ETV2

ETS variant transcription factor 2, the group of ETS transcription factor family

Basic information

Region (hg38): 19:35641745-35644871

Links

ENSG00000105672 ∙ NCBI:2116 ∙ OMIM:609358 ∙ HGNC:3491 ∙ Uniprot:O00321 ∙ 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 ETV2 gene.

• not_specified (51 variants)
• Hypoplastic_left_heart_syndrome (2 variants)
• Abnormal_vertebral_morphology (2 variants)
• Polydactyly (2 variants)
• Heart,_malformation_of (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETV2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014209.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	49	2		52
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	2	49	2	0

Highest pathogenic variant AF is 0.00092511345

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETV2	protein_coding	protein_coding	ENST00000402764	6	3127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-9	0.157	125556	0	10	125566	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.473	166	184	0.902	0.00000873	2125
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000160	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000925
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.237

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.711

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etv2
• Phenotype: embryo 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); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: etv2
• Affected structure: endothelial cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: blastocyst development;placenta development;regulation of transcription by RNA polymerase II;Notch signaling pathway;Wnt signaling pathway;cell differentiation;erythrocyte differentiation;positive regulation of endothelial cell differentiation;positive regulation of transcription by RNA polymerase II;blood vessel morphogenesis;BMP signaling pathway involved in mesodermal cell fate specification;positive regulation of mesoderm development
• Cellular component: nucleus
• 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