EBF1

protein-coding

EBF transcription factor 1, the group of Early B-cell factors|IPT domain containing

Gene summary

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of DNA-templated transcription. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

MANE transcript

NM_024007.5

Inheritance

—

ClinVar variants

U:57B:1

Top phenotype

EBF1-related condition

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr5:158,695,920-159,099,916

External References & Databases

Ensembl (ENSG00000164330)

Transcript & Mutation Effects

hg38 • Region Span ~404.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EBF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 46

EBF1-related conditionTotal: 3

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024007.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			53 clinvar			53
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	57	1	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024007.5	RefSeq	NP_076870.1	16	MANE Select
ENST00000313708.11	Ensembl	ENSP00000322898.6	16	MANE Select
NM_001290360.3	RefSeq	NP_001277289.1	16	Standard
NM_001324101.2	RefSeq	NP_001311030.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional regulation of white adipocyte differentiation
White fat cell differentiation
Adipogenesis
Prion disease pathway
White fat cell differentiation

Biological Process

multicellular organism development
positive regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding
protein dimerization activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313708
Coding exons: 16
Length: 403842
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.38	184	366	0.503	0.0000214	3874
Missense (PolyPhen)		43	122.32	0.35154		1265
Synonymous	0.768	134	146	0.919	0.00000957	1153
Loss of Function	4.59	3	30.3	0.0991	0.00000145	346

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3'. {ECO:0000250}.;

Recessive Scores

pRec: 0.289

Intolerance Scores

LoFtool: 0.124
RVIS EVS: -0.47
RVIS percentile EVS: 23.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium