EBF1

Summary

EBF1 (EBF transcription factor 1, HGNC:3126) is a protein-coding gene on chromosome 5q33.3, encoding Transcription factor COE1 (Q9UH73). Key pioneer transcription factor of B-cell specification and commitment.

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.

Source: NCBI Gene 1879 — RefSeq curated summary.

At a glance

• GWAS associations: 111
• Clinical variants (ClinVar): 62 total
• Cancer driver (intOGen): activating (oncogene-like) across 4 cancer types
• Transcription factor: yes — 41 downstream targets (CollecTRI)
• MANE Select transcript: NM_024007

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3126
Approved symbol	EBF1
Name	EBF transcription factor 1
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	OLF1, COE1
Ensembl gene	ENSG00000164330
Ensembl biotype	protein_coding
OMIM	164343
Entrez	1879

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000313708, ENST00000380654, ENST00000517373, ENST00000518323, ENST00000518836, ENST00000519739, ENST00000519890, ENST00000522192, ENST00000523315, ENST00000523464, ENST00000873114, ENST00000964682

RefSeq mRNA: 15 — MANE Select: NM_024007 NM_001290360, NM_001324101, NM_001324103, NM_001324106, NM_001324107, NM_001324108, NM_001324109, NM_001324111, NM_001364155, NM_001364156, NM_001364157, NM_001364158, NM_001364159, NM_024007, NM_182708

CCDS: CCDS4343, CCDS78081

Canonical transcript exons

ENST00000313708 — 16 exons

Exon	Start	End
ENSE00003473390	158712154	158712333
ENSE00003490681	158707979	158708173
ENSE00003491076	159084666	159084739
ENSE00003500297	158840029	158840110
ENSE00003540643	158796345	158796475
ENSE00003543030	158695920	158699142
ENSE00003552808	158731069	158731157
ENSE00003598895	158823176	158823317
ENSE00003604898	159073396	159073464
ENSE00003636930	159096343	159096406
ENSE00003647289	159095620	159095675
ENSE00003648058	158777413	158777539
ENSE00003650111	158714117	158714182
ENSE00003691447	158712970	158713147
ENSE00003692859	159096974	159097130
ENSE00003846074	159099345	159099916

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 99.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8913 / max 542.7415, expressed in 1039 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64591	7.7522	952
64585	1.2353	528
64589	0.7350	200
64580	0.2121	85
64587	0.1966	69
64586	0.1382	48
64558	0.1077	48
64577	0.1006	41
64579	0.0890	30
64581	0.0865	39

Top tissues by expression

257 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
synovial joint	UBERON:0002217	99.12	gold quality
layer of synovial tissue	UBERON:0007616	99.05	gold quality
calcaneal tendon	UBERON:0003701	98.92	gold quality
oocyte	CL:0000023	97.45	gold quality
buccal mucosa cell	CL:0002336	97.40	gold quality
skin of hip	UBERON:0001554	96.79	gold quality
cardiac muscle of right atrium	UBERON:0003379	96.66	gold quality
parietal pleura	UBERON:0002400	96.62	gold quality
vena cava	UBERON:0004087	96.62	gold quality
dorsal root ganglion	UBERON:0000044	96.40	gold quality
superficial temporal artery	UBERON:0001614	96.27	gold quality
urethra	UBERON:0000057	96.15	gold quality
saphenous vein	UBERON:0007318	95.70	gold quality
secondary oocyte	CL:0000655	95.64	gold quality
pericardium	UBERON:0002407	95.48	gold quality
sural nerve	UBERON:0015488	95.12	gold quality
tendon	UBERON:0000043	95.02	gold quality
mammary duct	UBERON:0001765	94.47	gold quality
thoracic mammary gland	UBERON:0005200	94.42	gold quality
subcutaneous adipose tissue	UBERON:0002190	94.32	gold quality
upper arm skin	UBERON:0004263	94.30	gold quality
mammary gland	UBERON:0001911	94.29	gold quality
epithelium of mammary gland	UBERON:0003244	94.25	gold quality
trigeminal ganglion	UBERON:0001675	94.21	gold quality
adipose tissue	UBERON:0001013	94.05	gold quality
cauda epididymis	UBERON:0004360	93.97	gold quality
endothelial cell	CL:0000115	93.73	gold quality
penis	UBERON:0000989	93.59	gold quality
cartilage tissue	UBERON:0002418	93.50	gold quality
left ventricle myocardium	UBERON:0006566	93.32	gold quality

Single-cell (SCXA)

Detected in 23 experiment(s), a significant marker in 23.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	3743.06
E-GEOD-131882	yes	3028.66
E-CURD-119	yes	2026.20
E-GEOD-180759	yes	1499.44
E-HCAD-56	yes	1388.16
E-MTAB-8894	yes	1198.82
E-CURD-6	yes	1062.87
E-GEOD-75140	yes	822.48
E-GEOD-98556	yes	816.53
E-MTAB-6678	yes	675.11
E-HCAD-5	yes	592.57
E-MTAB-9067	yes	479.57
E-HCAD-10	yes	54.13
E-HCAD-4	yes	49.60
E-CURD-112	yes	48.07

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

41 targets.

Target	Regulation
ACHE
ADCY3
ATF5	Unknown
BCR
BLK
CCL15-CCL14
CD19	Activation
CD79A	Activation
CD79B	Unknown
CEACAM1	Activation
CEBPA	Activation
CEL
CHGA
CNGA2
CREBBP
CXCL12	Activation
CXCL5	Activation
EBF1	Activation
EBF2
EN1	Unknown
FOXO1	Activation
GATA3	Unknown
GFI1
GFI1B
GNAL
IGLL1
OMP
PAX5
POSTN	Activation
PPARG	Activation

JASPAR motifs

Motif	Name	Family
MA0154.2	EBF1	Early B-Cell Factor-related factors
MA0154.3	EBF1	Early B-Cell Factor-related factors
MA0154.4	EBF1	Early B-Cell Factor-related factors
MA0154.5	EBF1	Early B-Cell Factor-related factors

JASPAR matrix evidence (PMIDs): PMID:17916232, PMID:8497258

Upstream regulators (CollecTRI, top): CEBPB, CEBPD, EBF1, EBF2, EOMES, ETS1, LMX1B, PAX5, SPI1, STAT5A, TCF3

miRNA regulators (miRDB)

193 targeting EBF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-1250-3P	99.96	70.04	4038

Literature-anchored findings (GeneRIF, showing 40)

• Three independent binding sites for EBF in the surrogate light chain VpreB promoter are important for the full function of the promoter and its collaborative activation by EBF and E47 in a preB cell line. (PMID:11994467)
• data suggest that Notch signaling may affect B-versus T-lineage commitment by the targeting of both EBF and E2A (PMID:15920012)
• EBF-1 and PPARgamma2 induce adipocyte differentiation with comparable kinetics and efficiency. (PMID:16106032)
• Two genetic markers within the EBF1 gene have been found associated with multiple sclerosis, indicative either of their causative role or that of some other polymorphism in linkage disequilibrium with them. (PMID:16255771)
• The regulation of Ebf1 via distinct promoters allows for the generation of several feedback loops and the coordination of multiple determinants of B lymphopoiesis in a regulatory network. (PMID:17101802)
• our studies not only provided molecular basis of ATF5 transcriptional regulation, but also identified ATF5 as a target gene of EBF1 transcription factor. (PMID:20423929)
• unique structural features of EBF domains and dimeerization motif (PMID:20592035)
• EBF1, BLK and TNFSF4 are all involved in B-cell differentiation and activation, and we conclude that polymorphisms in several susceptibility genes in the immune system contribute to the pathogenesis of primary SS. (PMID:20861858)
• Data show that ZNF521 can antagonize B-cell development and support the notion that it may contribute to conserve the multipotency of primitive lympho-myeloid progenitors by preventing or delaying their EBF1-driven commitment toward the B-cell lineage. (PMID:21593590)
• Ebf1 or Pax5 haploinsufficiency synergizes with STAT5 activation to initiate acute lymphoblastic leukemia (PMID:21606506)
• EBF1 functions as a tissue-specific regulator of chromatin structure at B cell-specific genes. [Review] (PMID:21735360)
• ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. (PMID:22473956)
• Loss of EBF1 expression is associated with Hodgkin lymphoma. (PMID:23174882)
• Using a capture sequencing strategy, we discovered the B-cell relevant genes IRF8, EBF1, and TNFSF13 as novel targets for IGH deregulation. (PMID:23775715)
• The transcription factor EBF1 is an interaction partner for TET2, suggesting a sequence-specific mechanism for regulating DNA methylation. (PMID:23863747)
• A novel cross talk between ERbeta and Early B-cell Factor 1 (EBF1) was also identified and characterized. (PMID:23951143)
• EBF1 plays a role in connecting chronic psychosocial stress and central obesity as a risk factor for CVD. (PMID:25271088)
• Studied whether EBF1 expression and biological activity in white adipose tissue is related to different metabolic parameters. (PMID:25791133)
• Epstein-Barr Virus EBNA1 bound to host genes of high significance for B-cell growth and function, including MEF2B, IL6R, and EBF1. (PMID:26468528)
• two multi-zinc finger transcription cofactors named ZNF423 and ZNF521 have been characterised as potent inhibitors of EBF1 and are emerging as potentially relevant contributors to the development of B-cell leukaemias (PMID:26788497)
• role in the expression of Latent membrane protein 1 (PMID:26819314)
• Among 15 childhood ALL patients with EBF1-PDGFRB fusion proteins, the fusion arose from interstitial deletion of 5q33 (n = 11), balanced rearrangement (n = 2), or complex rearrangement (n = 2). (PMID:26872634)
• early B cell factor-1 (EBF1) was identified as a co-regulator of gene expression with MEF2C. (PMID:26900922)
• EBF1 is critical for transcriptional control of SLAMF1 gene in human B cells. (PMID:27424222)
• The four single-nucleotide polymorphisms that had strong linkage disequilibrium relationships (rs10061900, rs10070743, rs4704967, and rs10056564) demonstrated significant interactions with the waist-hip ratio in the dominant model. (PMID:27744667)
• A genome-wide significant association was observed for rs35715456 (log10BF = 6.3) on chromosome 18 for the dichotomous trait of having at least one long-lived parent versus not having any long-lived parent. The most significant association among single nucleotide polymorphisms in longevity candidate genes (APOE, MINIPP1, FOXO3, EBF1, CAMKIV, and OTOL1) was observed in the EBF1 gene region (rs17056207, p = .0002). (PMID:27816938)
• EBF1 polymorphism is associated with metabolic diseases. (PMID:27918534)
• Data show that GS Homeobox 2 (Gsx2) and Early B-cell factor 1 (Ebf1) combined overexpression in human embryonic stem (hES) cells achieves high yields of medium spiny neurons (MSNs). (PMID:28137879)
• In a Chinese population the TT genotype and T alleles in rs36071027 in the EBF1 gene are associated with an increased risk of coronary artery disease and its severity. (PMID:28183271)
• EBF1-PDGFRB is sufficient to drive leukemogenesis. (PMID:28555080)
• In this genomewide association study, we found that variants at the EBF1, EEFSEC, AGTR2, WNT4, ADCY5, and RAP2C loci were associated with gestational duration and variants at the EBF1, EEFSEC, and AGTR2 loci with preterm birth. (PMID:28877031)
• this study demonstrates a role for the AHR in regulating human B cell development, and it suggests that transcriptional alterations of EBF1 by the AHR are involved in the underlying mechanism (PMID:28978690)
• EBF1 modifies the breast cancer subtype-specific methylation and gene expression program. (PMID:29099283)
• EBF1 was down-regulated in cholangiocarcinoma (CCA) tissues and cell lines. (PMID:29169115)
• EBF1 acts as a pioneer transcription factor that operates in a transcription factor network to activate B cell-specific genes and repress genes associated with alternative cell fates. (Review) (PMID:29336845)
• The results show that the mutation (CT+TT) at the rs987401919 and rs36071027 loci of EBF1 and its interaction with smoking and drinking are risk factors for coronary artery disease in Chinese patients. (PMID:29789399)
• Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene (PMID:30878028)
• EBF1 Gene mRNA Levels in Maternal Blood and Spontaneous Preterm Birth. (PMID:32046385)
• Maternal blood EBF1-based microRNA transcripts as biomarkers for detecting risk of spontaneous preterm birth: a nested case-control study. (PMID:32237936)
• Long intergenic noncoding RNA 00844 promotes apoptosis and represses proliferation of prostate cancer cells through upregulating GSTP1 by recruiting EBF1. (PMID:32329523)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	ebf1b	ENSDARG00000069196
danio_rerio	si:ch211-51e8.2	ENSDARG00000092635
danio_rerio	ebf1a	ENSDARG00000099849
mus_musculus	Ebf1	ENSMUSG00000057098
rattus_norvegicus	Ebf1	ENSRNOG00000028845
drosophila_melanogaster	kn	FBGN0001319
caenorhabditis_elegans		WBGENE00006743

Paralogs (3): EBF4 (ENSG00000088881), EBF3 (ENSG00000108001), EBF2 (ENSG00000221818)

Protein

Protein identifiers

Transcription factor COE1 — Q9UH73 (reviewed: Q9UH73)

Alternative names: Early B-cell factor

All UniProt accessions (2): E5RFQ1, Q9UH73

UniProt curated annotations — full annotation on UniProt →

Function. Key pioneer transcription factor of B-cell specification and commitment. Recognizes variations of the palindromic sequence 5’-ATTCCCNNGGGAATT-3’. Operates in a transcription factor network to activate B-cell-specific genes and repress genes associated with alternative cell fates. For instance, positively regulates many B-cell specific genes including BCR or CD40 while repressing genes that direct cells into alternative lineages, including GATA3 and TCF7 for the T-cell lineage. In addition to its role during lymphopoiesis, controls the thermogenic gene program in adipocytes during development and in response to environmental cold. (Microbial infection) Acts as a chromatin anchor for Epstein-Barr virus EBNA2 to mediate the assembly of EBNA2 chromatin complexes in B-cells. In addition, binds to the viral LMP1 proximal promoter and promotes its expression during latency.

Subunit / interactions. Homodimer. Interacts with ZNF423 and ZNF521, leading to prevent EBF1 to bind DNA and activate target genes. Interacts with CCR4-NOT component CNOT3. (Microbial infection) Interacts with Epstein-barr virus protein EBNA2.

Subcellular location. Nucleus.

Similarity. Belongs to the COE family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UH73-1	1	yes
Q9UH73-2	2

RefSeq proteins (15): NP_001277289, NP_001311030, NP_001311032, NP_001311035, NP_001311036, NP_001311037, NP_001311038, NP_001311040, NP_001351084, NP_001351085, NP_001351086, NP_001351087, NP_001351088, NP_076870, NP_874367 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002909	IPT_dom	Domain
IPR003523	Transcription_factor_COE	Family
IPR013783	Ig-like_fold	Homologous_superfamily
IPR014756	Ig_E-set	Homologous_superfamily
IPR018350	Transcription_factor_COE_CS	Conserved_site
IPR032200	COE_DBD	Domain
IPR032201	COE_HLH	Domain
IPR038006	COE_IPT	Domain
IPR038173	COE_DBD_sf	Homologous_superfamily

Pfam: PF01833, PF16422, PF16423

UniProt features (55 total): strand 22, sequence conflict 6, helix 6, region of interest 5, turn 4, site 2, cross-link 2, splice variant 2, chain 1, domain 1, modified residue 1, mutagenesis site 1, zinc finger region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3MQI	X-RAY DIFFRACTION	2.3
3LYR	X-RAY DIFFRACTION	2.51

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UH73-F1	72.07	0.47

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 172 (interaction with dna); 163 (interaction with dna)

Post-translational modifications (3): 1, 16, 16

Mutagenesis-validated functional residues (1):

Position	Phenotype
240	impaired ebf1-mediated cell differentiation and gene expression mostly without changing ebf1 occupancy.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-381340	Transcriptional regulation of white adipocyte differentiation
R-HSA-9752946	Expression and translocation of olfactory receptors

MSigDB gene sets: 295 (showing top): REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION, CREL_01, BENPORATH_ES_WITH_H3K27ME3, LU_IL4_SIGNALING, AREB6_03, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, ACTGCAG_MIR173P, NFKB_Q6, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, NFKB_C, SOX9_B1, KREPPEL_CD99_TARGETS_DN, IRF1_Q6, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, RIGGI_EWING_SARCOMA_PROGENITOR_DN

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Adipogenesis	1
Olfactory Signaling Pathway	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
cation binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2182 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EBF1	PAX5	Q02548	983
EBF1	TET2	Q6N021	968
EBF1	ZNF423	Q2M1K9	967
EBF1	TCF3	P15883	947
EBF1	IKZF1	Q13422	929
EBF1	IKZF3	Q9UKT9	879
EBF1	TMTC1	Q8IUR5	843
EBF1	ZNF521	Q96K83	794
EBF1	CD19	P15391	780
EBF1	LEF1	Q9UJU2	752
EBF1	BCL11A	Q9H165	729
EBF1	RAG1	P15918	716
EBF1	IGHV4-38-2	P0DP08	712
EBF1	SPIB	Q01892	705
EBF1	CD79A	P11912	699

IntAct

60 interactions, top by confidence:

A	B	Type	Score
ATPAF2	EBF1	psi-mi:“MI:0915”(physical association)	0.810
EBF1	ATPAF2	psi-mi:“MI:0915”(physical association)	0.810
EBF1	HOMEZ	psi-mi:“MI:0915”(physical association)	0.560
	EBF1	psi-mi:“MI:0915”(physical association)	0.560
POU6F2	EBF1	psi-mi:“MI:0915”(physical association)	0.560
EBF1	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
EBF1	ERO1A	psi-mi:“MI:0915”(physical association)	0.490
	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CCL22	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CCL24	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CCL3	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CCL3L1	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CCL4L1	EBF1	psi-mi:“MI:0915”(physical association)	0.370
CSF2	EBF1	psi-mi:“MI:0915”(physical association)	0.370
IFNG	EBF1	psi-mi:“MI:0915”(physical association)	0.370
IFNL4	EBF1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (25): HOMEZ (Two-hybrid), ATPAF2 (Two-hybrid), EBF1 (Affinity Capture-MS), EBF1 (Affinity Capture-MS), EBF1 (Affinity Capture-Western), EBF1 (Two-hybrid), EBF1 (Two-hybrid), ERO1L (Two-hybrid), CREBBP (Reconstituted Complex), CREBBP (Affinity Capture-Western), EBF1 (Two-hybrid), ATPAF2 (Two-hybrid), HOMEZ (Two-hybrid), EBF1 (Co-purification), EBF1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0R4IWI1, A5ABV9, B7ZRI2, B7ZRJ4, O08791, O08792, O13987, O73673, O73742, O74412, O74954, O93375, P06536, P06537, P49843, P49844, P56721, Q00858, Q03414, Q03571, Q07802, Q08DL5, Q10902, Q13761, Q13950, Q20937, Q23238, Q5H9I0, Q61X54, Q63398, Q64131, Q6E3C9, Q6E3D0, Q6E3D4, Q6E3D5, Q6P4K7, Q6PF39, Q700C2, Q8BYR2, Q8K4J2

Diamond homologs: A0A0R4IWI1, B7ZRI2, B7ZRJ4, O08791, O08792, O73742, O93375, P56721, Q07802, Q08DL5, Q63398, Q6P4K7, Q8K4J2, Q93705, Q9BQW3, Q9H4W6, Q9HAK2, Q9UH73, O13987

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ZNF521	down-regulates	EBF1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Interleukin-10 signaling	5	64.7×	7e-07

GO biological processes:

GO term	Partners	Fold	FDR
chemokine-mediated signaling pathway	5	67.5×	3e-06
antimicrobial humoral immune response mediated by antimicrobial peptide	5	33.8×	4e-05
positive regulation of cell migration	6	15.4×	1e-04
cell-cell signaling	5	14.5×	8e-04
inflammatory response	7	11.0×	1e-04
immune response	5	9.8×	3e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 4 cancer types — DLBCLNOS, LUSC, MLYM, NHL.

Clinical variants and AI predictions

ClinVar

62 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5294 predictions. Top by Δscore:

Variant	Effect	Δscore
5:158708169:CACTA:C	acceptor_gain	1.0000
5:158708171:CTA:C	acceptor_gain	1.0000
5:158708174:C:CC	acceptor_gain	1.0000
5:158712152:A:AC	donor_gain	1.0000
5:158712153:C:CC	donor_gain	1.0000
5:158712153:CTGG:C	donor_gain	1.0000
5:158712330:AAACC:A	acceptor_loss	1.0000
5:158712332:ACCTG:A	acceptor_loss	1.0000
5:158712334:C:G	acceptor_loss	1.0000
5:158712964:TCTGA:T	donor_loss	1.0000
5:158712965:CTGAC:C	donor_loss	1.0000
5:158712966:TGACC:T	donor_loss	1.0000
5:158712967:GACCC:G	donor_loss	1.0000
5:158712968:AC:A	donor_gain	1.0000
5:158712969:C:A	donor_gain	1.0000
5:158713144:TTTC:T	acceptor_gain	1.0000
5:158713146:TC:T	acceptor_gain	1.0000
5:158713147:CC:C	acceptor_gain	1.0000
5:158713148:C:CC	acceptor_gain	1.0000
5:158714111:GCTCA:G	donor_loss	1.0000
5:158714112:CTCAC:C	donor_loss	1.0000
5:158714113:TCACC:T	donor_loss	1.0000
5:158714114:CAC:C	donor_loss	1.0000
5:158714115:ACCT:A	donor_loss	1.0000
5:158714116:C:CG	donor_loss	1.0000
5:158714179:CTTC:C	acceptor_gain	1.0000
5:158731153:GAGCG:G	acceptor_gain	1.0000
5:158731154:AGCG:A	acceptor_gain	1.0000
5:158731154:AGCGC:A	acceptor_loss	1.0000
5:158731155:GCG:G	acceptor_gain	1.0000

AlphaMissense

3916 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:158708041:A:T	V561D	1.000
5:158708049:G:C	F558L	1.000
5:158708049:G:T	F558L	1.000
5:158708050:A:C	F558C	1.000
5:158708050:A:G	F558S	1.000
5:158708051:A:G	F558L	1.000
5:158708053:G:T	A557D	1.000
5:158714154:A:G	L385P	1.000
5:158714160:G:T	A383E	1.000
5:158714161:C:G	A383P	1.000
5:158714163:G:T	A382D	1.000
5:158714164:C:G	A382P	1.000
5:158714165:C:A	R381S	1.000
5:158714165:C:G	R381S	1.000
5:158714166:C:A	R381M	1.000
5:158714166:C:G	R381T	1.000
5:158714168:T:A	K380N	1.000
5:158714168:T:G	K380N	1.000
5:158714169:T:A	K380I	1.000
5:158714172:A:C	L379R	1.000
5:158714172:A:G	L379P	1.000
5:158714172:A:T	L379H	1.000
5:158731069:C:A	K375N	1.000
5:158731069:C:G	K375N	1.000
5:158731106:A:T	I363N	1.000
5:158731118:A:G	L359S	1.000
5:158731120:C:A	R358S	1.000
5:158731120:C:G	R358S	1.000
5:158731121:C:A	R358M	1.000
5:158731121:C:G	R358T	1.000

dbSNP variants (sampled 300 via entrez): RS1000011895 (5:158701562 C>T), RS1000015477 (5:158833847 G>A,C), RS1000017102 (5:159006154 G>A), RS1000021517 (5:158876428 A>G), RS1000025557 (5:158937254 C>A), RS1000037487 (5:158929179 A>G), RS1000038895 (5:159058988 C>T), RS1000041827 (5:158889044 T>C), RS1000042539 (5:158743860 G>A), RS1000054933 (5:158922500 G>C), RS1000063827 (5:159029202 A>G), RS1000070681 (5:158964313 G>A,C), RS1000070954 (5:159022087 C>T), RS1000072359 (5:158916242 C>T), RS1000074483 (5:159044142 A>G)

Disease associations

OMIM: gene MIM:164343 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

111 associations (top):

Study	Trait	p-value
GCST001227_4	Systolic blood pressure	3.000000e-11
GCST001228_6	Diastolic blood pressure	4.000000e-13
GCST001236_20	Blood pressure	1.000000e-11
GCST001238_4	Hypertension	2.000000e-07
GCST001762_526	Obesity-related traits	4.000000e-06
GCST001930_9	Breast cancer	7.000000e-06
GCST001937_56	Breast cancer	2.000000e-14
GCST002008_6	Adverse response to chemotherapy (neutropenia/leucopenia) (all anthracycline-based drugs)	5.000000e-07
GCST002403_2	Longevity (85 years and older)	4.000000e-06
GCST002404_2	Longevity (90 years and older)	2.000000e-08
GCST002563_20	Hypospadias	3.000000e-07
GCST002641_5	Hip circumference (psychosocial stress interaction)	3.000000e-08
GCST002740_83	Inflammatory skin disease	2.000000e-06
GCST003075_25	Cognitive decline rate in late mild cognitive impairment	8.000000e-07
GCST003114_1	Carotid intima media thickness	3.000000e-09
GCST003262_844	Post bronchodilator FEV1	1.000000e-06
GCST003272_15	Systolic blood pressure	2.000000e-07
GCST003968_4	Pericardial adipose tissue adjusted for height and weight	7.000000e-06
GCST003968_5	Pericardial adipose tissue adjusted for height and weight	1.000000e-09
GCST003971_1	Pericardial fat	3.000000e-09
GCST003983_7	Male-pattern baldness	7.000000e-22
GCST004278_65	Pulse pressure	6.000000e-11
GCST004279_22	Systolic blood pressure	1.000000e-13
GCST004280_70	Diastolic blood pressure	4.000000e-08
GCST004585_1	Anorexia nervosa (excluding migration to or from binge-eating disorder or bulimia nervosa)	2.000000e-07
GCST004609_58	Monocyte percentage of white cells	1.000000e-10
GCST004632_115	Lymphocyte percentage of white cells	4.000000e-09
GCST004775_23	Pulse pressure	7.000000e-06
GCST004776_22	Systolic blood pressure	2.000000e-11
GCST004777_10	Diastolic blood pressure	2.000000e-09

EFO canonical traits (37, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0006336	diastolic blood pressure
EFO:0006340	mean arterial pressure
EFO:0005188	CCL11 measurement
EFO:0005257	response to anthracycline-based chemotherapy
EFO:0006783	psychosocial stress measurement
EFO:0007710	cognitive decline measurement
EFO:0004314	forced expiratory volume
EFO:0004338	body weight
EFO:0005763	pulse pressure measurement
EFO:0007989	monocyte percentage of leukocytes
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0003917	premature birth
EFO:0005939	parental genotype effect measurement
EFO:0005112	gestational age
EFO:0004344	birth weight
EFO:0004534	creatine kinase measurement
EFO:0004329	alcohol drinking
EFO:0006527	smoking status measurement
EFO:0009270	heel bone mineral density
EFO:0008579	risk-taking behaviour
EFO:0004318	smoking behavior
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0004530	triglyceride measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0005670	smoking initiation
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004327	electrocardiography
EFO:0009819	comparative body size at age 10, self-reported
EFO:0004343	waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs4551053	EBF1		0.00	0

CTD chemical–gene interactions

54 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	6
bisphenol A	affects cotreatment, affects methylation, decreases expression, decreases methylation, increases expression (+1 more)	4
sodium arsenite	affects methylation, decreases expression, affects expression	4
trichostatin A	affects cotreatment, increases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Rotenone	decreases expression, increases expression	2
Aflatoxin B1	decreases methylation	2
Cadmium Chloride	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	increases expression	1
methyleugenol	decreases expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
arsenite	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	decreases expression	1
aflatoxin B2	increases methylation	1
cupric chloride	decreases expression	1
4-(2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acid	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
mercuric bromide	decreases expression	1
exemestane	increases expression	1
perfluorooctane sulfonic acid	affects expression, affects methylation	1
deguelin	decreases expression	1
2-palmitoylglycerol	increases expression	1
Chir 99021	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1

Cellosaurus cell lines

6 cell lines: 3 embryonic stem cell, 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A1D6	SEES3-1V human EBF1, clone1	Embryonic stem cell	Male
CVCL_A1D7	SEES3-1V human EBF1, clone2	Embryonic stem cell	Male
CVCL_A1D8	SEES3-1V human EBF1, clone3	Embryonic stem cell	Male
CVCL_B8F0	Abcam HCT 116 EBF1 KO	Cancer cell line	Male
CVCL_B8V2	Abcam MCF-7 EBF1 KO	Cancer cell line	Female
CVCL_B9H8	Abcam A-549 EBF1 KO	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.