chr1:226550829:T>C Detail (hg19) (PARP1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:226,550,829-226,550,829 |
| hg38 | chr1:226,363,128-226,363,128 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001618.3:c.2819A>G | NP_001609.2:p.Lys940Arg |
| Ensemble | ENST00000677203.1:c.2690A>G | ENST00000677203.1:p.Lys897Arg |
| ENST00000366794.10:c.2819A>G | ENST00000366794.10:p.Lys940Arg |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.059 |
| ToMMo:0.070 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.030 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2019-11-16 | criteria provided, single submitter | PARP1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.011 | colorectal cancer | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.003 | Malignant tumor of colon | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| <0.001 | Malignant tumor of colon | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.003 | colon carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.033 | colorectal cancer | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| <0.001 | colon carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| <0.001 | Rectal Carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.003 | colorectal carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| <0.001 | Rectal Carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.014 | colorectal carcinoma | We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... | BeFree | 18006925 | Detail |
| 0.010 | colorectal carcinoma | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
| 0.030 | colorectal cancer | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
| 0.058 | colorectal cancer | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
| 0.013 | colorectal carcinoma | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
| 0.006 | colorectal carcinoma | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
| 0.062 | colorectal cancer | In the present study, we investigated the role in colorectal cancer of single-nu... | BeFree | 18006925 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001618.4(PARP1):c.2819A>G (p.Lys940Arg) AND PARP1-related disorder | ClinVar | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | DisGeNET | Detail |
| In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... | 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
- -
- Genome
- hg19
- Position
- chr1:226,550,829-226,550,829
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1203
- Mean of sample read depth (HGVD)
- 127.74
- Standard deviation of sample read depth (HGVD)
- 57.07
- Number of reference allele (HGVD)
- 2265
- Number of alternative allele (HGVD)
- 141
- Allele Frequency (HGVD)
- 0.05860349127182045
- Gene Symbol (HGVD)
- PARP1
- 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))
- rs3219145
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0703
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1179
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8650
- East Asian Allele Counts (ExAC)
- 260
- East Asian Heterozygous Counts (ExAC)
- 246
- East Asian Homozygous Counts (ExAC)
- 7
- East Asian Allele Frequency (ExAC)
- 0.03005780346820809
- Chromosome Counts in All Race (ExAC)
- 121400
- Allele Counts in All Race (ExAC)
- 1634
- Heterozygous Counts in All Race (ExAC)
- 1498
- Homozygous Counts in All Race (ExAC)
- 68
- Allele Frequency in All Race (ExAC)
- 0.013459637561779243
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