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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PHACTR3
phosphatase and actin regulator 3
Chromosome 20 · 20q13.32-q13.33
NCBI Gene: 116154Ensembl: ENSG00000087495.18HGNC: HGNC:15833UniProt: B7Z339
25PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingnucleoplasmactin bindingactin cytoskeleton organizationintelligencemathematical abilityovarian dysfunctionskin disease
✦AI Summary

PHACTR3 (phosphatase and actin regulator 3), also known as scapinin, is a multifunctional protein primarily involved in actin cytoskeleton regulation and cell morphogenesis. The protein contains a putative regulatory subunit domain for protein phosphatase-1 (PP1) and binds directly to cytoplasmic actin 1. PHACTR3 localizes to the plasma membrane through basic and hydrophobic residues in its N-terminus, where it concentrates in lamellipodia and membrane ruffles to regulate actin dynamics and morphological changes in cells 2. The protein is predominantly expressed in mammalian brain tissue with complex, tissue-specific transcription patterns during development 1, suggesting specialized neurological functions. Clinically, PHACTR3 has emerged as a significant biomarker in cancer diagnostics. DNA methylation of PHACTR3 is progressively increased during HPV-induced cervical carcinogenesis, appearing in up to 100% of cervical carcinomas 3, and serves as a triage marker for detecting high-grade cervical disease 4. In colorectal cancer, PHACTR3 methylation shows 70-fold increased levels in advanced neoplasia, demonstrating 66% sensitivity and 100% specificity for CRC detection in stool samples with complementary value to fecal immunochemical testing 5. PHACTR3 methylation also appears useful for bladder cancer detection in urine 6 and lung cancer diagnosis 7, and shows prognostic significance in left-sided colon cancer 8.

Sources cited
1
PHACTR3/scapinin binds to cytoplasmic actin, is a putative PP1 regulatory subunit, and is predominantly expressed in brain tissue with complex developmental patterns
PMID: 16974080
2
PHACTR3 localizes to plasma membrane via N-terminal basic and hydrophobic residues and regulates cell morphogenesis
PMID: 25405772
3
PHACTR3 DNA methylation increases during HPV-induced cervical carcinogenesis with methylation in up to 100% of cervical carcinomas and is elevated in high-grade cervical disease
PMID: 23674368
4
PHACTR3 methylation progressively increases during HPV-induced immortalization of keratinocytes
PMID: 25580631
5
PHACTR3 methylation shows >70-fold increased levels in colorectal cancer with 66% sensitivity and 100% specificity in stool samples
PMID: 22135045
6
PHACTR3 methylation is significantly elevated in bladder cancer urine samples as a diagnostic marker
PMID: 35123558
7
PHACTR3 methylation is useful for lung cancer diagnosis in sputum samples
PMID: 25719833
8
PHACTR3 expression is prognostically significant in left-sided colon cancer
PMID: 30016783
Disease Associationsⓘ20
intelligenceOpen Targets
0.41Moderate
mathematical abilityOpen Targets
0.32Weak
ovarian dysfunctionOpen Targets
0.32Weak
skin diseaseOpen Targets
0.29Weak
sign or symptomOpen Targets
0.28Weak
benign neoplasm of pituitary glandOpen Targets
0.28Weak
alcohol drinkingOpen Targets
0.27Weak
Abnormality of refractionOpen Targets
0.25Weak
benign chondrogenic neoplasmOpen Targets
0.25Weak
ulcerative colitisOpen Targets
0.22Weak
tricuspid valve diseaseOpen Targets
0.19Weak
rheumatoid arthritisOpen Targets
0.18Weak
sialolithiasisOpen Targets
0.17Weak
Cerebral degenerationOpen Targets
0.16Weak
placenta praeviaOpen Targets
0.12Weak
neuroendocrine neoplasmOpen Targets
0.05Suggestive
LymphadenopathyOpen Targets
0.05Suggestive
atypical teratoid rhabdoid tumorOpen Targets
0.05Suggestive
response to COVID-19 vaccineOpen Targets
0.05Suggestive
Precordial painOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
FLNBShared pathway100%SPTAN1Shared pathway100%ACAP1Shared pathway100%PHACTR2Shared pathway100%THSD7BShared pathway100%SPECC1Shared pathway100%
Tissue Expression6 tissues
Brain
100%
Ovary
28%
Bone Marrow
16%
Heart
16%
Lung
16%
Liver
3%
Gene Interaction Network
Click a node to explore
PHACTR3FLNBSPTAN1ACAP1PHACTR2THSD7BSPECC1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q96KR7
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.30Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.18 [0.11–0.30]
RankingsWhere PHACTR3 stands among ~20K protein-coding genes
  • #13,036of 20,598
    Most Researched25
  • #1,171of 17,882
    Most Constrained (LOEUF)0.30 · top 10%
Genes detectedPHACTR3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Genomic organization and expression pattern of scapinin (PHACTR3) in mouse and human.
PMID: 16974080
Cytogenet Genome Res · 2006
1.00
2
Phactr3/scapinin, a member of protein phosphatase 1 and actin regulator (phactr) family, interacts with the plasma membrane via basic and hydrophobic residues in the N-terminus.
PMID: 25405772
PLoS One · 2014
0.90
3
Longitudinal assessment of DNA methylation changes during HPVE6E7-induced immortalization of primary keratinocytes.
PMID: 25580631
Epigenetics · 2015
0.80
4
DNA hypermethylation analysis in sputum for the diagnosis of lung cancer: training validation set approach.
PMID: 25719833
Br J Cancer · 2015
0.70
5
Bladder cancer detection in urine using DNA methylation markers: a technical and prospective preclinical validation.
PMID: 35123558
Clin Epigenetics · 2022
0.60