ETV4

ETS variant transcription factor 4, the group of ETS transcription factor family

Basic information

Region (hg38): 17:43527843-43579620

Links

ENSG00000175832 ∙ NCBI:2118 ∙ OMIM:600711 ∙ HGNC:3493 ∙ Uniprot:P43268 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ETV4 gene.

• not provided (28 variants)
• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETV4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			25	2	3	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					20	20
Total	0	0	25	3	23

Variants in ETV4

This is a list of pathogenic ClinVar variants found in the ETV4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-43528547-A-G		not specified	Uncertain significance (Apr 13, 2022)
17-43528581-A-G		not specified	Uncertain significance (Dec 15, 2022)
17-43528586-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-43528623-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-43528665-G-A			Benign (Aug 01, 2022)
17-43528676-G-A			Likely benign (Dec 14, 2017)
17-43528730-C-T		Congenital anomaly of kidney and urinary tract	Likely pathogenic (Aug 24, 2018)
17-43528880-T-C			Benign (Nov 11, 2018)
17-43529343-G-A			Benign (Nov 11, 2018)
17-43529554-T-C		not specified	Uncertain significance (Jan 25, 2023)
17-43529617-C-T		not specified	Uncertain significance (Feb 17, 2024)
17-43529628-T-C		not specified	Uncertain significance (Jul 09, 2021)
17-43529634-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-43529652-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-43529905-C-G		not specified	Uncertain significance (Jan 09, 2024)
17-43529905-C-T		not specified	Uncertain significance (Jun 22, 2021)
17-43529943-T-C		not specified	Uncertain significance (Nov 08, 2022)
17-43530108-C-G		not specified	Uncertain significance (Feb 21, 2024)
17-43530116-C-A		not specified	Uncertain significance (Feb 22, 2023)
17-43530602-ACG-A			Benign (Jun 19, 2021)
17-43530609-C-T			Benign (Jun 18, 2021)
17-43530609-CGTGTGTGT-C			Benign (Jun 18, 2021)
17-43530635-T-A			Benign (Jun 18, 2021)
17-43532694-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-43532769-T-C		not specified	Uncertain significance (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETV4	protein_coding	protein_coding	ENST00000319349	12	51777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.87e-8	0.980	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.558	263	290	0.908	0.0000169	3135
Missense in Polyphen		101	125	0.80799		1387
Synonymous	-0.132	126	124	1.01	0.00000768	950
Loss of Function	2.22	17	30.1	0.564	0.00000161	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.000871	0.000816
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000800	0.0000791
Middle Eastern	0.000871	0.000816
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator that binds to the enhancer of the adenovirus E1A gene; the core-binding sequence is 5'[AC]GGA[AT]GT-3'. {ECO:0000269|PubMed:19307308}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Androgen Receptor Network in Prostate Cancer;Signal Transduction;MAPK6/MAPK4 signaling;MAPK family signaling cascades;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.460

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.5

Haploinsufficiency Scores

• pHI: 0.565
• hipred: Y
• hipred_score: 0.758
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etv4
• Phenotype: renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; neoplasm; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: etv4
• Affected structure: pronephros
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;nucleolus
• 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;protein binding