PTPN2
Chr 18protein tyrosine phosphatase non-receptor type 2
Also known as: PTN2, PTPT, TC-PTP, TC45, TC48, TCELLPTP, TCPTP
This protein is a non-receptor tyrosine phosphatase that dephosphorylates multiple receptor and non-receptor protein tyrosine kinases, negatively regulating signaling pathways involved in immune system development, inflammatory responses, cell proliferation, and glucose homeostasis. Mutations cause autosomal recessive early-onset inflammatory bowel disease and T-cell immunodeficiency, typically presenting in infancy or early childhood. The gene is highly constrained against loss-of-function variants (pLI = 1.0, LOEUF = 0.18), indicating intolerance to protein-truncating mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Mild missense constraint
ClinVar Variant Classifications
161 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 83 | 0 | 83 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 36 | 9 | 0 | 45 |
Likely Benign | 0 | 1 | 0 | 4 | 5 |
Benign | 0 | 2 | 1 | 0 | 3 |
Conflicting | — | 1 | |||
| Total | 0 | 39 | 95 | 4 | 139 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PTPN2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
External Resources
Links to major genomics databases and tools