PTP4A1

Chr 6

protein tyrosine phosphatase 4A1

Also known as: HH72, PRL-1, PRL1, PTP(CAAX1), PTPCAAX1

NCBI Gene: 7803ENSG00000112245UniProt: Q93096

This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]

0
ClinVar variants
0
Pathogenic / LP
0.28
pLI score
0
Active trials
Clinical Summary— PTP4A1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.25) despite low pLI — interpret in context.
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.79LOEUF
pLI 0.282
Z-score 1.96
OE 0.25 (0.10–0.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.05Z-score
OE missense 0.43 (0.34–0.55)
44 obs / 102.4 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.25 (0.10–0.79)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.43 (0.34–0.55)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.99
0≤1.21.6
LoF obs/exp: 2 / 8.0Missense obs/exp: 44 / 102.4Syn Z: 0.04

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PTP4A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
GINS2 promotes oral squamous cell carcinoma progression and immune evasion by recruiting PD-L1(+) neutrophils and modulating the PTP4A1/PKM2 axis.
Wei B et al.·Front Immunol
2025
Oxidative stress promotes fibrosis in systemic sclerosis through stabilization of a kinase-phosphatase complex.
Zhang R et al.·JCI Insight
2022
Expression of PTP4A1 in circulating tumor cells and its efficacy evaluation in patients with early- and intermediate-stage esophageal cancer.
Wu J et al.·Medicine (Baltimore)
2023Cohort
Protein tyrosine phosphatase PTP4A1 promotes proliferation and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma via the PI3K/AKT pathway.
Liu LZ et al.·Oncotarget
2016
A New Genomewide Association Meta-Analysis of Alcohol Dependence.
Zuo L et al.·Alcohol Clin Exp Res
2015Meta-analysis
Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence.
Zuo L et al.·Am J Addict
2014
WTAP promotes proliferation of esophageal squamous cell carcinoma via m(6)A-dependent epigenetic promoting of PTP4A1.
Zou J et al.·Cancer Sci
2024
Suppression of cell migration is promoted by miR-944 through targeting of SIAH1 and PTP4A1 in breast cancer cells.
Flores-Pérez A et al.·BMC Cancer
2016
An organoid library of salivary gland tumors reveals subtype-specific characteristics and biomarkers.
Wang B et al.·J Exp Clin Cancer Res
2022
Identification of PRL1 as a novel diagnostic and therapeutic target for castration-resistant prostate cancer by the Escherichia coli ampicillin secretion trap (CAST) method.
Shinmei S et al.·Urol Oncol
2014
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools