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]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
12
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.79
LOEUF
Multiple*
Mechanism· predicted
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?
0.79LOEUF
pLI 0.282
Z-score 1.96
OE 0.25 (0.10–0.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
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?
LoF OE?0.25 (0.10–0.79)
0≤0.351.4
Missense OE?0.43 (0.34–0.55)
0≤0.61.4
Synonymous OE?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.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients