ZNF540
protein-codingzinc finger protein 540, the group of Zinc fingers C2H2-type
Gene summary
Enables mRNA regulatory element binding translation repressor activity. Involved in negative regulation of DNA-templated transcription and negative regulation of translation. Located in cytosol and nucleoplasm. [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 ~62.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZNF540 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001172225.3. 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 | 0 | |||||
| missense | 83 | 4 | 87 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 83 | 4 | 0 | 87 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001165696.1 | 4 | MANE Select | |
| Ensembl | ENSP00000324598.3 | 4 | MANE Select | |
| RefSeq | NP_001165697.1 | 3 | Standard | |
| RefSeq | NP_689819.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- Generic Transcription Pathway
- RNA Polymerase II Transcription
Biological Process
- regulation of transcription by RNA polymerase II
- negative regulation of translation
- negative regulation of transcription, DNA-templated
Molecular Function
- translation repressor activity, mRNA regulatory element binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- protein binding
- metal ion binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- cytosol
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000592533
- Coding exons
- 4
- Length
- 62691
- Individuals with no LoFs
- 125627
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125628
- p
- 0.00000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.659 | 316 | 351 | 0.901 | 0.0000180 | 4398 |
| Missense (PolyPhen) | 100 | 114.96 | 0.86987 | 1464 | ||
| Synonymous | 0.781 | 107 | 118 | 0.908 | 0.00000588 | 1147 |
| Loss of Function | 1.64 | 1 | 4.94 | 0.202 | 2.07e-7 | 67 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| 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: May act as a transcriptional repressor. {ECO:0000269|PubMed:16815308}.;
Recessive Scores
- pRec
- 0.0835
Intolerance Scores
- LoFtool
- 0.771
- RVIS EVS
- -0.96
- RVIS percentile EVS
- 9.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0100
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |