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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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ZKSCAN3
zinc finger with KRAB and SCAN domains 3
Chromosome 6 · 6p22.1
NCBI Gene: 80317Ensembl: ENSG00000189298.15HGNC: HGNC:13853UniProt: Q9BRR0
37PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
nucleuscytoplasmDNA-binding transcription repressor activity, RNA polymerase II-specificDNA bindingneoplasmhepatocellular carcinomacancerurinary bladder carcinoma
✦AI Summary

ZKSCAN3 is a zinc finger transcription factor that functions as a master repressor of autophagy and lysosomal biogenesis in human cells 1. It binds to consensus DNA sequences and transcriptionally represses autophagy-related genes including MAP1LC3B, ULK1, and WIPI2, opposing the autophagy-promoting effects of TFEB 1. ZKSCAN3 regulates autophagy through mTORC1-independent pathways via protein kinase C 2. Beyond autophagy regulation, ZKSCAN3 maintains heterochromatin stability and genomic integrity by interacting with heterochromatin-associated and nuclear lamina proteins, thereby attenuating cellular senescence 3. This epigenetic function is independent of its autophagy-repressing activity 3. In disease contexts, ZKSCAN3 is significantly upregulated across multiple cancer types and correlates with poor prognosis and therapeutic resistance 4. In Parkinson's disease models, ZKSCAN3 overexpression suppresses autophagy-lysosome pathway activation through TFEB inhibition, exacerbating pathology 5. Functionally, ZKSCAN3 exhibits context-dependent plasticity: it promotes cancer progression, invasion, and metastasis while inhibiting apoptosis 4, yet paradoxically suppresses tumor initiation through genomic stability maintenance 6. Its subcellular localization and activity are dynamically regulated by post-translational modifications including phosphorylation and ubiquitination 6. ZKSCAN3 represents both a prognostic biomarker and promising therapeutic target in oncology and neurodegenerative diseases.

Sources cited
1
ZKSCAN3 is the master transcriptional repressor of autophagy in human cell lines and is functionally homologous to Drosophila M1BP in autophagy repression
PMID: 32541927
2
ZKSCAN3 regulates lysosomal digestive functions through mTORC1-independent pathways via PKC
PMID: 27684505
3
ZKSCAN3 maintains heterochromatin stability and attenuates cellular senescence through interaction with heterochromatin-associated and nuclear lamina proteins
PMID: 32427330
4
ZKSCAN3 is overexpressed in multiple cancer types and associated with adverse prognosis, drug resistance, and promotion of tumor proliferation, invasion, and metastasis
PMID: 39519085
5
ZKSCAN3 suppresses the autophagy-lysosome pathway through TFEB inhibition in Parkinson's disease models
PMID: 40083599
6
ZKSCAN3 undergoes post-translational modifications (phosphorylation, ubiquitination) that modulate its subcellular localization and activity, enabling context-dependent functional plasticity
PMID: 40723888
Disease Associationsⓘ20
neoplasmOpen Targets
0.09Suggestive
hepatocellular carcinomaOpen Targets
0.09Suggestive
cancerOpen Targets
0.08Suggestive
urinary bladder carcinomaOpen Targets
0.08Suggestive
ovarian cancerOpen Targets
0.07Suggestive
permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndromeOpen Targets
0.07Suggestive
prostate cancerOpen Targets
0.06Suggestive
SepsisOpen Targets
0.04Suggestive
adenomaOpen Targets
0.04Suggestive
Parkinson diseaseOpen Targets
0.03Suggestive
breast cancerOpen Targets
0.03Suggestive
colorectal cancerOpen Targets
0.03Suggestive
melanomaOpen Targets
0.03Suggestive
gastric cancerOpen Targets
0.03Suggestive
Huntington diseaseOpen Targets
0.02Suggestive
bladder tumorOpen Targets
0.02Suggestive
multiple myelomaOpen Targets
0.02Suggestive
cervical cancerOpen Targets
0.02Suggestive
gastric carcinomaOpen Targets
0.02Suggestive
cervical squamous intraepithelial neoplasiaOpen Targets
0.02Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ZNF444Protein interaction84%ZNF396Protein interaction83%ITGB4Protein interaction83%PGBD1Protein interaction83%ZNF397Protein interaction79%ZNF24Protein interaction77%
Tissue Expression6 tissues
Ovary
100%
Heart
77%
Liver
70%
Brain
67%
Lung
60%
Bone Marrow
17%
Gene Interaction Network
Click a node to explore
ZKSCAN3ZNF444ZNF396ITGB4PGBD1ZNF397ZNF24
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9BRR0
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.93LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.66 [0.48–0.93]
RankingsWhere ZKSCAN3 stands among ~20K protein-coding genes
  • #10,725of 20,598
    Most Researched37
  • #8,551of 17,882
    Most Constrained (LOEUF)0.93
Genes detectedZKSCAN3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Trehalose induces autophagy via lysosomal-mediated TFEB activation in models of motoneuron degeneration.
PMID: 30335591
Autophagy · 2019
1.00
2
Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation.
PMID: 32541927
Sci Rep · 2020
0.90
3
LRRK2 is required for CD38-mediated NAADP-Ca
PMID: 34313548
Autophagy · 2022
0.80
4
Turn up the lysosome.
PMID: 27684505
Nat Cell Biol · 2016
0.70
5
The Biological Roles of ZKSCAN3 (ZNF306) in the Hallmarks of Cancer: From Mechanisms to Therapeutics.
PMID: 39519085
Int J Mol Sci · 2024
0.60