EBF4

EBF family member 4, the group of Early B-cell factors|IPT domain containing

Basic information

Region (hg38): 20:2692780-2760108

Links

ENSG00000088881NCBI:57593OMIM:609935HGNC:29278Uniprot:Q9BQW3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EBF4 gene.

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
clinvar
2
missense
50
clinvar
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)3086840
20-2693673-C-G not specified Uncertain significance (Dec 13, 2023)3086845
20-2693724-T-A not specified Uncertain significance (Feb 22, 2023)2487286
20-2705581-G-A not specified Uncertain significance (Aug 02, 2021)2349935
20-2705636-C-G not specified Uncertain significance (Nov 08, 2021)2204041
20-2705653-G-A not specified Uncertain significance (Oct 10, 2023)3086847
20-2705662-A-C not specified Uncertain significance (Mar 11, 2022)2278086
20-2705671-C-T not specified Uncertain significance (Jun 27, 2022)2257002
20-2705672-G-A not specified Uncertain significance (Dec 15, 2022)2207863
20-2705712-C-T Benign (Apr 26, 2018)783856
20-2705980-G-A not specified Uncertain significance (Nov 17, 2023)3086848
20-2705984-C-T not specified Uncertain significance (Apr 12, 2022)2388430
20-2706014-G-A not specified Uncertain significance (Aug 02, 2021)2388685
20-2706020-G-T not specified Uncertain significance (Jan 31, 2024)3086850
20-2706035-A-G not specified Uncertain significance (Jul 06, 2021)2367987
20-2706247-G-A not specified Uncertain significance (Aug 12, 2021)2244202
20-2707972-A-G not specified Uncertain significance (May 27, 2022)2292436
20-2709577-G-T Benign (Apr 26, 2018)783857
20-2709615-C-T not specified Uncertain significance (Feb 02, 2022)2275161
20-2709635-A-G not specified Uncertain significance (Feb 10, 2022)2341962
20-2709638-G-A not specified Uncertain significance (Jun 22, 2023)2590587
20-2749628-C-A not specified Uncertain significance (Jun 23, 2023)2606230
20-2749688-G-A not specified Uncertain significance (Jul 08, 2022)2225667
20-2749709-G-T not specified Uncertain significance (Jul 06, 2021)2216021
20-2749719-A-G not specified Uncertain significance (Oct 04, 2022)2316737

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EBF4protein_codingprotein_codingENST00000380648 1767230
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003150.99700000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.811982840.6970.00001743803
Missense in Polyphen80120.580.663461434
Synonymous1.161051210.8660.000007961217
Loss of Function2.661024.10.4150.00000128325

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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