chr1:114394689:C>T Detail (hg19) (PTPN22)

Information

Genome

Assembly Position
hg19 chr1:114,394,689-114,394,689
hg38 chr1:113,852,067-113,852,067 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001193431.2:c.788G>A NP_001180360.1:p.Arg263Gln
NM_015967.6:c.788G>A NP_057051.3:p.Arg263Gln
NM_012411.5:c.750+2404G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

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 tgv2864931 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
0.226 Autoimmune Diseases Two independent functional missense single nucleotide polymorphisms (SNPs) locat... BeFree 23559857 Detail
0.524 rheumatoid arthritis The PTPN22 R263Q polymorphism is a risk factor for rheumatoid arthritis in Cauca... BeFree 21279993 Detail
0.276 Lupus Erythematosus, Systemic Recently, a functional PTPN22 variant (R263Q; rs33996649) was found to be associ... BeFree 21279993 Detail
Annotation

Annotations

DescrptionSourceLinks
Two independent functional missense single nucleotide polymorphisms (SNPs) located within the PTPN22... DisGeNET Detail
The PTPN22 R263Q polymorphism is a risk factor for rheumatoid arthritis in Caucasian case-control sa... DisGeNET Detail
Recently, a functional PTPN22 variant (R263Q; rs33996649) was found to be associated with systemic l... 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
rs33996649 dbSNP
Genome
hg19
Position
chr1:114,394,689-114,394,689
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs33996649
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8550
East Asian Allele Counts (ExAC)
4
East Asian Heterozygous Counts (ExAC)
4
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
4.6783625730994154E-4
Chromosome Counts in All Race (ExAC)
116786
Allele Counts in All Race (ExAC)
2043
Heterozygous Counts in All Race (ExAC)
1989
Homozygous Counts in All Race (ExAC)
27
Allele Frequency in All Race (ExAC)
0.017493535184011783
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