ETV5

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

Basic information

Region (hg38): 3:186046313-186110318

Links

ENSG00000244405 ∙ NCBI:2119 ∙ OMIM:601600 ∙ HGNC:3494 ∙ Uniprot:P41161 ∙ 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 ETV5 gene.

• not provided (13 variants)
• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETV5 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					3	3
missense			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					9	9
Total	0	0	13	0	13

Variants in ETV5

This is a list of pathogenic ClinVar variants found in the ETV5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-186048702-G-A		ETV5-related disorder	Likely benign (Aug 07, 2019)
3-186048703-G-A		not specified	Uncertain significance (Nov 18, 2022)
3-186048726-C-T			Benign (Feb 26, 2018)
3-186048758-C-T		not specified	Uncertain significance (Nov 17, 2022)
3-186048773-G-A			Benign (Apr 19, 2018)
3-186048777-C-T			Benign (Apr 19, 2018)
3-186048922-G-A			Benign (Nov 10, 2018)
3-186052307-G-T			Benign (Jun 19, 2021)
3-186057024-C-A			Benign (Jun 19, 2021)
3-186057125-T-C		not specified	Uncertain significance (Feb 06, 2024)
3-186057491-C-G		not specified	Uncertain significance (Jul 25, 2023)
3-186064176-T-C			Benign (Jun 18, 2021)
3-186065855-T-C		not specified	Uncertain significance (Jun 11, 2021)
3-186065947-G-C		not specified	Uncertain significance (Jan 19, 2024)
3-186065989-C-T		not specified	Uncertain significance (Feb 22, 2023)
3-186066019-A-G		not specified	Uncertain significance (Oct 03, 2022)
3-186079836-G-C		not specified	Uncertain significance (Feb 23, 2023)
3-186079931-T-G		Myoepithelial tumor	Pathogenic (Nov 01, 2022)
3-186080012-G-T		not specified	Uncertain significance (Apr 07, 2023)
3-186080022-G-C			Benign (Jun 14, 2018)
3-186080081-G-C		not specified	Uncertain significance (Feb 27, 2024)
3-186080097-C-T		not specified	Uncertain significance (Feb 17, 2023)
3-186080236-C-T			Benign (Nov 11, 2018)
3-186080939-A-G			Benign (Jun 19, 2021)
3-186081074-A-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETV5	protein_coding	protein_coding	ENST00000306376	12	64011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000938	125362	0	1	125363	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	203	300	0.677	0.0000169	3314
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to DNA sequences containing the consensus nucleotide core sequence 5'-GGAA.-3'. {ECO:0000269|PubMed:8152800}.
• Pathway: 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;FGF;FOXM1 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0779
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.709
• hipred: Y
• hipred_score: 0.825
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etv5
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; skeleton phenotype; renal/urinary system phenotype; embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; 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); 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)

Zebrafish Information Network

• Gene name: etv5b
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;neuromuscular synaptic transmission;locomotory behavior;cell differentiation;cellular response to oxidative stress;positive regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;male germ-line stem cell asymmetric division;regulation of synapse organization;positive regulation of glial cell proliferation;regulation of branching involved in mammary gland duct morphogenesis;skeletal muscle acetylcholine-gated channel clustering
• Cellular component: nucleus;nucleoplasm;plasma membrane
• 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;protein binding;transcription regulatory region DNA binding