ETV2
protein-codingETS variant transcription factor 2, the group of ETS transcription factor family
Gene summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including cell surface receptor signaling pathway; positive regulation of endothelial cell differentiation; and regulation of gene expression. Predicted to be active in nucleus. Implicated in limb ischemia. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0005453
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ETV2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014209.4. 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 | 0 | |||||
| missense | 1 | 56 | 2 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 2 | 56 | 2 | 0 | 60 |
Highest pathogenic variant AF is 0.00092511345
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055024.2 | 6 | MANE Select | |
| Ensembl | ENSP00000384524.2 | 6 | MANE Select | |
| RefSeq | NP_001287903.1 | 3 | Standard | |
| RefSeq | NP_001291478.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| etv2 | Danio rerio | Structure: endothelial cell Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- blastocyst development
- placenta development
- regulation of transcription by RNA polymerase II
- Notch signaling pathway
- Wnt signaling pathway
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription activator activity, RNA polymerase II-specific
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000402764
- Coding exons
- 6
- Length
- 3127
- Individuals with no LoFs
- 125556
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125566
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.473 | 166 | 184 | 0.902 | 0.00000873 | 2125 |
| Missense (PolyPhen) | 44 | 51.215 | 0.85912 | 605 | ||
| Synonymous | -0.456 | 87 | 81.8 | 1.06 | 0.00000422 | 704 |
| Loss of Function | 0.333 | 14 | 15.4 | 0.908 | 6.70e-7 | 158 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000030 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to DNA sequences containing the consensus pentanucleotide 5'-CGGA[AT]-3'. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0791
Intolerance Scores
- LoFtool
- 0.805
- RVIS EVS
- 0.53
- RVIS percentile EVS
- 80.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.711
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |