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4 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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ZNF541
zinc finger protein 541
Chromosome 19 · 19q13.33
NCBI Gene: 84215Ensembl: ENSG00000118156.13HGNC: HGNC:25294UniProt: Q9H0D2
11PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingregulation of DNA-templated transcriptionregulation of transcription by RNA polymerase IImale meiotic nuclear divisioninfectionazoospermiaRomano-Ward syndromeFamilial progressive cardiac conduction defect
✦AI Summary

ZNF541 is a zinc finger transcription factor essential for male fertility and meiotic progression in spermatocytes [UniProt]. As a transcriptional regulator, ZNF541 activates expression of genes required for pachytene stage advancement during spermatogenesis while maintaining repression of pre-pachytene programs, including meiotic double-strand break (DSB) formation genes [UniProt]. This dual regulatory role ensures proper meiosis progression by suppressing aberrant DSB formation after mid-pachytene [UniProt]. ZNF541 functions through transcriptional corepressor activity and histone deacetylase complex interactions [GO Annotations]. Beyond its canonical role in reproduction, ZNF541 appears relevant to cancer biology. In cervical cancer, ZNF541 was identified as an upstream modulator of genes differentially expressed in HPV16-positive tissues, suggesting involvement in HPV-mediated oncogenic transcriptional programs 1. Similarly, in head and neck squamous cell carcinoma, ZNF541 was among genes significantly associated with natural killer cell infiltration and patient survival outcomes 2. Expression analysis revealed ZNF541 as differentially expressed between HPV-positive and HPV-negative head and neck cancers 3. Additionally, ZNF541 haploinsufficiency through 19q13.32 microdeletion contributes to developmental abnormalities including facial dysmorphia, neurological defects, and orofacial clefting 4, indicating broader developmental significance beyond spermatogenesis.

Sources cited
1
ZNF541 identified as upstream modulator of differentially expressed genes in HPV16-positive cervical cancer tissues
PMID: 31456134
2
ZNF541 associated with natural killer cell infiltration and patient survival in head and neck squamous cell carcinoma
PMID: 38384136
3
ZNF541 haploinsufficiency through 19q13.32 microdeletion causes developmental abnormalities including facial asymmetry, ptosis, orofacial clefting, and neurological defects
PMID: 25230004
4
ZNF541 differentially expressed between HPV-positive and HPV-negative head and neck cancer samples
PMID: 38643268
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
infectionOpen Targets
0.12Weak
azoospermiaOpen Targets
0.09Suggestive
Romano-Ward syndromeOpen Targets
0.08Suggestive
Familial progressive cardiac conduction defectOpen Targets
0.08Suggestive
partial chromosome Y deletionOpen Targets
0.08Suggestive
familial atrial fibrillationOpen Targets
0.07Suggestive
Familial short QT syndromeOpen Targets
0.07Suggestive
catecholaminergic polymorphic ventricular tachycardiaOpen Targets
0.07Suggestive
Brugada syndromeOpen Targets
0.07Suggestive
Arrhythmogenic right ventricular dysplasiaOpen Targets
0.07Suggestive
spermatogenic failure 57Open Targets
0.07Suggestive
spermatogenic failure 50Open Targets
0.07Suggestive
spermatogenic failure 25Open Targets
0.07Suggestive
hypertrophic cardiomyopathyOpen Targets
0.07Suggestive
Rare familial disorder with hypertrophic cardiomyopathyOpen Targets
0.07Suggestive
spermatogenic failure, X-linked, 2Open Targets
0.06Suggestive
spermatogenic failure 59Open Targets
0.06Suggestive
spermatogenic failure 60Open Targets
0.06Suggestive
spermatogenic failure 73Open Targets
0.06Suggestive
spermatogenic failure 74Open Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
DNTTIP1Protein interaction73%KCTD19Shared pathway50%HSF5Shared pathway50%TEX14Shared pathway33%ASZ1Shared pathway33%SPDYAShared pathway25%
Tissue Expression6 tissues
Ovary
100%
Heart
37%
Bone Marrow
15%
Lung
6%
Liver
5%
Brain
4%
Gene Interaction Network
Click a node to explore
ZNF541DNTTIP1KCTD19HSF5TEX14ASZ1SPDYA
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9H0D2
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.28Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.20 [0.14–0.28]
RankingsWhere ZNF541 stands among ~20K protein-coding genes
  • #16,957of 20,598
    Most Researched11
  • #976of 17,882
    Most Constrained (LOEUF)0.28 · top 10%
Genes detectedZNF541
Sources retrieved4 papers
Response time—
📄 Sources
4
1
Transcriptome sequencing profiles of cervical cancer tissues and SiHa cells.
PMID: 31456134
Funct Integr Genomics · 2020
1.00
2
Natural killer cell-based signature: Prognostic analysis in head and neck squamous cell carcinoma.
PMID: 38384136
J Gene Med · 2024
0.75
3
19q13.32 microdeletion syndrome: three new cases.
PMID: 25230004
Eur J Med Genet · 2014
0.50
4
Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers.
PMID: 38643268
Sci Rep · 2024
0.25