ZNF93
protein-codingzinc finger protein 93, the group of Zinc fingers C2H2-type
Gene summary
Enables DNA-binding transcription repressor activity, RNA polymerase II-specific. Involved in transposable element silencing. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- ZNF505
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~62.6 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 ZNF93 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031218.4. 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 | 1 | 1 | 2 | |||
| missense | 101 | 2 | 1 | 104 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 102 | 3 | 3 | 108 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112495.2 | 4 | MANE Select | |
| Ensembl | ENSP00000342002.4 | 4 | MANE Select | |
| Ensembl | ENSP00000468563.1 | 4 | Standard | |
| Ensembl | ENSP00000467553.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- negative regulation of transcription, DNA-templated
- negative regulation of transposon integration
Molecular Function
- transcription regulatory region sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription factor activity
- zinc ion binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343769
- Coding exons
- 4
- Length
- 34663
- Individuals with no LoFs
- 125700
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125747
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0441 | 312 | 310 | 1.01 | 0.0000140 | 4077 |
| Missense (PolyPhen) | 70 | 74.166 | 0.94383 | 1093 | ||
| Synonymous | -0.418 | 114 | 108 | 1.05 | 0.00000503 | 1074 |
| Loss of Function | -0.00829 | 5 | 4.98 | 1.00 | 2.11e-7 | 58 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.0011 | 0.0011 | notable |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription factor specifically required to repress long interspersed nuclear element 1 (L1) retrotransposons: recognizes and binds L1 sequences and repress their expression by recruiting a repressive complex containing TRIM28/KAP1 (PubMed:25274305). Not able to repress expression of all subtypes of L1 elements. Binds to the 5' end of L1PA4, L1PA5 and L1PA6 subtypes, and some L1PA3 subtypes. Does not bind to L1PA7 or older subtypes nor at the most recently evolved L1PA2 and L1Hs. 50% of L1PA3 elements have lost the ZNF93-binding site, explaining why ZNF93 is not able to repress their expression (PubMed:25274305). {ECO:0000269|PubMed:25274305}.;
Intolerance Scores
- LoFtool
- 0.769
- RVIS EVS
- 1.04
- RVIS percentile EVS
- 91.29
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |