chr1:114363459:G>A Detail (hg19) (PTPN22)

Information

Genome

Assembly Position
hg19 chr1:114,363,459-114,363,459
hg38 chr1:113,820,837-113,820,837 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001308297.1:c.2210-1183C>T
NM_012411.5:c.2117-1183C>T
NM_001193431.2:c.2282-1183C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.141
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600716 OMIM
HGNC 9652 HGNC
Ensembl ENSG00000134242 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2863863 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
0.145 Graves Disease We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3... BeFree 20615141 Detail
0.001 Autoimmune thyroid disease We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3... BeFree 20615141 Detail
<0.001 thyroiditis We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3... BeFree 20615141 Detail
0.001 thyroiditis We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3... BeFree 20615141 Detail
Annotation

Annotations

DescrptionSourceLinks
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2... DisGeNET Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2... DisGeNET Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2... DisGeNET Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2476599 dbSNP
Genome
hg19
Position
chr1:114,363,459-114,363,459
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs2476599
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.141
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2363
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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