EBF4

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

Basic information

Region (hg38): 20:2692779-2760108

Links

ENSG00000088881 ∙ NCBI:57593 ∙ OMIM:609935 ∙ HGNC:29278 ∙ Uniprot:Q9BQW3 ∙ 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 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	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: gnomAD

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: 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
• 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

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