chr11:48166267:G>C Detail (hg19) (PTPRJ)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr11:48,166,267-48,166,267 |
| hg38 | chr11:48,144,715-48,144,715 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002843.3:c.2616G>C | NP_002834.3:p.Glu872Asp |
| Ensemble | ENST00000418331.7:c.2616G>C | ENST00000418331.7:p.Glu872Asp |
| ENST00000698881.1:c.2958G>C | ENST00000698881.1:p.Glu986Asp |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.498 |
| ToMMo:0.503 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.421 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.003 | Thyroid Neoplasm | We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons... | BeFree | 15378013 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons 5, 6 and 13 of PTPR... | 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
- chr11:48,166,267-48,166,267
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1200
- Mean of sample read depth (HGVD)
- 81.55
- Standard deviation of sample read depth (HGVD)
- 36.62
- Number of reference allele (HGVD)
- 1203
- Number of alternative allele (HGVD)
- 1195
- Allele Frequency (HGVD)
- 0.4983319432860717
- Gene Symbol (HGVD)
- PTPRJ
- 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))
- rs4752904
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5031
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8431
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8616
- East Asian Allele Counts (ExAC)
- 3630
- East Asian Heterozygous Counts (ExAC)
- 2068
- East Asian Homozygous Counts (ExAC)
- 781
- East Asian Allele Frequency (ExAC)
- 0.4213091922005571
- Chromosome Counts in All Race (ExAC)
- 121200
- Allele Counts in All Race (ExAC)
- 62451
- Heterozygous Counts in All Race (ExAC)
- 27645
- Homozygous Counts in All Race (ExAC)
- 17403
- Allele Frequency in All Race (ExAC)
- 0.5152722772277227
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