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5 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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ZNF398
zinc finger protein 398
Chromosome 7 · 7q36.1
NCBI Gene: 57541Ensembl: ENSG00000197024.10HGNC: HGNC:18373UniProt: A0A090N7S8
26PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingDNA-binding transcription factor activity, RNA polymerase II-specificRNA polymerase II transcription regulatory region sequence-specific DNA bindingregulation of transcription by RNA polymerase IIaortic diseasecomplicationhypertensionretinal degeneration
✦AI Summary

ZNF398 is a transcriptional regulator belonging to the KRAB domain-containing zinc finger protein family, functioning primarily as a transcriptional repressor 1. In human pluripotent stem cells (hPSCs), ZNF398 acts as a transcriptional activator mediating pluripotency and epithelial character downstream of TGF-beta signaling 2. Mechanistically, ZNF398 binds active promoters and enhancers together with SMAD3 and the histone acetyltransferase EP300 to enable TGF-beta target gene transcription 2. During epiblast development, ZNF398 acts downstream of TGFβ1 to activate the epithelial master regulator ESRP1 while repressing mesenchymal factors CDH2 and ZEB2 3. The p52 isoform of ZNF398 (also called p52-ZER6) is predominantly expressed in brain tissue and suppresses the antioxidant metallothionein-3, thereby increasing reactive oxygen species in neuronal cells 1. Upregulation of p52-ZER6 in Alzheimer's disease models correlates with reduced MT3 levels, suggesting a potential pathological mechanism in neurodegeneration 1. Additionally, p52-ZER6 overexpression enhances MDM2-p53 binding and reduces tumor cell sensitivity to MDM2-p53 inhibitors, identifying it as a potential cancer biomarker 4. ZNF398 has clinical implications for regenerative medicine applications and understanding neurodegenerative disease pathogenesis.

Sources cited
1
ZNF398 mediates pluripotency and epithelial character in hPSCs downstream of TGF-beta, binding active promoters and enhancers with SMAD3 and EP300
PMID: 32398665
2
ZNF398 acts downstream of TGFβ1 during epiblast development, activating ESRP1 and repressing CDH2 and ZEB2
PMID: 41339717
3
p52-ZER6 (ZNF398 isoform) is a KRAB-containing zinc finger protein predominantly expressed in brain that suppresses MT3, increasing ROS in neurons and is upregulated in Alzheimer's disease models
PMID: 39809138
4
p52-ZER6 overexpression enhances MDM2-p53 binding, promotes p53 degradation, and reduces tumor cell sensitivity to MDM2-p53 inhibitors
PMID: 35995868
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
aortic diseaseOpen Targets
0.31Weak
complicationOpen Targets
0.30Weak
hypertensionOpen Targets
0.30Weak
retinal degenerationOpen Targets
0.25Weak
fracture of pelvisOpen Targets
0.19Weak
fasciitisOpen Targets
0.12Weak
neoplasmOpen Targets
0.10Suggestive
colorectal carcinomaOpen Targets
0.07Suggestive
cancerOpen Targets
0.04Suggestive
ProptosisOpen Targets
0.03Suggestive
colon carcinomaOpen Targets
0.03Suggestive
ovarian cancerOpen Targets
0.03Suggestive
colorectal cancerOpen Targets
0.02Suggestive
breast cancerOpen Targets
0.02Suggestive
lung cancerOpen Targets
0.02Suggestive
prostate carcinomaOpen Targets
0.01Suggestive
acute myeloid leukemiaOpen Targets
0.01Suggestive
chronic myelogenous leukemiaOpen Targets
0.01Suggestive
squamous cell carcinomaOpen Targets
0.01Suggestive
infectionOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ZNF746Protein interaction84%ZNF212Protein interaction83%ZNF282Protein interaction83%DDX17Protein interaction82%ELMO1Protein interaction77%ZNF783Protein interaction73%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
92%
Ovary
52%
Lung
49%
Heart
48%
Liver
41%
Gene Interaction Network
Click a node to explore
ZNF398ZNF746ZNF212ZNF282DDX17ELMO1ZNF783
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q8TD17
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.78LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.55 [0.40–0.78]
RankingsWhere ZNF398 stands among ~20K protein-coding genes
  • #12,926of 20,598
    Most Researched26
  • #6,331of 17,882
    Most Constrained (LOEUF)0.78
Genes detectedZNF398
Sources retrieved5 papers
Response time—
📄 Sources
5
1
The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs.
PMID: 32398665
Nat Commun · 2020
1.00
2
A human epiblast model reveals dynamic TGFβ-mediated control of epithelial identity during mammalian epiblast development.
PMID: 41339717
Nat Cell Biol · 2026
0.80
3
The association of GNB5 with Alzheimer disease revealed by genomic analysis restricted to variants impacting gene function.
PMID: 38354736
Am J Hum Genet · 2024
0.60
4
Upregulation of p52-ZER6 (ZNF398) increases reactive oxygen species by suppressing metallothionein-3 in neuronal cells.
PMID: 39809138
Biochem Biophys Res Commun · 2025
0.40
5
p52-ZER6: a determinant of tumor cell sensitivity to MDM2-p53 binding inhibitors.
PMID: 35995868
Acta Pharmacol Sin · 2023
0.20