Seroatlas · Human Serome Atlas

PTPN22

Tyrosine-protein phosphatase non-receptor type 22

Also known as: Lyp, Lyp1, Lyp2, PTN22_HUMAN, PTPN8

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9Y2R2
Gene
PTPN22
Ensembl
ENSG00000134242
Chromosome
1
Canonical length
807 aa
Protein class
Disease related genes, Enzymes, Human disease related genes, Plasma proteins, Potential drug targets, Predicted intracellular proteins
Subcellular location
Nucleoplasm,Vesicles,Plasma membrane

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

807 residues, UniProt reviewed canonical sequence.

>Q9Y2R2|PTPN22
     1  MDQREILQKF LDEAQSKKIT KEEFANEFLK LKRQSTKYKA DKTYPTTVAE KPKNIKKNRY
    61  KDILPYDYSR VELSLITSDE DSSYINANFI KGVYGPKAYI ATQGPLSTTL LDFWRMIWEY
   121  SVLIIVMACM EYEMGKKKCE RYWAEPGEMQ LEFGPFSVSC EAEKRKSDYI IRTLKVKFNS
   181  ETRTIYQFHY KNWPDHDVPS SIDPILELIW DVRCYQEDDS VPICIHCSAG CGRTGVICAI
   241  DYTWMLLKDG IIPENFSVFS LIREMRTQRP SLVQTQEQYE LVYNAVLELF KRQMDVIRDK
   301  HSGTESQAKH CIPEKNHTLQ ADSYSPNLPK STTKAAKMMN QQRTKMEIKE SSSFDFRTSE
   361  ISAKEELVLH PAKSSTSFDF LELNYSFDKN ADTTMKWQTK AFPIVGEPLQ KHQSLDLGSL
   421  LFEGCSNSKP VNAAGRYFNS KVPITRTKST PFELIQQRET KEVDSKENFS YLESQPHDSC
   481  FVEMQAQKVM HVSSAELNYS LPYDSKHQIR NASNVKHHDS SALGVYSYIP LVENPYFSSW
   541  PPSGTSSKMS LDLPEKQDGT VFPSSLLPTS STSLFSYYNS HDSLSLNSPT NISSLLNQES
   601  AVLATAPRID DEIPPPLPVR TPESFIVVEE AGEFSPNVPK SLSSAVKVKI GTSLEWGGTS
   661  EPKKFDDSVI LRPSKSVKLR SPKSELHQDR SSPPPPLPER TLESFFLADE DCMQAQSIET
   721  YSTSYPDTME NSTSSKQTLK TPGKSFTRSK SLKILRNMKK SICNSCPPNK PAESVQSNNS
   781  SSFLNFGFAN RFSKPKGPRN PPPTWNI

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PTPN22 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.54
Highest tissue expression
36 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 36 nTPM
  • lymph node: 19 nTPM
  • thymus: 19 nTPM
  • tonsil: 13 nTPM
  • spleen: 13 nTPM
  • appendix: 11 nTPM

Single-cell type

  • t-cells: 561 nCPM
  • neutrophil progenitors: 555 nCPM
  • nk-cells: 506 nCPM
  • innate lymphoid cells: 465 nCPM
  • thymocytes: 247 nCPM
  • neutrophils: 194 nCPM

Immune cell

  • eosinophil: 25 nTPM
  • MAIT T-cell: 20 nTPM
  • gdT-cell: 17 nTPM
  • basophil: 16 nTPM
  • T-reg: 15 nTPM
  • memory CD8 T-cell: 14 nTPM

Brain region

  • white matter: 1.8 nTPM
  • thalamus: 1.5 nTPM
  • choroid plexus: 1.4 nTPM
  • medulla oblongata: 1.3 nTPM
  • cerebral cortex: 1.2 nTPM
  • cerebellum: 1 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PTPN22.

Disease | AllUniProt

Conditions PTPN22 is implicated in, by any mechanism.

Disease | ImmuneIEDB

Conditions an epitope on PTPN22 was assayed in.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
1.09
gnomAD pLI
0
gnomAD missense Z
0.87
DepMap mean gene effect
-0.06
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PTPN22 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PTPN22 as an antibody target. Whether an autoantibody or antibody against PTPN22 could matter depends on whether native PTPN22 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PTPN22 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Source-annotated serology context

The source annotations explicitly mention antibody, autoantibody, autoantigen, or autoimmune context. This is biological context, not study-specific reactivity.

  • 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.

Canonical record: https://seroatlas.com/gene/PTPN22. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

© 2026 · Seroatlas, Discover Oregon LLC · Terms of use

Loading the interactive Seroatlas protein explorer...