chr3:49394834:G>A Detail (hg19) (GPX1)

Information

Genome

Assembly Position
hg19 chr3:49,394,834-49,394,834
hg38 chr3:49,357,401-49,357,401 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_201397.1:c.*581C>T
NM_000581.2:c.599C>T NP_000572.2:p.Pro200Leu
Ensemble ENST00000419349.3:c.*581C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.077
ToMMo:0.074
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.063

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 138320 OMIM
HGNC 4553 HGNC
Ensembl ENSG00000233276 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12407284 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 1999-01-01 no assertion criteria provided GLUTATHIONE PEROXIDASE POLYMORPHISM germline Detail
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
Benign 2021-08-16 criteria provided, single submitter Gluthathione peroxidase deficiency unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.223 Hypertensive disease After adjustment for age, body mass index, fibrinogen level and high sensitivity... BeFree 23701472 Detail
<0.001 Prostatic Diseases Three SNPs, namely GPx1 rs1050450, SEL15 rs5845 and CAT rs1001179, were signific... BeFree 23363810 Detail
0.025 Diabetes Mellitus, Non-Insulin-Dependent After adjustment for age, body mass index, fibrinogen level and high sensitivity... BeFree 23701472 Detail
0.045 Malignant neoplasm of prostate In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
0.002 Carcinoma of lung We evaluated potential associations between gene variants that result in reduced... BeFree 17548672 Detail
0.004 prostate carcinoma In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
0.013 Malignant neoplasm of prostate The rs1050450 C &gt; T polymorphism of GPX1 is associated with the risk of bladd... BeFree 23975365 Detail
0.003 Carcinoma of lung We evaluated potential associations between gene variants that result in reduced... BeFree 17548672 Detail
0.004 prostate carcinoma The rs1050450 C &gt; T polymorphism of GPX1 is associated with the risk of bladd... BeFree 23975365 Detail
0.120 Peripheral neuropathy Association between the rs1050450 glutathione peroxidase-1 (C &gt; T) gene varia... BeFree 21185702 Detail
0.005 prostate carcinoma In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
0.013 Malignant neoplasm of prostate In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
<0.001 Kashin-Beck Disease In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs180066... BeFree 24058403 Detail
<0.001 Kashin-Beck Disease In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs180066... BeFree 24058403 Detail
0.007 Restenosis Minor alleles of polymorphisms 298G/T of the eNOS gene and 599C/T of the GPx-1 g... BeFree 22890915 Detail
0.087 Malignant neoplasm of prostate In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
<0.001 Kashin-Beck Disease Haplotypes TCC, TTC and TTT of rs1050450, rs1800668 and rs3811699 in GPX1 showed... BeFree 24058403 Detail
0.003 Coronary heart disease Our results confirmed that GPX1 rs1050450 was associated with susceptibility to ... BeFree 23906684 Detail
0.022 Malignant neoplasm of lung We evaluated potential associations between gene variants that result in reduced... BeFree 17548672 Detail
0.002 Carcinoma of bladder The present meta-analysis provides evidence that the GPX1 rs1050450 C &gt; T pol... BeFree 23975365 Detail
0.002 Carcinoma of lung However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and... BeFree 18298806 Detail
0.026 Malignant neoplasm of lung However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and... BeFree 18298806 Detail
0.004 prostate carcinoma However, the GPx1 rs1050450 allele T in association with prostate cancer recorde... BeFree 23363810 Detail
0.066 Malignant neoplasm of lung However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and... BeFree 18298806 Detail
0.026 prostate carcinoma In the present study we investigated the association of a number of polymorphic ... BeFree 24610081 Detail
0.012 Malignant neoplasm of urinary bladder The present meta-analysis provides evidence that the GPX1 rs1050450 C &gt; T pol... BeFree 23975365 Detail
0.009 Carcinoma of lung However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and... BeFree 18298806 Detail
0.026 Malignant neoplasm of lung We evaluated potential associations between gene variants that result in reduced... BeFree 17548672 Detail
<0.001 Restenosis Minor alleles of polymorphisms 298G/T of the eNOS gene and 599C/T of the GPx-1 g... BeFree 22890915 Detail
0.006 diabetes mellitus Association between the rs1050450 glutathione peroxidase-1 (C &gt; T) gene varia... BeFree 21185702 Detail
0.013 Malignant neoplasm of prostate However, the GPx1 rs1050450 allele T in association with prostate cancer recorde... BeFree 23363810 Detail
<0.001 Prostatic Diseases Three SNPs, namely GPx1 rs1050450, SEL15 rs5845 and CAT rs1001179, were signific... BeFree 23363810 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000581.4(GPX1):c.599C>T (p.Pro200Leu) AND GLUTATHIONE PEROXIDASE POLYMORPHISM ClinVar Detail
NM_000581.4(GPX1):c.599C>T (p.Pro200Leu) AND not provided ClinVar Detail
NM_000581.4(GPX1):c.599C>T (p.Pro200Leu) AND Gluthathione peroxidase deficiency ClinVar Detail
After adjustment for age, body mass index, fibrinogen level and high sensitivity C-reactive protein ... DisGeNET Detail
Three SNPs, namely GPx1 rs1050450, SEL15 rs5845 and CAT rs1001179, were significantly associated wit... DisGeNET Detail
After adjustment for age, body mass index, fibrinogen level and high sensitivity C-reactive protein ... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
We evaluated potential associations between gene variants that result in reduced neutralization of r... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
The rs1050450 C &gt; T polymorphism of GPX1 is associated with the risk of bladder but not prostate ... DisGeNET Detail
We evaluated potential associations between gene variants that result in reduced neutralization of r... DisGeNET Detail
The rs1050450 C &gt; T polymorphism of GPX1 is associated with the risk of bladder but not prostate ... DisGeNET Detail
Association between the rs1050450 glutathione peroxidase-1 (C &gt; T) gene variant and peripheral ne... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs1800668 and rs3811699), Tr... DisGeNET Detail
In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs1800668 and rs3811699), Tr... DisGeNET Detail
Minor alleles of polymorphisms 298G/T of the eNOS gene and 599C/T of the GPx-1 gene are associated w... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
Haplotypes TCC, TTC and TTT of rs1050450, rs1800668 and rs3811699 in GPX1 showed a significant assoc... DisGeNET Detail
Our results confirmed that GPX1 rs1050450 was associated with susceptibility to CHD in Chinese and I... DisGeNET Detail
We evaluated potential associations between gene variants that result in reduced neutralization of r... DisGeNET Detail
The present meta-analysis provides evidence that the GPX1 rs1050450 C &gt; T polymorphism leads to a... DisGeNET Detail
However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and the C-Allele of EPH... DisGeNET Detail
However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and the C-Allele of EPH... DisGeNET Detail
However, the GPx1 rs1050450 allele T in association with prostate cancer recorded a significantly hi... DisGeNET Detail
However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and the C-Allele of EPH... DisGeNET Detail
In the present study we investigated the association of a number of polymorphic changes in antioxida... DisGeNET Detail
The present meta-analysis provides evidence that the GPX1 rs1050450 C &gt; T polymorphism leads to a... DisGeNET Detail
However, this study provides some support for the T-Allel of GPX1(Pro200Leu) and the C-Allele of EPH... DisGeNET Detail
We evaluated potential associations between gene variants that result in reduced neutralization of r... DisGeNET Detail
Minor alleles of polymorphisms 298G/T of the eNOS gene and 599C/T of the GPx-1 gene are associated w... DisGeNET Detail
Association between the rs1050450 glutathione peroxidase-1 (C &gt; T) gene variant and peripheral ne... DisGeNET Detail
However, the GPx1 rs1050450 allele T in association with prostate cancer recorded a significantly hi... DisGeNET Detail
Three SNPs, namely GPx1 rs1050450, SEL15 rs5845 and CAT rs1001179, were significantly associated wit... 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
rs1050450 dbSNP
Genome
hg19
Position
chr3:49,394,834-49,394,834
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
LowQual
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
Filtering Status (HGVD)
VQSRTrancheSNP99.90to100.00
# of samples (HGVD)
537
Mean of sample read depth (HGVD)
8.25
Standard deviation of sample read depth (HGVD)
16.50
Number of reference allele (HGVD)
991
Number of alternative allele (HGVD)
83
Allele Frequency (HGVD)
0.07728119180633147
Gene Symbol (HGVD)
GPX1
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))
rs1050450
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0739
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1239
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8474
East Asian Allele Counts (ExAC)
535
East Asian Heterozygous Counts (ExAC)
507
East Asian Homozygous Counts (ExAC)
14
East Asian Allele Frequency (ExAC)
0.06313429313193297
Chromosome Counts in All Race (ExAC)
114832
Allele Counts in All Race (ExAC)
32216
Heterozygous Counts in All Race (ExAC)
22122
Homozygous Counts in All Race (ExAC)
5047
Allele Frequency in All Race (ExAC)
0.2805489758952208
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