PTPN22 Gene (Protein Coding)

Protein Tyrosine Phosphatase Non-Receptor Type 22

GC01M113813
GIFtS:
48
This gene encodes of member of the non-receptor class 4 subfamily of the protein-tyrosine phosphatase family. The encoded protein is a lymphoid-specific intracellular phosphatase that associates with the molecular adapter protein CBL and may be involved in regulating CBL function in the T-cell receptor signaling pathway. Mutations in this gene may be associated with a range of ... See more...

Aliases for PTPN22 Gene

Aliases for PTPN22 Gene

  • Protein Tyrosine Phosphatase Non-Receptor Type 22 2 3 5
  • Protein Tyrosine Phosphatase, Non-Receptor Type 22 (Lymphoid) 2 3
  • Hematopoietic Cell Protein-Tyrosine Phosphatase 70Z-PEP 3 4
  • Protein Tyrosine Phosphatase, Non-Receptor Type 8 2 3
  • Tyrosine-Protein Phosphatase Non-Receptor Type 22 3 4
  • PEST-Domain Phosphatase 3 4
  • PTPN8 3 4
  • PEP 3 4
  • Lymphoid-Specific Protein Tyrosine Phosphatase 3
  • Lymphoid Phosphatase 4
  • EC 3.1.3.48 4
  • PTPN22.5 3
  • PTPN22.6 3
  • PTPN22 5
  • LYP1 3
  • LYP2 3
  • Lyp1 2
  • Lyp2 2
  • LYP 3
  • Lyp 2
  • LyP 4

External Ids for PTPN22 Gene

Previous HGNC Symbols for PTPN22 Gene

  • PTPN8

Previous GeneCards Identifiers for PTPN22 Gene

  • GC01M114770
  • GC01M113238
  • GC01M113456
  • GC01M113655
  • GC01M114003
  • GC01M114157
  • GC01M114356
  • GC01M112214

Summaries for PTPN22 Gene

Entrez Gene Summary for PTPN22 Gene

  • This gene encodes of member of the non-receptor class 4 subfamily of the protein-tyrosine phosphatase family. The encoded protein is a lymphoid-specific intracellular phosphatase that associates with the molecular adapter protein CBL and may be involved in regulating CBL function in the T-cell receptor signaling pathway. Mutations in this gene may be associated with a range of autoimmune disorders including Type 1 Diabetes, rheumatoid arthritis, systemic lupus erythematosus and Graves' disease. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Mar 2009]

GeneCards Summary for PTPN22 Gene

PTPN22 (Protein Tyrosine Phosphatase Non-Receptor Type 22) is a Protein Coding gene. Diseases associated with PTPN22 include Systemic Lupus Erythematosus and Rheumatoid Arthritis. Among its related pathways are Innate Immune System and Translocation of ZAP-70 to Immunological synapse. Gene Ontology (GO) annotations related to this gene include phosphatase activity and protein tyrosine phosphatase activity. An important paralog of this gene is PTPN12.

UniProtKB/Swiss-Prot Summary for PTPN22 Gene

  • Acts as negative regulator of T-cell receptor (TCR) signaling by direct dephosphorylation of the Src family kinases LCK and FYN, ITAMs of the TCRz/CD3 complex, as well as ZAP70, VAV, VCP and other key signaling molecules (PubMed:16461343, PubMed:18056643). Associates with and probably dephosphorylates CBL. Dephosphorylates LCK at its activating 'Tyr-394' residue (PubMed:21719704). Dephosphorylates ZAP70 at its activating 'Tyr-493' residue (PubMed:16461343). Dephosphorylates the immune system activator SKAP2 (PubMed:21719704). Positively regulates toll-like receptor (TLR)-induced type 1 interferon production (PubMed:23871208). Promotes host antiviral responses mediated by type 1 interferon (By similarity). Regulates NOD2-induced pro-inflammatory cytokine secretion and autophagy (PubMed:23991106). Dephosphorylates phospho-anandamide (p-AEA), an endocannabinoid to anandamide (also called N-arachidonoylethanolamide) (By similarity).

Gene Wiki entry for PTPN22 Gene

Additional gene information for PTPN22 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTPN22 Gene

Genomics for PTPN22 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PTPN22 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPN22 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTPN22

Top Transcription factor binding sites by QIAGEN in the PTPN22 gene promoter:
  • AML1a
  • GATA-3
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for PTPN22 Gene

Latest Assembly
chr1:113,813,811-113,871,761
(GRCh38/hg38)
Size:
57,951 bases
Orientation:
Minus strand

Previous Assembly
chr1:114,356,433-114,414,381
(GRCh37/hg19 by Entrez Gene)
Size:
57,949 bases
Orientation:
Minus strand

chr1:114,356,433-114,414,381
(GRCh37/hg19 by Ensembl)
Size:
57,949 bases
Orientation:
Minus strand

Genomic View for PTPN22 Gene

Genes around PTPN22 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPN22 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPN22 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PTPN22 Gene

Proteins for PTPN22 Gene

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  • Protein details for PTPN22 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2R2-PTN22_HUMAN
    Recommended name:
    Tyrosine-protein phosphatase non-receptor type 22
    Protein Accession:
    Q9Y2R2
    Secondary Accessions:
    • A0N0K6
    • B1ALC8
    • D4NZ71
    • E9PLD8
    • E9PPI1
    • O95063
    • O95064
    • Q6IPX8
    • Q8WVM1

    Protein attributes for PTPN22 Gene

    Size:
    807 amino acids
    Molecular mass:
    91705 Da
    Quaternary structure:
    • Interacts with CSK (PubMed:15208781). Interacts with LPXN (By similarity). Interacts with CBL (PubMed:10068674). Interacts with TRAF3 (via MATH domain); the interaction promotes TRAF3 polyubiquitination (PubMed:23871208).
    Miscellaneous:
    • [Isoform 2]: Due to intron retention.
    • [Isoform 6]: Lacks most of the phosphatase domain and functions as a dominant negative isoform of the full length PTPN22.

    Three dimensional structures from OCA and Proteopedia for PTPN22 Gene

    Alternative splice isoforms for PTPN22 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTPN22 Gene

Protein Expression for PTPN22 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PTPN22 Gene

  • Phosphorylation on Ser-35 by PKC/PRKCD abrogates its ability to dephosphorylate and inactivate the SRC family kinases.
  • Ubiquitination at Lys315, Lys411, Lys429, Lys448, and Lys506
  • Modification sites at PhosphoSitePlus

Other Protein References for PTPN22 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PTPN22 Gene

Domains & Families for PTPN22 Gene

Gene Families for PTPN22 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PTPN22 Gene

InterPro:
Blocks:
  • Protein tyrosine phosphatase signature
ProtoNet:

Suggested Antigen Peptide Sequences for PTPN22 Gene

GenScript: Design optimal peptide antigens:
  • Protein tyrosine phosphatase, non-receptor type 22 (Lymphoid) (B1ALC9_HUMAN)
  • Lymphoid phosphatase (PTN22_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y2R2

UniProtKB/Swiss-Prot:

PTN22_HUMAN :
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class 4 subfamily.
Family:
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class 4 subfamily.
genes like me logo Genes that share domains with PTPN22: view

Function for PTPN22 Gene

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Molecular function for PTPN22 Gene

UniProtKB/Swiss-Prot Function:
Acts as negative regulator of T-cell receptor (TCR) signaling by direct dephosphorylation of the Src family kinases LCK and FYN, ITAMs of the TCRz/CD3 complex, as well as ZAP70, VAV, VCP and other key signaling molecules (PubMed:16461343, PubMed:18056643). Associates with and probably dephosphorylates CBL. Dephosphorylates LCK at its activating 'Tyr-394' residue (PubMed:21719704). Dephosphorylates ZAP70 at its activating 'Tyr-493' residue (PubMed:16461343). Dephosphorylates the immune system activator SKAP2 (PubMed:21719704). Positively regulates toll-like receptor (TLR)-induced type 1 interferon production (PubMed:23871208). Promotes host antiviral responses mediated by type 1 interferon (By similarity). Regulates NOD2-induced pro-inflammatory cytokine secretion and autophagy (PubMed:23991106). Dephosphorylates phospho-anandamide (p-AEA), an endocannabinoid to anandamide (also called N-arachidonoylethanolamide) (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate; Xref=Rhea:RHEA:10684, Rhea:RHEA-COMP:10136, Rhea:RHEA-COMP:10137, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:46858, ChEBI:CHEBI:82620; EC=3.1.3.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU10044, ECO:0000269|PubMed:21719704};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine phosphate = N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + phosphate; Xref=Rhea:RHEA:56532, ChEBI:CHEBI:2700, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:131894; Evidence={ECO:0000250|UniProtKB:P29352};.
UniProtKB/Swiss-Prot Induction:
By muramyl-dipeptide and lipopolysaccharide.
UniProtKB/Swiss-Prot EnzymeRegulation:
Down-regulated by phosphorylation.
GENATLAS Biochemistry:
Protein tyrosine-phosphatase non receptor type 22,lymphoid-specific,involved in regulation of the function of protooncogene CBL

Enzyme Numbers (IUBMB) for PTPN22 Gene

Phenotypes From GWAS Catalog for PTPN22 Gene

Gene Ontology (GO) - Molecular Function for PTPN22 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004725 protein tyrosine phosphatase activity IEA,TAS --
GO:0004726 non-membrane spanning protein tyrosine phosphatase activity IBA 21873635
GO:0005515 protein binding IPI 10068674
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PTPN22: view
genes like me logo Genes that share phenotypes with PTPN22: view

Human Phenotype Ontology for PTPN22 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTPN22 Gene

MGI Knock Outs for PTPN22:

Animal Models for research

  • Taconic Biosciences Mouse Models for PTPN22

miRNA for PTPN22 Gene

miRTarBase miRNAs that target PTPN22

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPN22

No data available for Transcription Factor Targets and HOMER Transcription for PTPN22 Gene

Localization for PTPN22 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPN22 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTPN22 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
  • Nucleoplasm (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PTPN22 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 10940933
GO:0005737 cytoplasm IEA,TAS 20401454
GO:0005829 cytosol TAS --
GO:0009898 cytoplasmic side of plasma membrane IEA,IDA 10940933
GO:0048471 perinuclear region of cytoplasm IDA 10068674
genes like me logo Genes that share ontologies with PTPN22: view

Pathways & Interactions for PTPN22 Gene

genes like me logo Genes that share pathways with PTPN22: view

Pathways by source for PTPN22 Gene

1 GeneGo (Thomson Reuters) pathway for PTPN22 Gene
  • Anandamide biosynthesis and metabolism
2 Qiagen pathways for PTPN22 Gene
  • CTLA4 Signaling
  • Epithelial Adherens Junctions
1 Cell Signaling Technology pathway for PTPN22 Gene

SIGNOR curated interactions for PTPN22 Gene

Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for PTPN22 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002230 positive regulation of defense response to virus by host IEA,IBA 21873635
GO:0002376 immune system process IEA --
GO:0002685 regulation of leukocyte migration IEA --
GO:0006470 protein dephosphorylation IEA,TAS 21044313
GO:0006914 autophagy IEA --
genes like me logo Genes that share ontologies with PTPN22: view

Drugs & Compounds for PTPN22 Gene

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(4) Drugs for PTPN22 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Phosphate Experimental Pharma 0

(1) Additional Compounds for PTPN22 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PTPN22: view

Transcripts for PTPN22 Gene

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mRNA/cDNA for PTPN22 Gene

4 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPN22

Alternative Splicing Database (ASD) splice patterns (SP) for PTPN22 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^ 22
SP1: - - - -
SP2: - -
SP3: -
SP4: - - - - - - - - - - - - - - -
SP5:

Relevant External Links for PTPN22 Gene

GeneLoc Exon Structure for
PTPN22

Expression for PTPN22 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTPN22 Gene

mRNA expression in normal human tissues for PTPN22 Gene
mRNA expression by GTEx for PTPN22 GenemRNA expression by BioGPS for PTPN22 Gene

mRNA differential expression in normal tissues according to GTEx for PTPN22 Gene

This gene is overexpressed in Whole Blood (x13.5).

Protein differential expression in normal tissues from HIPED for PTPN22 Gene

This gene is overexpressed in CD8 Tcells (48.3) and Spleen (14.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTPN22 Gene



Protein tissue co-expression partners for PTPN22 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTPN22

SOURCE GeneReport for Unigene cluster for PTPN22 Gene:

Hs.535276

mRNA Expression by UniProt/SwissProt for PTPN22 Gene:

Q9Y2R2-PTN22_HUMAN
Tissue specificity: Expressed in bone marrow, B and T-cells, PBMCs, natural killer cells, monocytes, dendritic cells and neutrophils (PubMed:15208781). Both isoform 1 and 4 are predominantly expressed in lymphoid tissues and cells. Isoform 1 is expressed in thymocytes and both mature B and T-cells.

Evidence on tissue expression from TISSUES for PTPN22 Gene

  • Thyroid gland(2.9)
  • Spleen(2.8)
  • Blood(2.8)
  • Lymph node(2.7)
  • Bone marrow(2.5)
  • Pancreas(2.5)
  • Heart(2.3)
  • Intestine(2.3)
  • Skin(2.3)
  • Muscle(2.2)
  • Adrenal gland(2)
  • Nervous system(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPN22 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pituitary gland
  • sinus
  • skull
  • tooth
Thorax:
  • bronchus
  • esophagus
  • heart
  • lung
  • trachea
Abdomen:
  • kidney
  • stomach
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with PTPN22: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for PTPN22 Gene

Orthologs for PTPN22 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPN22 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PTPN22 30 31
  • 99.79 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PTPN22 30 31
  • 86.8 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PTPN22 30 31
  • 86.65 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ptpn22 30 17 31
  • 79.95 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ptpn22 30
  • 78.65 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia PTPN22 31
  • 77 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PTPN22 31
  • 63 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PTPN22 30 31
  • 59.5 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PTPN22 31
  • 42 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ptpn22 30
  • 54.03 (n)
Zebrafish
(Danio rerio)
 Actinopterygii ptpn22 31
  • 30 (a)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea T22C1.8 32
  • 34 (a)
ZK616.7 32
  • 33 (a)
M04G7.2 32
  • 31 (a)
Y41D4A.5 31 32
  • 25 (a)
 OneToMany
Species where no ortholog for PTPN22 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PTPN22 Gene

ENSEMBL:
Gene Tree for PTPN22 (if available)
TreeFam:
Gene Tree for PTPN22 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTPN22: view image

Paralogs for PTPN22 Gene

Paralogs for PTPN22 Gene

(67) SIMAP similar genes for PTPN22 Gene using alignment to 7 proteins:

  • PTN22_HUMAN
  • E9PLD8_HUMAN
  • E9PM87_HUMAN
  • E9PMK2_HUMAN
  • E9PMT0_HUMAN
  • F5H2S8_HUMAN
  • G3K0T4_HUMAN
genes like me logo Genes that share paralogs with PTPN22: view

Variants for PTPN22 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTPN22 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1011039090 Likely Benign: not provided 113,859,053(-) G/A
NM_015967.7(PTPN22):c.222C>T (p.Ser74=) 		SYNONYMOUS
rs1045662456 Likely Benign: not provided 113,837,852(-) C/T
NM_015967.7(PTPN22):c.1548G>A (p.Lys516=) 		SYNONYMOUS
rs114092230 Likely Benign: not provided 113,837,773(-) T/C
NM_015967.7(PTPN22):c.1627A>G (p.Ser543Gly) 		MISSENSE
rs149915690 Benign: not provided 113,834,363(-) A/T
NM_015967.7(PTPN22):c.1971T>A (p.Gly657=) 		SYNONYMOUS_VARIANT,INTRON
rs183145687 Benign: not provided 113,830,008(-) G/C
NM_015967.7(PTPN22):c.2075C>G (p.Ser692Cys) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PTPN22 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PTPN22 Gene

Variant ID Type Subtype PubMed ID
esv23869 CNV loss 19812545
esv3587239 CNV loss 21293372
esv3587240 CNV loss 21293372
esv3587250 CNV loss 21293372
esv3587251 CNV loss 21293372
nsv473902 CNV novel sequence insertion 20440878
nsv831093 CNV loss 17160897
nsv951398 CNV duplication 24416366

Variation tolerance for PTPN22 Gene

Residual Variation Intolerance Score: 86.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.56; 55.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPN22 Gene

Human Gene Mutation Database (HGMD)
PTPN22
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTPN22

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTPN22 Gene

Disorders for PTPN22 Gene

MalaCards: The human disease database

(58) MalaCards diseases for PTPN22 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PTN22_HUMAN
  • Systemic lupus erythematosus (SLE) [MIM:152700]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269 PubMed:15273934}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.
  • Diabetes mellitus, insulin-dependent (IDDM) [MIM:222100]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269 PubMed:15004560}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.
  • Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269 PubMed:15208781}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.
  • Vitiligo (VTLG) [MIM:193200]: A pigmentary disorder of the skin and mucous membranes. It is characterized by circumscribed depigmented macules and patches, commonly on extensor aspects of extremities, on the face or neck and in skin folds. Vitiligo is a progressive disorder in which some or all of the melanocytes in the affected skin are selectively destroyed. It is a multifactorial disorder with a complex etiology probably including autoimmune mechanisms, and is associated with an elevated risk of other autoimmune diseases. {ECO:0000269 PubMed:16015369}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.

Additional Disease Information for PTPN22

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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No data available for Genatlas for PTPN22 Gene

Publications for PTPN22 Gene

  1. Systematic search for single nucleotide polymorphisms in a lymphoid tyrosine phosphatase gene (PTPN22): association between a promoter polymorphism and type 1 diabetes in Asian populations. (PMID: 16470599) Kawasaki E … Eguchi K (American journal of medical genetics. Part A 2006) 3 23 41 74
  2. A single-nucleotide polymorphism in the gene encoding lymphoid protein tyrosine phosphatase (PTPN22) confers susceptibility to generalised vitiligo. (PMID: 16015369) Cantón I … Kemp EH (Genes and immunity 2005) 3 4 23 41
  3. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. (PMID: 15208781) Begovich AB … Gregersen PK (American journal of human genetics 2004) 3 4 23 41
  4. The codon 620 tryptophan allele of the lymphoid tyrosine phosphatase (LYP) gene is a major determinant of Graves' disease. (PMID: 15531553) Velaga MR … Pearce SH (The Journal of clinical endocrinology and metabolism 2004) 3 4 23 41
  5. Cloning and characterization of a lymphoid-specific, inducible human protein tyrosine phosphatase, Lyp. (PMID: 10068674) Cohen S … Roifman CM (Blood 1999) 2 3 4 23

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