EBF4
Basic information
Region (hg38): 20:2692780-2760108
Links
Phenotypes
GenCC
Source:
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 EBF4 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 | 50 | 50 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 50 | 0 | 2 |
Variants in EBF4
This is a list of pathogenic ClinVar variants found in the EBF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-2693667-C-G | not specified | Uncertain significance (Feb 26, 2024) | ||
20-2693673-C-G | not specified | Uncertain significance (Dec 13, 2023) | ||
20-2693724-T-A | not specified | Uncertain significance (Feb 22, 2023) | ||
20-2705581-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
20-2705636-C-G | not specified | Uncertain significance (Nov 08, 2021) | ||
20-2705653-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
20-2705662-A-C | not specified | Uncertain significance (Mar 11, 2022) | ||
20-2705671-C-T | not specified | Uncertain significance (Jun 27, 2022) | ||
20-2705672-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
20-2705712-C-T | Benign (Apr 26, 2018) | |||
20-2705980-G-A | not specified | Uncertain significance (Nov 17, 2023) | ||
20-2705984-C-T | not specified | Uncertain significance (Apr 12, 2022) | ||
20-2706014-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
20-2706020-G-T | not specified | Uncertain significance (Jan 31, 2024) | ||
20-2706035-A-G | not specified | Uncertain significance (Jul 06, 2021) | ||
20-2706247-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
20-2707972-A-G | not specified | Uncertain significance (May 27, 2022) | ||
20-2709577-G-T | Benign (Apr 26, 2018) | |||
20-2709615-C-T | not specified | Uncertain significance (Feb 02, 2022) | ||
20-2709635-A-G | not specified | Uncertain significance (Feb 10, 2022) | ||
20-2709638-G-A | not specified | Uncertain significance (Jun 22, 2023) | ||
20-2749628-C-A | not specified | Uncertain significance (Jun 23, 2023) | ||
20-2749688-G-A | not specified | Uncertain significance (Jul 08, 2022) | ||
20-2749709-G-T | not specified | Uncertain significance (Jul 06, 2021) | ||
20-2749719-A-G | not specified | Uncertain significance (Oct 04, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EBF4 | protein_coding | protein_coding | ENST00000380648 | 17 | 67230 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000315 | 0.997 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.81 | 198 | 284 | 0.697 | 0.0000174 | 3803 |
Missense in Polyphen | 80 | 120.58 | 0.66346 | 1434 | ||
Synonymous | 1.16 | 105 | 121 | 0.866 | 0.00000796 | 1217 |
Loss of Function | 2.66 | 10 | 24.1 | 0.415 | 0.00000128 | 325 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional factor which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3'. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0932
Haploinsufficiency Scores
- pHI
- 0.199
- hipred
- N
- hipred_score
- 0.331
- ghis
- 0.439
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.379
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ebf4
- Phenotype
Gene ontology
- Biological process
- multicellular organism development;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding;protein dimerization activity