ETV3

ETS variant transcription factor 3, the group of ETS transcription factor family

Basic information

Region (hg38): 1:157121191-157138474

Links

ENSG00000117036 ∙ NCBI:2117 ∙ OMIM:164873 ∙ HGNC:3492 ∙ Uniprot:P41162 ∙ 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 ETV3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETV3 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						0
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in ETV3

This is a list of pathogenic ClinVar variants found in the ETV3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157124941-C-A		not specified	Uncertain significance (Nov 21, 2022)
1-157124996-G-A		not specified	Uncertain significance (Aug 12, 2024)
1-157125043-T-A		not specified	Uncertain significance (Dec 15, 2024)
1-157125068-T-C		not specified	Uncertain significance (May 02, 2024)
1-157125077-C-A		not specified	Uncertain significance (Nov 14, 2023)
1-157125121-C-T		not specified	Uncertain significance (Jun 26, 2024)
1-157125148-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-157125202-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-157125203-G-A		not specified	Uncertain significance (Sep 09, 2021)
1-157125227-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-157125271-G-A		not specified	Uncertain significance (Dec 30, 2024)
1-157125278-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-157125287-A-C		not specified	Uncertain significance (Dec 14, 2023)
1-157125300-C-G		not specified	Uncertain significance (Sep 04, 2024)
1-157125418-C-T		not specified	Uncertain significance (May 31, 2023)
1-157125520-C-T		not specified	Uncertain significance (Aug 03, 2022)
1-157125524-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-157125553-T-C		not specified	Uncertain significance (Dec 25, 2024)
1-157125563-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-157125565-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-157125614-C-T		not specified	Uncertain significance (Nov 15, 2024)
1-157125616-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-157125617-G-A		not specified	Uncertain significance (Jan 07, 2025)
1-157125626-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-157125635-C-A		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETV3	protein_coding	protein_coding	ENST00000368192	4	17284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0240	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	185	296	0.624	0.0000171	3331
Missense in Polyphen		46	108.06	0.42569		1175
Synonymous	0.124	106	108	0.985	0.00000549	1054
Loss of Function	3.46	1	15.9	0.0630	7.67e-7	198

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)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that contribute to growth arrest during terminal macrophage differentiation by repressing target genes involved in Ras-dependent proliferation. Represses MMP1 promoter activity. {ECO:0000269|PubMed:12007404}.
• Pathway: mets affect on macrophage differentiation (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.447
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etv3

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;biological_process;negative regulation of cell population proliferation;cell differentiation;cellular response to granulocyte macrophage colony-stimulating factor stimulus
• Cellular component: nuclear chromatin;nucleus;RNA polymerase II transcription repressor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;molecular_function;DEAD/H-box RNA helicase binding