ZNF541
protein-codingzinc finger protein 541, the group of Zinc fingers C2H2-type|Myb/SANT domain containing
Gene summary
Predicted to enable transcription corepressor activity. Predicted to be involved in male meiotic nuclear division and regulation of DNA-templated transcription. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex and transcription regulator complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~52.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0018393
Submitter: King Faisal Specialist Hospital and Research Center
Alhathal et al., 2020 (PMID: 32719396) reported a missense variant in a large male infertility cohort (n=285 infertile man and case–control fertile man). Gene is scored according ClinGen classification. Limited with total score of 4. Single variant segregation (3 points), experimental evidence: testicular expression (1 points) (PMID: 27965440).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZNF541 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001277075.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | 4 | |||
| missense | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 4 | 2 | 0 | 6 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001264004.1 | 15 | MANE Select | |
| Ensembl | ENSP00000375770.3 | 15 | MANE Select | |
| Ensembl | ENSP00000263351.5 | 7 | Standard | |
| Ensembl | ENSP00000471665.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- multicellular organism development
- spermatogenesis
- cell differentiation
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription factor activity
- transcription factor binding
- transcription regulatory region DNA binding
- metal ion binding
Cellular Component
- histone deacetylase complex
- nucleus
- transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000314121
- Coding exons
- 15
- Length
- 35172
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.64 | 534 | 736 | 0.726 | 0.0000452 | 8798 |
| Missense (PolyPhen) | 108 | 203.9 | 0.52968 | 2516 | ||
| Synonymous | 1.50 | 294 | 328 | 0.895 | 0.0000227 | 2820 |
| Loss of Function | 6.17 | 3 | 50.1 | 0.0598 | 0.00000289 | 603 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of some chromatin remodeling multiprotein complex that plays a role during spermatogenesis. {ECO:0000250|UniProtKB:Q0GGX2}.;
Intolerance Scores
- RVIS EVS
- 1.02
- RVIS percentile EVS
- 90.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.216
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |