GeneBe

ELF3

E74 like ETS transcription factor 3, the group of ETS transcription factor family

Basic information

Region (hg38): 1:202007945-202017183

Previous symbols: [ "ESX" ]

Links

ENSG00000163435 ∙ NCBI:1999 ∙ OMIM:602191 ∙ HGNC:3318 ∙ Uniprot:P78545 ∙ 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 ELF3 gene.

  • not_specified (19 variants)
  • not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004433.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
 3
missense
18
clinvar
1
clinvar
 19
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 18 3 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ELF3protein_codingprotein_codingENST00000359651 89244
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9830.0168125744041257480.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.881522330.6530.00001472435
Missense in Polyphen4185.8580.47753927
Synonymous0.5978794.40.9220.00000620707
Loss of Function3.87221.30.09410.00000136203

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002650.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional activator that binds and transactivates ETS sequences containing the consensus nucleotide core sequence GGA[AT]. Acts synergistically with POU2F3 to transactivate the SPRR2A promoter and with RUNX1 to transactivate the ANGPT1 promoter. Also transactivates collagenase, CCL20, CLND7, FLG, KRT8, NOS2, PTGS2, SPRR2B, TGFBR2 and TGM3 promoters. Represses KRT4 promoter activity. Involved in mediating vascular inflammation. May play an important role in epithelial cell differentiation and tumorigenesis. May be a critical downstream effector of the ERBB2 signaling pathway. May be associated with mammary gland development and involution. Plays an important role in the regulation of transcription with TATA-less promoters in preimplantation embryos, which is essential in preimplantation development (By similarity). {ECO:0000250, ECO:0000269|PubMed:10391676, ECO:0000269|PubMed:10644990, ECO:0000269|PubMed:10773884, ECO:0000269|PubMed:11036073, ECO:0000269|PubMed:11313868, ECO:0000269|PubMed:12414801, ECO:0000269|PubMed:12624109, ECO:0000269|PubMed:12682075, ECO:0000269|PubMed:12713734, ECO:0000269|PubMed:14715662, ECO:0000269|PubMed:14767472, ECO:0000269|PubMed:15075319, ECO:0000269|PubMed:15169914, ECO:0000269|PubMed:15794755, ECO:0000269|PubMed:16307850, ECO:0000269|PubMed:17060315, ECO:0000269|PubMed:9129154, ECO:0000269|PubMed:9234700, ECO:0000269|PubMed:9336459, ECO:0000269|PubMed:9395241, ECO:0000269|PubMed:9417054}.;
Pathway
Signal Transduction;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH;EGFR1 (Consensus)

Recessive Scores

pRec
0.314

Intolerance Scores

loftool
0.0980
rvis_EVS
0.04
rvis_percentile_EVS
57.31

Haploinsufficiency Scores

pHI
0.139
hipred
Y
hipred_score
0.786
ghis
0.412

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.884

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Elf3
Phenotype
growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary 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);

Gene ontology

Biological process
blastocyst development;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;inflammatory response;multicellular organism development;epidermis development;cell differentiation;extracellular matrix organization;epithelial cell differentiation;positive regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;mammary gland involution
Cellular component
nucleus;nucleoplasm;Golgi apparatus;cytosol
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;DNA-binding transcription factor activity;transcription coactivator activity;protein binding