chr11:48123823:A>C Detail (hg38) (PTPRJ)

Information

Genome

Assembly Position
hg19 chr11:48,145,375-48,145,375 View the variant detail on this assembly version.
hg38 chr11:48,123,823-48,123,823

HGVS

Type Transcript Protein
RefSeq NM_002843.3:c.827A>C NP_002834.3:p.Gln276Pro
NM_001098503.1:c.827A>C NP_001091973.1:p.Gln276Pro
Ensemble ENST00000418331.7:c.827A>C ENST00000418331.7:p.Gln276Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.211
ToMMo:0.207
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.266

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
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 tgv42476864 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2002-07-01 no assertion criteria provided Carcinoma of colon somatic Detail
Benign 2022-05-04 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-12-10 criteria provided, single submitter colorectal cancer unknown Detail
Likely benign 2019-10-23 criteria provided, single submitter PTPRJ-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.122 colon carcinoma NA CLINVAR Detail
0.003 Thyroid Neoplasm We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons... BeFree 15378013 Detail
<0.001 Malignant neoplasm of thyroid We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human ... BeFree 15384144 Detail
0.006 Thyroid carcinoma We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human ... BeFree 15384144 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002843.4(PTPRJ):c.827A>C (p.Gln276Pro) AND Carcinoma of colon ClinVar Detail
NM_002843.4(PTPRJ):c.827A>C (p.Gln276Pro) AND not specified ClinVar Detail
NM_002843.4(PTPRJ):c.827A>C (p.Gln276Pro) AND Colorectal cancer ClinVar Detail
NM_002843.4(PTPRJ):c.827A>C (p.Gln276Pro) AND PTPRJ-related disorder ClinVar Detail
NA DisGeNET Detail
We also looked for the Gln276Pro, Arg326Gln and Asp872Glu polymorphisms in exons 5, 6 and 13 of PTPR... DisGeNET Detail
We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTP... 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
-
dbSNP
rs1566734 dbSNP
Genome
hg38
Position
chr11:48,123,823-48,123,823
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
965
Mean of sample read depth (HGVD)
24.99
Standard deviation of sample read depth (HGVD)
16.96
Number of reference allele (HGVD)
1522
Number of alternative allele (HGVD)
408
Allele Frequency (HGVD)
0.21139896373056996
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))
rs1566734
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2072
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3472
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
Homozygous Counts in All Race (ExAC)
1993
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
2292
East Asian Heterozygous Counts (ExAC)
1678
East Asian Homozygous Counts (ExAC)
307
East Asian Allele Frequency (ExAC)
0.2655236329935125
Chromosome Counts in All Race (ExAC)
121116
Allele Counts in All Race (ExAC)
20511
Heterozygous Counts in All Race (ExAC)
16525
Allele Frequency in All Race (ExAC)
0.16935004458535619
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