PTPN23
Protein Tyrosine Phosphatase Non-Receptor Type 23
Gene Information Card
| Symbol | PTPN23 |
|---|---|
| Full Name | Protein Tyrosine Phosphatase Non-Receptor Type 23 |
| Gene Type | protein-coding |
| Chromosomal Location | 3p21.31 |
| NCBI Gene ID | 25930 ncbi.nlm.nih.gov/gene/25930 |
| Ensembl ID | ENSG00000114544 |
| UniProt ID | Q9H3S7 |
| OMIM ID | 606584 |
| HGNC ID | 9643 |
| Aliases | HD-PTP, KIAA1471, PTP-TD14 |
Description
PTPN23 encodes a non-receptor protein tyrosine phosphatase that functions as a tumor suppressor and regulator of endosomal trafficking. The protein contains a N-terminal Bro1 domain, a central phosphatase domain, and a C-terminal proline-rich region. It dephosphorylates specific substrates involved in cell growth, migration, and vesicle sorting. Loss of PTPN23 expression is associated with several cancers and neurodevelopmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Breast cancer | Reduced PTPN23 expression correlates with poor prognosis; loss of phosphatase activity promotes cell proliferation and invasion | PMID: 23431147 |
| Lung cancer | Frequent downregulation; re-expression suppresses tumor growth in vitro | PMID: 21502567 |
| Colorectal cancer | Mutations and decreased expression linked to metastasis | PMID: 25686123 |
| Neurodevelopmental disorder with hypotonia and brain anomalies | Biallelic loss-of-function variants impair endosomal trafficking | PMID: 31965077 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Lung | 8.3 | Low |
| Liver | 15.2 | Medium |
| Kidney | 10.1 | Medium |
| Breast | 9.8 | Low |
| Colon | 11.4 | Medium |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| MCF7 (breast cancer) | 14.2 | Moderate expression |
| A549 (lung cancer) | 7.6 | Low expression |
| HCT116 (colorectal cancer) | 10.5 | Moderate expression |
| HEK293 (embryonic kidney) | 18.9 | High expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1234C>T (p.Arg412*) | Nonsense | <0.1% in general population | Truncation; loss of phosphatase domain |
| c.1567G>A (p.Gly523Arg) | Missense | 0.2% in COSMIC | Impaired catalytic activity |
| c.2101_2102del (p.Gln701fs) | Frameshift | Rare | Loss of function; associated with neurodevelopmental disorder |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations that truncate the protein or disrupt the phosphatase domain lead to loss of tumor suppressor activity.
Gain of Function (GOF)
No evidence of gain-of-function mutations in PTPN23.
Dominant Negative (DN)
Not reported for PTPN23.
View complete mutation data：
Gene Ontology (GO)
| • protein tyrosine phosphatase activity | • endosomal transport |
| • negative regulation of cell proliferation | • protein dephosphorylation |
| • vesicle-mediated transport |
Pathways
• Endosomal sorting complex required for transport (ESCRT)
• EGFR signaling pathway
• Cell cycle regulation
Protein Summary
PTPN23 is a 1636-amino acid protein with a Bro1 domain that binds to CHMP4B, a phosphatase domain that dephosphorylates substrates such as EGFR and STAT3, and a proline-rich region mediating protein-protein interactions. It localizes to endosomes and regulates multivesicular body formation, receptor downregulation, and cell migration. The protein is widely expressed with highest levels in brain and liver.
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