chr3:49395757:G>A Detail (hg19) (GPX1)

Information

Genome

Assembly Position
hg19 chr3:49,395,757-49,395,757
hg38 chr3:49,358,324-49,358,324 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000581.2:c.-46C>T
Ensemble ENST00000419783.3:c.-46C>T
ENST00000496791.3:c.-46C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.074
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.088

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 tgv12407542 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Stage IV Prostate Cancer AJCC v7 Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Stage IV Prostate Cancer AJCC v7 Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Stage IV Prostate Cancer AJCC v7 Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Stage IV Prostate Carcinoma Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Stage IV Prostate Carcinoma Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Stage IV Prostate Carcinoma Seven interactions were statistically significant after adjusting for multiple t... BeFree 25315963 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 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
<0.001 Kashin-Beck Disease Haplotypes TCC, TTC and TTT of rs1050450, rs1800668 and rs3811699 in GPX1 showed... BeFree 24058403 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000581.4(GPX1):c.-46C>T AND not provided ClinVar Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Seven interactions were statistically significant after adjusting for multiple testing (FDR Q-value ... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... 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
Haplotypes TCC, TTC and TTT of rs1050450, rs1800668 and rs3811699 in GPX1 showed a significant assoc... 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
rs1800668 dbSNP
Genome
hg19
Position
chr3:49,395,757-49,395,757
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs1800668
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0741
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1241
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
226
East Asian Allele Counts (ExAC)
20
East Asian Heterozygous Counts (ExAC)
20
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.08849557522123894
Chromosome Counts in All Race (ExAC)
6474
Allele Counts in All Race (ExAC)
2252
Heterozygous Counts in All Race (ExAC)
1560
Homozygous Counts in All Race (ExAC)
346
Allele Frequency in All Race (ExAC)
0.34785295026258883
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