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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 2 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 2 | 1 |
Variants in ELF3
This is a list of pathogenic ClinVar variants found in the ELF3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-202011149-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 1-202011297-C-A | not specified | Uncertain significance (May 18, 2023) | ||
| 1-202011969-G-T | not specified | Uncertain significance (Feb 03, 2022) | ||
| 1-202012105-T-C | Benign (May 30, 2017) | |||
| 1-202012418-C-G | not specified | Uncertain significance (May 06, 2024) | ||
| 1-202012677-C-T | Likely benign (May 01, 2023) | |||
| 1-202012678-G-A | not specified | Likely benign (Nov 30, 2022) | ||
| 1-202012739-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 1-202012997-G-A | not specified | Uncertain significance (Jul 14, 2023) | ||
| 1-202013193-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 1-202013891-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
| 1-202013927-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 1-202015315-C-T | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ELF3 | protein_coding | protein_coding | ENST00000359651 | 8 | 9244 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.983 | 0.0168 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.88 | 152 | 233 | 0.653 | 0.0000147 | 2435 |
| Missense in Polyphen | 41 | 85.858 | 0.47753 | 927 | ||
| Synonymous | 0.597 | 87 | 94.4 | 0.922 | 0.00000620 | 707 |
| Loss of Function | 3.87 | 2 | 21.3 | 0.0941 | 0.00000136 | 203 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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