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 |
![]() |
Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
![]() |
2018-11-12 | criteria provided, single submitter | not provided |
![]() |
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
Descrption | Source | Links |
---|---|---|
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
Genome browser