-Dependent Cellular characterisation of the GCKR P446L variant associated with type 2 diabe... BeFree 22038520 Detail
0.249 Hypertriglyceridemia Genomic study in Mexicans identifies a new locus for triglycerides and refines E... GWASCAT 23505323 Detail
0.249 Hypertriglyceridemia [Excess of rare variants in genes identified by genome-wide association study of... GAD 20657596 Detail
0.125 gout Genome-wide association study of clinically defined gout identifies multiple ris... GWASCAT 25646370 Detail
0.005 myocardial infarction The goal of this study was to test whether TRIB1-rs2954029 and GCKR-rs1260326 as... BeFree 21071687 Detail
0.162 Diabetes Mellitus, Non-Insulin-Dependent The common P446L polymorphism in GCKR inversely modulates fasting glucose and tr... BeFree 18556336 Detail
<0.001 Nonalcoholic Steatohepatitis Herein, we aimed to study the association between hepatic fat accumulation as as... BeFree 23275357 Detail
0.005 Kidney Diseases [New loci associated with kidney function and chronic kidney disease.] GAD 20383146 Detail
0.156 hyperglycemia Moreover, an additive effect of GCKR rs1260326(T) and GCK (-30G) alleles conferr... BeFree 18556336 Detail
0.005 myocardial infarction The goal of this study was to test whether TRIB1-rs2954029 and GCKR-rs1260326 as... BeFree 21071687 Detail
0.007 Dyslipidemias A polymorphism in the GCKR gene predicted dyslipidaemia (rs1260326, OR 1.15, 95%... BeFree 18853134 Detail
<0.001 Diabetes Mellitus, Insulin-Dependent The study group included 129 children with GCK-MODY from the Polish Registry of ... BeFree 24918535 Detail
0.001 hyperglycemia Moreover, an additive effect of GCKR rs1260326(T) and GCK (-30G) alleles conferr... BeFree 18556336 Detail
0.162 Diabetes Mellitus, Non-Insulin-Dependent Recently, the association of the natural variants rs1260326 and rs780094 of the ... BeFree 21511510 Detail
0.249 Hypertriglyceridemia Excess of rare variants in genes identified by genome-wide association study of ... GWASCAT 20657596 Detail
<0.001 Nonalcoholic Steatohepatitis Herein, we aimed to study the association between hepatic fat accumulation as as... BeFree 23275357 Detail
0.121 Chronic Kidney Diseases Follow-up of the 23 new genome-wide-significant loci (P &lt; 5 x 10(-8)) in 22,9... GWASCAT 20383146 Detail
0.129 Metabolic syndrome X A polymorphism in the GCKR gene predicted dyslipidaemia (rs1260326, OR 1.15, 95%... BeFree 18853134 Detail
0.026 diabetes mellitus The intronic single-nucleotide polymorphism (SNP) rs780094 (intron 16) and the m... BeFree 21525158 Detail
0.013 Diabetes The intronic single-nucleotide polymorphism (SNP) rs780094 (intron 16) and the m... BeFree 21525158 Detail
0.129 Hypertriglyceridemia result Genomic study in Mexicans identifies a new locus for triglycerides and refines E... GWASCAT 23505323 Detail
<0.001 Nonalcoholic Steatohepatitis Herein, we aimed to study the association between hepatic fat accumulation as as... BeFree 23275357 Detail
0.002 Nonalcoholic Steatohepatitis Herein, we aimed to study the association between hepatic fat accumulation as as... BeFree 23275357 Detail
0.127 Cardiovascular Diseases Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with... GWASCAT 21943158 Detail
0.129 Hypertriglyceridemia result [Excess of rare variants in genes identified by genome-wide association study of... GAD 20657596 Detail
0.129 Hypertriglyceridemia result Excess of rare variants in genes identified by genome-wide association study of ... GWASCAT 20657596 Detail
0.088 Diabetes Mellitus, Insulin-Dependent The study group included 129 children with GCK-MODY from the Polish Registry of ... BeFree 24918535 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001486.4(GCKR):c.1337T>C (p.Leu446Pro) AND Fasting plasma glucose level quantitative trait locus ... ClinVar Detail
NM_001486.4(GCKR):c.1337T>C (p.Leu446Pro) AND not provided ClinVar Detail
Cellular characterisation of the GCKR P446L variant associated with type 2 diabetes risk. DisGeNET Detail
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. DisGeNET Detail
[Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemi... DisGeNET Detail
Genome-wide association study of clinically defined gout identifies multiple risk loci and its assoc... DisGeNET Detail
The goal of this study was to test whether TRIB1-rs2954029 and GCKR-rs1260326 associate with lipid l... DisGeNET Detail
The common P446L polymorphism in GCKR inversely modulates fasting glucose and triglyceride levels an... DisGeNET Detail
Herein, we aimed to study the association between hepatic fat accumulation as assessed by magnetic r... DisGeNET Detail
[New loci associated with kidney function and chronic kidney disease.] DisGeNET Detail
Moreover, an additive effect of GCKR rs1260326(T) and GCK (-30G) alleles conferred lower fasting gly... DisGeNET Detail
The goal of this study was to test whether TRIB1-rs2954029 and GCKR-rs1260326 associate with lipid l... DisGeNET Detail
A polymorphism in the GCKR gene predicted dyslipidaemia (rs1260326, OR 1.15, 95% CI 1.09-1.22, p &lt... DisGeNET Detail
The study group included 129 children with GCK-MODY from the Polish Registry of Monogenic Diabetes a... DisGeNET Detail
Moreover, an additive effect of GCKR rs1260326(T) and GCK (-30G) alleles conferred lower fasting gly... DisGeNET Detail
Recently, the association of the natural variants rs1260326 and rs780094 of the glucokinase regulato... DisGeNET Detail
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia... DisGeNET Detail
Herein, we aimed to study the association between hepatic fat accumulation as assessed by magnetic r... DisGeNET Detail
Follow-up of the 23 new genome-wide-significant loci (P &lt; 5 x 10(-8)) in 22,982 replication sampl... DisGeNET Detail
A polymorphism in the GCKR gene predicted dyslipidaemia (rs1260326, OR 1.15, 95% CI 1.09-1.22, p &lt... DisGeNET Detail
The intronic single-nucleotide polymorphism (SNP) rs780094 (intron 16) and the missense SNP rs126032... DisGeNET Detail
The intronic single-nucleotide polymorphism (SNP) rs780094 (intron 16) and the missense SNP rs126032... DisGeNET Detail
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. DisGeNET Detail
Herein, we aimed to study the association between hepatic fat accumulation as assessed by magnetic r... DisGeNET Detail
Herein, we aimed to study the association between hepatic fat accumulation as assessed by magnetic r... DisGeNET Detail
Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovasc... DisGeNET Detail
[Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemi... DisGeNET Detail
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia... DisGeNET Detail
The study group included 129 children with GCK-MODY from the Polish Registry of Monogenic Diabetes a... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1260326 dbSNP
Genome
hg19
Position
chr2:27,730,940-27,730,940
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1113
Mean of sample read depth (HGVD)
31.19
Standard deviation of sample read depth (HGVD)
14.39
Number of reference allele (HGVD)
1225
Number of alternative allele (HGVD)
1001
Allele Frequency (HGVD)
0.449685534591195
Gene Symbol (HGVD)
GCKR
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1260326
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4377
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7336
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8624
East Asian Allele Counts (ExAC)
4365
East Asian Heterozygous Counts (ExAC)
2185
East Asian Homozygous Counts (ExAC)
1090
East Asian Allele Frequency (ExAC)
0.5061456400742115
Chromosome Counts in All Race (ExAC)
121246
Allele Counts in All Race (ExAC)
77943
Heterozygous Counts in All Race (ExAC)
26359
Homozygous Counts in All Race (ExAC)
25792
Allele Frequency in All Race (ExAC)
0.6428500734044834
Genome browser