chr11:48125070:G>A Detail (hg38) (PTPRJ)

Information

Genome

Assembly Position
hg19 chr11:48,146,622-48,146,622 View the variant detail on this assembly version.
hg38 chr11:48,125,070-48,125,070

HGVS

Type Transcript Protein
RefSeq NM_002843.3:c.977G>A NP_002834.3:p.Arg326Gln
NM_001098503.1:c.977G>A NP_001091973.1:p.Arg326Gln
Ensemble ENST00000418331.7:c.977G>A ENST00000418331.7:p.Arg326Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.217
ToMMo:0.207
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.265

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600925 OMIM
HGNC 9673 HGNC
Ensembl ENSG00000149177 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv42476929 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Malignant tumor of colon Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homo... BeFree 19672627 Detail
0.122 colon carcinoma Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homo... BeFree 19672627 Detail
0.022 Malignant neoplasm of breast Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.003 Thyroid Neoplasm We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons... BeFree 15378013 Detail
0.001 colorectal carcinoma Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homo... BeFree 19672627 Detail
<0.001 Malignant neoplasm of thyroid We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human ... BeFree 15384144 Detail
0.003 colorectal cancer Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homo... BeFree 19672627 Detail
0.008 breast carcinoma Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.006 Thyroid carcinoma We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human ... BeFree 15384144 Detail
Annotation

Annotations

DescrptionSourceLinks
Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homologue of the mouse S... DisGeNET Detail
Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homologue of the mouse S... DisGeNET Detail
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons 5, 6 and 13 of PTPR... DisGeNET Detail
Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homologue of the mouse S... DisGeNET Detail
We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTP... DisGeNET Detail
Compared with the major homozygotes at the Arg326Gln SNP in PTPRJ, a likely homologue of the mouse S... DisGeNET Detail
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTP... 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
hg38
Position
chr11:48,125,070-48,125,070
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
115.95
Standard deviation of sample read depth (HGVD)
53.90
Number of reference allele (HGVD)
1895
Number of alternative allele (HGVD)
525
Allele Frequency (HGVD)
0.21694214876033058
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))
rs1503185
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.207
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3469
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
2283
East Asian Heterozygous Counts (ExAC)
1671
East Asian Homozygous Counts (ExAC)
306
East Asian Allele Frequency (ExAC)
0.2646036161335188
Chromosome Counts in All Race (ExAC)
121294
Allele Counts in All Race (ExAC)
21917
Heterozygous Counts in All Race (ExAC)
17443
Homozygous Counts in All Race (ExAC)
2237
Allele Frequency in All Race (ExAC)
0.18069319174897358
Genome browser