PTPN2 (P17706) variants and mutations

PTPN2 (also known as P17706) is a human protein-coding gene encoding a tyrosine-protein phosphatase non-receptor type 2 protein. It restrains cytokine and growth-factor signaling by dephosphorylating JAK-STAT and related pathway components. Haploinsufficiency can cause early-onset immune dysregulation with autoimmunity, while common variants influence inflammatory bowel disease and other autoimmune risks. This analysis covers 651 PTPN2 variants and mutations. Of these, 81% have computational variant effect predictions. Disease context includes rheumatoid arthritis, type 1 diabetes mellitus, and inflammatory bowel disease. Example PTPN2 variants include P2H, P2L, and P2R.

Variant analysis overview

Gene: PTPN2
Protein: P17706
UniProt accession: P17706
Organism: Homo sapiens
Variants analyzed: 651
Variant scope: all variants
Completed: 2026-08-21

Variant and mutation evidence

Variant composition: 412 unspecified-consequence records; 83 synonymous variants; 120 missense variants; 23 frameshift variants; 7 in-frame deletions; 6 stop-gained variants; 1 splice-region variants; 1 in-frame insertions; 1 protein altering variant
Prediction scores: 525 variants have prediction scores (81% of the analyzed set).

Clinical, disease, and population context

Disease context: 25 disease associations are represented. Top associations: rheumatoid arthritis, type 1 diabetes mellitus, inflammatory bowel disease, Crohn disease, autoimmune disease, psoriasis, systemic lupus erythematosus, hypothyroidism, Arthritis, arthritic joint disease, celiac disease, common variable immunodeficiency.

Protein structure and variant hotspots

Protein features: 1 domains; 3 binding sites; 8 post-translational modification sites.
Structural context: 341 variants have structural context.
PTM context: 10 variants overlap post-translational modification sites.

Data sources

Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.

Notable PTPN2 variants

Examples include P2H, P2L, P2R, P2S, T3A, T3I, T3S, T4A. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.

PTPN2 analysis run — PTPN2 (651 variants) — completed 2026-08-21