ETV5

protein-coding

ETS variant transcription factor 5, the group of ETS transcription factor family

Gene summary

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in cellular response to oxidative stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_004454.3

Inheritance

—

ClinVar variants

P:1U:62B:9

Top phenotype

ETV5-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:186,046,314-186,110,318

External References & Databases

Ensembl (ENSG00000244405)

Transcript & Mutation Effects

hg38 • Region Span ~64.0 kb

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GenCC 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 ETV5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 4

ETV5-related disorderTotal: 4

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004454.3. 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				3 clinvar	3 clinvar	6
missense	1 clinvar		54 clinvar	2 clinvar	1 clinvar	58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	1	0	62	5	4	72

Highest pathogenic variant AF is 0.01696762

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004454.3	RefSeq	NP_004445.1	12	MANE Select
ENST00000306376.10	Ensembl	ENSP00000306894.5	12	MANE Select
ENST00000413301.5	Ensembl	ENSP00000405157.1	6	Standard
ENST00000421809.5	Ensembl	ENSP00000412171.1	6	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
etv5b	Danio rerio	Structure: motor neuron Quality: branchiness abnormal

Gene / Model

Organism

Observed Phenotype

etv5b

Danio rerio

Structure: motor neuron

Quality: branchiness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prostate cancer - Homo sapiens (human)
Transcriptional misregulation in cancer - Homo sapiens (human)
Androgen receptor signaling pathway
il12 and stat4 dependent signaling pathway in th1 development
IL12 signaling mediated by STAT4

Biological Process

regulation of transcription by RNA polymerase II
neuromuscular synaptic transmission
locomotory behavior
cell differentiation
cellular response to oxidative stress

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity

Cellular Component

nucleus
nucleoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306376
Coding exons: 12
Length: 64011
Individuals with no LoFs: 125362
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125363
p: 0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.99	203	300	0.677	0.0000169	3314
Missense (PolyPhen)		70	141.47	0.49481		1497
Synonymous	0.531	108	115	0.937	0.00000682	989
Loss of Function	5.28	0	32.5	0.00	0.00000192	330

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	0.000054	0.000054	rare
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: dbNSFP

Function: FUNCTION: Binds to DNA sequences containing the consensus nucleotide core sequence 5'-GGAA.-3'. {ECO:0000269|PubMed:8152800}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.0779
RVIS EVS: -0.36
RVIS percentile EVS: 29.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.956

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium