chr4:86785353:T>G Detail (hg38) (PTPN13)

Information

Genome

Assembly Position
hg19 chr4:87,706,506-87,706,506 View the variant detail on this assembly version.
hg38 chr4:86,785,353-86,785,353

HGVS

Type Transcript Protein
RefSeq NM_080684.2:c.5668T>G NP_542415.1:p.Tyr1890Asp
NM_080683.2:c.6241T>G NP_542414.1:p.Tyr2081Asp
NM_006264.2:c.6184T>G NP_006255.1:p.Tyr2062Asp
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.472
ToMMo:0.444
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.408

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600267 OMIM
HGNC 9646 HGNC
Ensembl ENSG00000163629 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17758944 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
0.022 Malignant neoplasm of breast Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.008 breast carcinoma Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.127 Malignant neoplasm of breast Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN... BeFree 24338422 Detail
0.001 breast carcinoma Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN... BeFree 24338422 Detail
0.004 breast carcinoma Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN... BeFree 24338422 Detail
0.001 Malignant neoplasm of breast Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN... BeFree 24338422 Detail
Annotation

Annotations

DescrptionSourceLinks
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN13, and rs7003146 in... DisGeNET Detail
Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN13, and rs7003146 in... DisGeNET Detail
Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN13, and rs7003146 in... DisGeNET Detail
Our results confirmed the association of rs7014346 in POU5F1P1, rs989902 in PTPN13, and rs7003146 in... 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
chr4:86,785,353-86,785,353
Variant Type
snv
Reference Allele
T
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1024
Mean of sample read depth (HGVD)
17.52
Standard deviation of sample read depth (HGVD)
18.16
Number of reference allele (HGVD)
1081
Number of alternative allele (HGVD)
966
Allele Frequency (HGVD)
0.47191011235955055
Gene Symbol (HGVD)
PTPN13
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))
rs989902
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4435
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7433
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8472
East Asian Allele Counts (ExAC)
3459
East Asian Heterozygous Counts (ExAC)
2017
East Asian Homozygous Counts (ExAC)
721
East Asian Allele Frequency (ExAC)
0.40828611898017
Chromosome Counts in All Race (ExAC)
117912
Allele Counts in All Race (ExAC)
50887
Heterozygous Counts in All Race (ExAC)
27433
Homozygous Counts in All Race (ExAC)
11727
Allele Frequency in All Race (ExAC)
0.43156760974285907
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