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6 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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ZNF540
zinc finger protein 540
Chromosome 19 · 19q13.12
NCBI Gene: 163255Ensembl: ENSG00000171817.18HGNC: HGNC:25331UniProt: Q8NDQ6
10PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
mRNA regulatory element binding translation repressor activitynegative regulation of translationnegative regulation of DNA-templated transcriptionnucleuscardiac transplantneurodegenerative diseaseSensorineural hearing impairmentprostate carcinoma
✦AI Summary

ZNF540 is a zinc finger transcription factor that functions as a transcriptional repressor in multiple cellular contexts. The protein contains 660 amino acids and localizes to both the nucleus and cytoplasm 1. Mechanistically, ZNF540 interacts with MVP, a MAPK scaffold protein, and inhibits transcriptional activities of the ERK signaling pathway by repressing SRE and ELK-1 dependent gene expression 1. This regulatory function is consistent with its characterized DNA-binding and RNA polymerase II-specific transcriptional activity. Clinically, ZNF540 has emerged as a significant biomarker in cancer prognosis. In clear cell renal cell carcinomas (ccRCCs), ZNF540 promoter hypermethylation is a hallmark feature of the CpG island methylator phenotype (CIMP), which characterizes aggressive tumors with significantly lower cancer-free and overall survival rates 2. ZNF540 methylation status provides prognostic utility, with criteria combining ZNF540 CpG sites achieving 100% sensitivity and specificity in distinguishing CIMP-positive from CIMP-negative ccRCCs 3. In head and neck squamous cell carcinomas, higher ZNF540 expression correlates with HPV infection and improved overall survival, suggesting a tumor-suppressive role 4. Additionally, ZNF540 was identified as a component of a prognostic model for bicalutamide resistance in prostate cancer 5, indicating broader relevance in endocrine therapy resistance.

Sources cited
1
ZNF540 is a 660 amino acid zinc finger protein localized to nucleus and cytoplasm that interacts with MVP and represses transcriptional activities of SRE and ELK-1 in the MAPK signaling pathway
PMID: 16815308
2
ZNF540 promoter hypermethylation is a hallmark of CpG island methylator phenotype in aggressive clear cell renal cell carcinomas with lower survival rates
PMID: 22610075
3
ZNF540 methylation status is part of criteria that discriminate CIMP-positive from CIMP-negative ccRCCs with 100% sensitivity and specificity, and predicts patient survival
PMID: 25332168
4
Higher ZNF540 expression correlates with HPV infection in head and neck squamous cell carcinomas and is associated with better overall survival
PMID: 36547193
5
ZNF540 was identified as part of a prognostic model for bicalutamide resistance prediction in prostate cancer
PMID: 37143720
Disease Associationsⓘ20
cardiac transplantOpen Targets
0.25Weak
neurodegenerative diseaseOpen Targets
0.15Weak
Sensorineural hearing impairmentOpen Targets
0.12Weak
prostate carcinomaOpen Targets
0.06Suggestive
hearing lossOpen Targets
0.04Suggestive
Abnormality of refractionOpen Targets
0.04Suggestive
head and neck squamous cell carcinomaOpen Targets
0.04Suggestive
breast carcinomaOpen Targets
0.03Suggestive
neoplasmOpen Targets
0.03Suggestive
glioblastoma multiformeOpen Targets
0.02Suggestive
ependymomaOpen Targets
0.02Suggestive
prostate cancerOpen Targets
0.02Suggestive
lung cancerOpen Targets
0.02Suggestive
human papilloma virus infectionOpen Targets
0.01Suggestive
astrocytomaOpen Targets
0.01Suggestive
lung adenocarcinomaOpen Targets
0.01Suggestive
SepsisOpen Targets
0.01Suggestive
psoriasisOpen Targets
0.01Suggestive
cirrhosis of liverOpen Targets
0.00Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
TCEAL1Shared pathway50%CNPY2Shared pathway50%SFMBT2Shared pathway50%ZNF410Shared pathway50%IFRD2Shared pathway50%PURBShared pathway50%
Tissue Expression6 tissues
Ovary
100%
Heart
58%
Brain
27%
Liver
23%
Lung
18%
Bone Marrow
15%
Gene Interaction Network
Click a node to explore
ZNF540TCEAL1CNPY2SFMBT2ZNF410IFRD2PURB
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q8NDQ6
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.75LoF Tolerant
pLIⓘ
0.67Intermediate
Observed/Expected LoF0.29 [0.13–0.75]
RankingsWhere ZNF540 stands among ~20K protein-coding genes
  • #17,235of 20,598
    Most Researched10
  • #6,009of 17,882
    Most Constrained (LOEUF)0.75
Genes detectedZNF540
Sources retrieved6 papers
Response time—
📄 Sources
6▼
1
Identification of bicalutamide resistance-related genes and prognosis prediction in patients with prostate cancer.
PMID: 37143720
Front Endocrinol (Lausanne) · 2023
1.00
2
A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway.
PMID: 16815308
Biochem Biophys Res Commun · 2006
0.83
3
Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas.
PMID: 22610075
Carcinogenesis · 2012
0.67
4
Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes.
PMID: 25332168
BMC Cancer · 2014
0.50
5
Defining the prognostic value of urine extracellular vesicles ZNF540 in bladder cancer based on GEO database.
PMID: 38296684
Asian J Surg · 2024
0.33