CBFB

Summary

CBFB (core-binding factor subunit beta, HGNC:1539) is a protein-coding gene on chromosome 16q22.1, encoding Core-binding factor subunit beta (Q13951). Forms the heterodimeric complex core-binding factor (CBF) with RUNX family proteins (RUNX1, RUNX2, and RUNX3). It is a selective cancer dependency (DepMap: 21.6% of cell lines).

The protein encoded by this gene is the beta subunit of a heterodimeric core-binding transcription factor belonging to the PEBP2/CBF transcription factor family which master-regulates a host of genes specific to hematopoiesis (e.g., RUNX1) and osteogenesis (e.g., RUNX2). The beta subunit is a non-DNA binding regulatory subunit; it allosterically enhances DNA binding by alpha subunit as the complex binds to the core site of various enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers and GM-CSF promoters. Alternative splicing generates two mRNA variants, each encoding a distinct carboxyl terminus. In some cases, a pericentric inversion of chromosome 16 [inv(16)(p13q22)] produces a chimeric transcript consisting of the N terminus of core-binding factor beta in a fusion with the C-terminal portion of the smooth muscle myosin heavy chain 11. This chromosomal rearrangement is associated with acute myeloid leukemia of the M4Eo subtype. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 865 — RefSeq curated summary.

At a glance

• Gene–disease (curated): cleidocranial dysplasia 2 (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 35 total — 2 pathogenic
• Phenotypes (HPO): 27
• Druggable target: yes — 2 molecules with ChEMBL bioactivity
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
• Cancer dependency (DepMap): dependent in 21.6% of screened cell lines
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_022845

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1539
Approved symbol	CBFB
Name	core-binding factor subunit beta
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	PEBP2B
Ensembl gene	ENSG00000067955
Ensembl biotype	protein_coding
OMIM	121360
Entrez	865

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 11 protein_coding, 3 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000290858, ENST00000412916, ENST00000561924, ENST00000563939, ENST00000564034, ENST00000565389, ENST00000566281, ENST00000567947, ENST00000568858, ENST00000650873, ENST00000651988, ENST00000652116, ENST00000652360, ENST00000862089, ENST00000862090, ENST00000862091, ENST00000862092, ENST00000929055, ENST00000958716

RefSeq mRNA: 6 — MANE Select: NM_022845 NM_001368707, NM_001368708, NM_001368709, NM_001368710, NM_001755, NM_022845

CCDS: CCDS10827, CCDS45508

Canonical transcript exons

ENST00000412916 — 6 exons

Exon	Start	End
ENSE00001297396	67029149	67029485
ENSE00001620506	67082213	67082308
ENSE00001696905	67098710	67101058
ENSE00003462846	67029727	67029813
ENSE00003599426	67036639	67036755
ENSE00003658049	67066682	67066798

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 96.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.7610 / max 597.0157, expressed in 1812 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154559	15.8689	1796
154561	5.2138	1622
154558	2.1546	1255
154560	0.7051	410
154565	0.6294	214
154566	0.6240	194
154562	0.5809	339
154563	0.3914	202
207915	0.3698	147
154564	0.2230	80

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	96.31	gold quality
sural nerve	UBERON:0015488	96.30	gold quality
tibia	UBERON:0000979	96.26	gold quality
calcaneal tendon	UBERON:0003701	95.99	gold quality
periodontal ligament	UBERON:0008266	95.44	gold quality
tibialis anterior	UBERON:0001385	95.16	gold quality
oocyte	CL:0000023	94.92	gold quality
cartilage tissue	UBERON:0002418	94.88	gold quality
bone marrow cell	CL:0002092	94.82	gold quality
islet of Langerhans	UBERON:0000006	94.70	gold quality
choroid plexus epithelium	UBERON:0003911	94.53	gold quality
tendon	UBERON:0000043	94.52	gold quality
vermiform appendix	UBERON:0001154	94.46	gold quality
tonsil	UBERON:0002372	94.18	gold quality
epithelial cell of pancreas	CL:0000083	94.07	gold quality
lymph node	UBERON:0000029	94.05	gold quality
mononuclear cell	CL:0000842	94.00	gold quality
leukocyte	CL:0000738	93.95	gold quality
thymus	UBERON:0002370	93.94	gold quality
monocyte	CL:0000576	93.92	gold quality
epithelium of nasopharynx	UBERON:0001951	93.86	gold quality
nasopharynx	UBERON:0001728	93.84	gold quality
ileal mucosa	UBERON:0000331	93.66	gold quality
oviduct epithelium	UBERON:0004804	93.53	gold quality
hair follicle	UBERON:0002073	93.50	gold quality
dorsal root ganglion	UBERON:0000044	93.40	gold quality
tendon of biceps brachii	UBERON:0008188	93.33	gold quality
stromal cell of endometrium	CL:0002255	93.03	gold quality
visceral pleura	UBERON:0002401	92.97	gold quality
endometrium	UBERON:0001295	92.81	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	9.31
E-ANND-3	yes	7.24
E-ENAD-27	yes	3.83

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
GATA1	Unknown
RUNX1	Unknown
RUNX2	Unknown
RUNX3	Unknown

Upstream regulators (CollecTRI, top): ESR1, GATA1, MYC, SP1

miRNA regulators (miRDB)

272 targeting CBFB, 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-3925-3P	100.00	69.95	1237
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 21.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• has a role in hematopoiesis; preturbations result from expression of the leukemogenic fusion gene Cbfb-MYH11 (PMID:12239155)
• review: genetics of CBFB and RUNX1 and roles in hematopoiesis and leukemogenesis, with emphasis on human and knockout mice studies (PMID:12495904)
• Expression of CBFB is down regulated in a significant portion of gastric cancer cases; may be involved in gastric carcinogenesis (PMID:15386419)
• Plag1 and Plagl2 are novel leukemia oncogenes that act by expanding hematopoietic progenitors expressing CbF beta-SMMHC. (PMID:15585652)
• Detection of acute myeloid leukemic cells that are characterized by a CBFB-MYH11 gene fusion. (PMID:16502584)
• These observations suggest that when abdominal GS is diagnosed, an analysis of the CBFB/MYH11 fusion gene is necessary to make an appropriate decision regarding treatment options, even if no chromosomal abnormalities are found. (PMID:16504290)
• Agents interacting with the outer surface of the CBFbeta-SMMHC ACD that prevent multimerization may be effective as novel therapeutics in AML (PMID:16767164)
• Rare fusion transcripts were correlated with an atypical cytomorphology not primarily suggestive for the FAB subtype acute myelocytic leukemia. (PMID:17287858)
• Cbfb enhances osteogenic differentiation of mesenchymal stem cells by stabilizing Cbfa-1 proteins. (PMID:17379770)
• Examine consequences of expression of abnormal chimeric protein CBFbeta-MYH11 in acute myelomonocytic leukemia. (PMID:17571080)
• interaction with PEBP2-beta leads to the phosphorylation of RUNX1, which in turn induces p300 phosphorylation (PMID:18695000)
• high CBFB protein level was an independent predictor of survival in colorectal cancer (PMID:19156145)
• CBFbeta is essential for TEL-AML1’s ability to promote self-renewal of B cell precursors in vitro. (PMID:19179469)
• For routine clinical practice, it may be meaningful to screen for C-KIT mutations in AML1/ETO-positive patients, as well as for FLT3(D835) mutations in CBF-AML. (PMID:19603346)
• Loss of DNA binding, but not nuclear localization or CBF-beta heterodimerization, causes RUNX2 haploinsufficiency in patients with the RUNX2(R131G) mutation. (PMID:20225274)
• The structural features of RUNX1/CBFbeta and their derivatives, their roles in transcriptional control, and their contributions to normal and malignant hematopoiesis are discussed. Review. (PMID:20306249)
• Studies show that FISH technic for the detection of CBF chromosomal aberrations was significantly higher than conventional cytogenetics. (PMID:20306685)
• The expression of Cbfbeta which were the key factors in osteogenic differentiation was also up-regulated. (PMID:20433876)
• conclude that CBFbeta is required for a subset of Runx2-target genes that are sufficient to maintain the invasive phenotype of the cells (PMID:20591170)
• Data collectively suggest that CBFbeta is required for malignant phenotype in prostate and ovarian cancer cells. (PMID:20607802)
• Vif and CBF-beta physically interact, and that the amino-terminal region of Vif is required for this interaction (PMID:22190036)
• CBF-beta is required for Vif-mediated degradation of APOBEC3G and therefore for preserving HIV-1 infectivity (PMID:22190037)
• Vif proteins of human and simian immunodeficiency viruses require cellular CBFbeta to degrade APOBEC3G. (PMID:22205746)
• These separation-of-function mutants demonstrate that HIV-1 Vif and the RUNX transcription factors interact with cellular CBFbeta on genetically distinct surfaces. (PMID:22725134)
• A comparison of heat capacity changes supports a model in which CBFbeta prestabilizes Vif((1-192)) relative to Vif((95-192)) (PMID:23098073)
• Our data indicate that the CBFbeta-SMMHC’s C-terminus is essential to induce embryonic hematopoietic defects and leukemogenesis. (PMID:23152542)
• We conclude that non-type A CBFB-MYH11 fusion types associate with distinct clinical and genetic features, including lack of KIT mutations, and a unique gene-expression profile in acute myeloid leukemia (PMID:23160462)
• Authors revealed that different lengths and regions are required for CBFbeta to assist HIV-1 Vif or RUNX1. (PMID:23175372)
• This report of recurring FLT3 N676 mutations in core-binding factor (CBF) leukemias suggests a defined subgroup of CBF leukemias. (PMID:23878140)
• Transcriptional analysis revealed that upon fusion protein knockdown, a small subset of the CBFbeta-MYH11 target genes show increased expression, confirming a role in transcriptional repression (PMID:24002588)
• In the absence of CBFbeta, Vif does not bind Cul5, thus preventing the assembly of the E3 ligase complex. (PMID:24390320)
• CBF-beta is critical for the formation of the Vif-ElonginB/ElonginC-Cul5 core E3 ubiquitin ligase complex. (PMID:24390335)
• data reveal the structural basis for Vif hijacking of the CBF-beta and CUL5 E3 ligase complex, laying a foundation for rational design of novel anti-HIV drugs (PMID:24402281)
• Vif conserved residues E88/W89 are crucial for CBFbeta binding. (PMID:24418540)
• Authors propose that CBFbeta acts as a chaperone to stabilize HIV-1 Vif during and after synthesis and to facilitate interaction of Vif with cellular cofactors required for the efficient degradation of APOBEC3G. (PMID:24522927)
• Suggest that CBFbeta retention in the midbody during cytokinesis reflects a novel function that contributes to epigenetic control. (PMID:24648201)
• Our findings indicate that RUNX1 and CBF-beta cooperate in cells to modulate HIV-1 replication (PMID:24651404)
• CBFB contributes to the transcriptional regulation of ribosomal gene expression and provide further understanding of the epigenetic role of CBFB-SMMHC in proliferation and maintenance of the leukemic phenotype. (PMID:25079347)
• suggest that a different mechanism exists for the Vif-APOBEC interaction and that non-primates are not suitable animal models for exploring pharmacological interventions that disrupt Vif-CBF-beta interaction (PMID:25122780)
• we report a novel hypomethylation pattern, specific to CBFB-MYH11 fusion resulting from inv(16) rearrangement in acute myeloid leukemia the expression of which correlated with PBX3 differential methylation (PMID:25266220)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	cbfb	ENSDARG00000040917
mus_musculus	Cbfb	ENSMUSG00000031885
rattus_norvegicus	Cbfb	ENSRNOG00000014647
drosophila_melanogaster	Bgb	FBGN0013753
drosophila_melanogaster	Bro	FBGN0013755
caenorhabditis_elegans	bro-1	WBGENE00000272

Protein

Protein identifiers

Core-binding factor subunit beta — Q13951 (reviewed: Q13951)

Alternative names: Polyomavirus enhancer-binding protein 2 beta subunit, SL3-3 enhancer factor 1 subunit beta, SL3/AKV core-binding factor beta subunit

All UniProt accessions (6): Q13951, A0A494C0A9, H3BSC0, J3KRT0, J3KS23, J3KTD8

UniProt curated annotations — full annotation on UniProt →

Function. Forms the heterodimeric complex core-binding factor (CBF) with RUNX family proteins (RUNX1, RUNX2, and RUNX3). RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5’-TGTGGT-3’, or very rarely, 5’-TGCGGT-3’, within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. (Microbial infection) Following infection, hijacked by the HIV-1 Vif protein, leading to the formation a cullin-5-RING E3 ubiquitin-protein ligase complex (ECS complex) that catalyzes ubiquitination and degradation of APOBEC3F and APOBEC3G. The complex can also ubiquitinate APOBEC3H to some extent. Association with HIV-1 Vif protein also inhibits the transcription coactivator activity of CBFB/CBF-beta.

Subunit / interactions. Heterodimer with RUNX1, RUNX2 and RUNX3. Interacts with COPRS. Found in a complex with PRMT5 and RUNX1. (Microbial infection) Interacts with HIV-1 Vif; forming an active cullin-5-RING E3 ubiquitin-protein ligase complex (ECS complex).

Subcellular location. Nucleus.

Disease relevance. A chromosomal aberration involving CBFB is associated with acute myeloid leukemia of M4EO subtype. Pericentric inversion inv(16)(p13;q22). The inversion produces a fusion protein that consists of the 165 N-terminal residues of CBF-beta (PEPB2) with the tail region of MYH11. Cleidocranial dysplasia 2 (CLCD2) [MIM:620099] A form of cleidocranial dysplasia, a rare skeletal disorder with significant clinical variability, even within families. Patients typically present with delayed closure of cranial sutures and fontanels with multiple Wormian bones, retarded ossification of the skull, shortening of the distal phalanges, dental anomalies including supernumerary teeth and eruption failure, clavicular hypoplasia or aplasia, wide pubic symphysis, vertebral anomalies, and short stature. Craniofacial features are subtle and characterized by prominent parietal and frontal bones, widely spaced eyes, depressed nasal bridge and small maxilla. Some CLCD2 patients present mild to moderate developmental delay. CLCD2 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the CBF-beta family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q13951-1	1	yes
Q13951-2	2

RefSeq proteins (6): NP_001355636, NP_001355637, NP_001355638, NP_001355639, NP_001746, NP_074036* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003417	CBF_beta	Family
IPR036552	CBF_bsu_sf	Homologous_superfamily

Pfam: PF02312

UniProt features (25 total): strand 8, helix 6, turn 3, sequence variant 2, mutagenesis site 2, chain 1, site 1, splice variant 1, modified residue 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
8J62	ELECTRON MICROSCOPY	2.5
1E50	X-RAY DIFFRACTION	2.6
1H9D	X-RAY DIFFRACTION	2.6
8CX0	ELECTRON MICROSCOPY	2.7
8H0I	ELECTRON MICROSCOPY	2.8
6P59	X-RAY DIFFRACTION	2.94
8CX2	ELECTRON MICROSCOPY	3.2
8FVI	ELECTRON MICROSCOPY	3.24
4N9F	X-RAY DIFFRACTION	3.3
8CX1	ELECTRON MICROSCOPY	3.3
8FVJ	ELECTRON MICROSCOPY	3.54
8E40	ELECTRON MICROSCOPY	3.57
8SZK	ELECTRON MICROSCOPY	3.58
9E93	ELECTRON MICROSCOPY	3.58
6NIL	ELECTRON MICROSCOPY	3.9
9E9V	ELECTRON MICROSCOPY	4
6VGD	X-RAY DIFFRACTION	4.2
6VGE	X-RAY DIFFRACTION	4.25
6VGG	X-RAY DIFFRACTION	4.31
1CL3	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13951-F1	85.81	0.56

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 (1): 165–166 (breakpoint for translocation to form cbf-beta-myh11 oncogene in aml, subtype m4eo)

Post-translational modifications (1): 173

Mutagenesis-validated functional residues (2):

Position	Phenotype
35–43	abolished ability to promote ubiquitination and degradation of apobec3f following interaction with hiv-1 vif. does not a
54	abolished ability to promote ubiquitination and degradation of apobec3f following interaction with hiv-1 vif. does not a

Function

Pathways and Gene Ontology

Reactome pathways

25 pathways

ID	Pathway
R-HSA-8877330	RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs)
R-HSA-8878166	Transcriptional regulation by RUNX2
R-HSA-8931987	RUNX1 regulates estrogen receptor mediated transcription
R-HSA-8934593	Regulation of RUNX1 Expression and Activity
R-HSA-8935964	RUNX1 regulates expression of components of tight junctions
R-HSA-8936459	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-8939242	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes
R-HSA-8939243	RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8939245	RUNX1 regulates transcription of genes involved in BCR signaling
R-HSA-8939246	RUNX1 regulates transcription of genes involved in differentiation of myeloid cells
R-HSA-8939247	RUNX1 regulates transcription of genes involved in interleukin signaling
R-HSA-8939256	RUNX1 regulates transcription of genes involved in WNT signaling
R-HSA-8939902	Regulation of RUNX2 expression and activity
R-HSA-8940973	RUNX2 regulates osteoblast differentiation
R-HSA-8941284	RUNX2 regulates chondrocyte maturation
R-HSA-8941326	RUNX2 regulates bone development
R-HSA-8941332	RUNX2 regulates genes involved in cell migration
R-HSA-8941333	RUNX2 regulates genes involved in differentiation of myeloid cells
R-HSA-8941858	Regulation of RUNX3 expression and activity
R-HSA-8949275	RUNX3 Regulates Immune Response and Cell Migration
R-HSA-8951911	RUNX3 regulates RUNX1-mediated transcription
R-HSA-8951936	RUNX3 regulates p14-ARF
R-HSA-9018519	Estrogen-dependent gene expression
R-HSA-9616222	Transcriptional regulation of granulopoiesis

MSigDB gene sets: 518 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_REGULATION_OF_CELL_ACTIVATION, MORF_DNMT1, RRAGTTGT_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GOBP_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, YAGI_AML_WITH_INV_16_TRANSLOCATION, chr16q22, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GOBP_OSTEOBLAST_DIFFERENTIATION

GO Biological Process (14): negative regulation of transcription by RNA polymerase II (GO:0000122), protein polyubiquitination (GO:0000209), osteoblast differentiation (GO:0001649), regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366), lymphocyte differentiation (GO:0030098), myeloid cell differentiation (GO:0030099), negative regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043371), positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378), positive regulation of transcription by RNA polymerase II (GO:0045944), cell maturation (GO:0048469), definitive hemopoiesis (GO:0060216), ossification (GO:0001503), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (4): transcription coactivator activity (GO:0003713), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), membrane (GO:0016020), core-binding factor complex (GO:0016513), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Transcriptional regulation by RUNX1	12
Transcriptional regulation by RUNX2	4
RUNX2 regulates bone development	2
Generic Transcription Pathway	1
Transcriptional regulation by RUNX3	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	3
regulation of transcription by RNA polymerase II	2
cell differentiation	2
regulation of DNA-templated transcription	2
DNA-templated transcription	2
hemopoiesis	2
positive regulation of DNA-templated transcription	2
cellular anatomical structure	2
negative regulation of DNA-templated transcription	1
protein ubiquitination	1
ossification	1
lymphocyte activation	1
mononuclear cell differentiation	1
CD4-positive, alpha-beta T cell differentiation	1
regulation of CD4-positive, alpha-beta T cell differentiation	1
negative regulation of alpha-beta T cell differentiation	1
negative regulation of CD4-positive, alpha-beta T cell activation	1
CD8-positive, alpha-beta T cell differentiation	1
regulation of CD8-positive, alpha-beta T cell differentiation	1
positive regulation of alpha-beta T cell differentiation	1
positive regulation of CD8-positive, alpha-beta T cell activation	1
cell development	1
cellular developmental process	1
anatomical structure maturation	1
multicellular organismal process	1
positive regulation of RNA biosynthetic process	1
transcription coregulator activity	1
DNA binding	1
nucleic acid binding	1
binding	1
nuclear lumen	1
RNA polymerase II transcription regulator complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CBFB	RUNX1	Q01196	999
CBFB	RUNX3	Q13761	997
CBFB	RUNX2	Q13950	996
CBFB	ELOB	Q15370	994
CBFB	CUL5	Q93034	994
CBFB	ELOC	Q15369	992
CBFB	RNF7	Q9UBF6	989
CBFB	MYH11	P35749	978
CBFB	LYL1	P12980	922
CBFB	FLNA	P21333	882
CBFB	TCF3	P15883	869
CBFB	RUNX1T1	Q06455	780
CBFB	APOBEC3G	Q9HC16	774
CBFB	GATA1	P15976	760
CBFB	CBFA2T3	O75081	754

IntAct

86 interactions, top by confidence:

A	B	Type	Score
CBFB	RUNX1	psi-mi:“MI:0407”(direct interaction)	0.870
CBFB	RUNX1	psi-mi:“MI:0915”(physical association)	0.870
CBFB	RUNX1	psi-mi:“MI:0914”(association)	0.870
RUNX1	CBFB	psi-mi:“MI:0915”(physical association)	0.870
CUL5	vif	psi-mi:“MI:0915”(physical association)	0.740
CUL5	vif	psi-mi:“MI:0914”(association)	0.740
CRYBA4	CRYBB1	psi-mi:“MI:0914”(association)	0.730
CBFB	vif	psi-mi:“MI:0914”(association)	0.690
vif	CBFB	psi-mi:“MI:0914”(association)	0.690
vif	CBFB	psi-mi:“MI:0915”(physical association)	0.690
RUNX2	CBFB	psi-mi:“MI:0915”(physical association)	0.670
vif	CUL2	psi-mi:“MI:0914”(association)	0.660
RUNX3	CBFB	psi-mi:“MI:0915”(physical association)	0.560
RUNX1	CBFB	psi-mi:“MI:0915”(physical association)	0.560
LHFPL4	ATP5F1B	psi-mi:“MI:0914”(association)	0.530
ARF5	ARF3	psi-mi:“MI:0914”(association)	0.530
DNAJB8	DNAJB6	psi-mi:“MI:0914”(association)	0.530
CBFB	INTS13	psi-mi:“MI:0915”(physical association)	0.520
RUNX3	CBFB	psi-mi:“MI:0915”(physical association)	0.500
vif	UBL4A	psi-mi:“MI:0914”(association)	0.500
vif	HDAC3	psi-mi:“MI:0914”(association)	0.500
vif	BAG6	psi-mi:“MI:0914”(association)	0.460
vif	DNAJB2	psi-mi:“MI:0914”(association)	0.460
vif	CBFB	psi-mi:“MI:0915”(physical association)	0.400
RUNX1	CBFB	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (183): vif (Affinity Capture-Western), CBFB (Affinity Capture-Western), CBFB (Co-purification), CBFB (Affinity Capture-Western), vif (Co-purification), TCEB1 (Co-purification), CBFB (Reconstituted Complex), CBFB (Affinity Capture-Western), TCEB2 (Co-purification), RUNX1 (Co-purification), RUNX1 (Affinity Capture-Western), RUNX2 (Affinity Capture-Western), RUNX3 (Affinity Capture-Western), CBFB (Affinity Capture-MS), CBFB (Affinity Capture-MS)

ESM2 similar proteins: A4GCJ2, A4GCM5, A7WQL9, B4URE2, O41649, O41665, O57268, O57276, O89748, O92548, P03496, P08270, P08272, P08274, P13139, P13142, P16857, P22385, P36349, P69252, P69417, Q08024, Q09227, Q0A2H0, Q0A2Q8, Q0A3Q3, Q13951, Q20NN7, Q20NS3, Q20PL8, Q24040, Q2VC87, Q3SBF0, Q5PQ44, Q67256, Q6DP28, Q6DP62, Q6DP66, Q6DP70, Q6J871

Diamond homologs: Q08024, Q13951, Q24039, Q24040

SIGNOR signaling

7 interactions.

A	Effect	B	Mechanism
CBFB	“form complex”	“Core Binding Factor complex”	binding
MLL-AF9	“down-regulates quantity by repression”	CBFB	“transcriptional regulation”
MLL-ENL	“down-regulates quantity by repression”	CBFB	“transcriptional regulation”
MLL-AF4	“down-regulates quantity by repression”	CBFB	“transcriptional regulation”
GATA1	“down-regulates quantity by repression”	CBFB	“transcriptional regulation”
CBFB	“up-regulates quantity by stabilization”	RUNX1	binding

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — BRCA.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	8
Likely benign	3
Benign	5

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1712242	NM_022845.3(CBFB):c.78+1G>T	Pathogenic
1712243	NM_022845.3(CBFB):c.283-1039_400-7568del	Pathogenic

SpliceAI

1422 predictions. Top by Δscore:

Variant	Effect	Δscore
16:67029464:G:GT	donor_gain	1.0000
16:67029468:C:G	donor_gain	1.0000
16:67029484:AGG:A	donor_loss	1.0000
16:67029485:GG:G	donor_loss	1.0000
16:67029486:GTGAG:G	donor_loss	1.0000
16:67029722:TGCA:T	acceptor_loss	1.0000
16:67029723:GCA:G	acceptor_loss	1.0000
16:67029724:CAGAT:C	acceptor_loss	1.0000
16:67029725:A:AG	acceptor_gain	1.0000
16:67029725:A:G	acceptor_loss	1.0000
16:67029726:G:GG	acceptor_gain	1.0000
16:67029726:GA:G	acceptor_gain	1.0000
16:67029812:TC:T	donor_gain	1.0000
16:67029814:G:GG	donor_gain	1.0000
16:67036634:A:AG	acceptor_gain	1.0000
16:67036634:AAAAG:A	acceptor_gain	1.0000
16:67036635:A:G	acceptor_gain	1.0000
16:67036752:CAAG:C	donor_loss	1.0000
16:67036753:AAG:A	donor_loss	1.0000
16:67036754:AGGT:A	donor_loss	1.0000
16:67036756:GT:G	donor_loss	1.0000
16:67036757:T:A	donor_loss	1.0000
16:67040332:C:G	donor_gain	1.0000
16:67082211:A:AG	acceptor_gain	1.0000
16:67082212:G:GG	acceptor_gain	1.0000
16:67029479:GT:G	donor_gain	0.9900
16:67029483:GAG:G	donor_gain	0.9900
16:67029487:T:G	donor_loss	0.9900
16:67029726:GAT:G	acceptor_gain	0.9900
16:67029726:GATT:G	acceptor_gain	0.9900

AlphaMissense

1236 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:67029431:G:C	Q8H	1.000
16:67029431:G:T	Q8H	1.000
16:67029441:T:C	F12L	1.000
16:67029442:T:C	F12S	1.000
16:67029442:T:G	F12C	1.000
16:67029443:C:A	F12L	1.000
16:67029443:C:G	F12L	1.000
16:67029460:T:C	F18S	1.000
16:67029463:G:C	R19T	1.000
16:67029463:G:T	R19M	1.000
16:67029464:G:C	R19S	1.000
16:67029464:G:T	R19S	1.000
16:67029469:T:C	L21P	1.000
16:67029732:G:C	K28N	1.000
16:67029732:G:T	K28N	1.000
16:67029733:T:C	Y29H	1.000
16:67029733:T:G	Y29D	1.000
16:67029734:A:C	Y29S	1.000
16:67029740:G:A	G31D	1.000
16:67029742:T:C	F32L	1.000
16:67029744:C:A	F32L	1.000
16:67029744:C:G	F32L	1.000
16:67029746:G:T	R33M	1.000
16:67029766:C:A	R40S	1.000
16:67029779:T:C	F44S	1.000
16:67029799:G:C	G51R	1.000
16:67029800:G:A	G51D	1.000
16:67029800:G:T	G51V	1.000
16:67036640:C:A	A56D	1.000
16:67036642:T:C	F57L	1.000

dbSNP variants (sampled 300 via entrez): RS1000097241 (16:67055029 A>G), RS1000107266 (16:67096785 T>A,C), RS1000149531 (16:67054839 G>A), RS1000215572 (16:67070857 A>G), RS1000305955 (16:67068865 T>C), RS1000311474 (16:67067086 T>C), RS1000357171 (16:67068436 A>G), RS1000397160 (16:67097067 T>A), RS1000398726 (16:67097391 C>T), RS1000546864 (16:67067596 C>G), RS1000565970 (16:67060966 T>A), RS1000567463 (16:67062016 G>A), RS1000667661 (16:67027939 A>C,G), RS1000675155 (16:67065168 G>A,T), RS1000688244 (16:67033671 G>A)

Disease associations

OMIM: gene MIM:121360 | disease phenotypes: MIM:620099, MIM:601626

GenCC curated gene-disease

Disease	Classification	Inheritance
cleidocranial dysplasia 2	Strong	Autosomal dominant
acute myeloid leukemia	Limited	Unknown

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
cleidocranial dysplasia 2	Definitive	AD

Mondo (2): cleidocranial dysplasia 2 (MONDO:0859307), acute myeloid leukemia (MONDO:0018874)

Orphanet (1): Acute myeloid leukemia (Orphanet:519)

HPO phenotypes

27 total (27 of 27 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000260	Wide anterior fontanel
HP:0000307	Pointed chin
HP:0000327	Hypoplasia of the maxilla
HP:0000365	Hearing impairment
HP:0000680	Delayed eruption of primary teeth
HP:0000894	Short clavicles
HP:0000938	Osteopenia
HP:0001216	Delayed ossification of carpal bones
HP:0001263	Global developmental delay
HP:0001357	Plagiocephaly
HP:0001508	Failure to thrive
HP:0001763	Pes planus
HP:0002673	Coxa valga
HP:0002857	Genu valgum
HP:0003577	Congenital onset
HP:0003621	Juvenile onset
HP:0006585	Congenital pseudoarthrosis of the clavicle
HP:0006660	Aplastic clavicle
HP:0008788	Delayed pubic bone ossification
HP:0009882	Short distal phalanx of finger
HP:0011069	Supernumerary tooth
HP:0011220	Prominent forehead
HP:0011304	Broad thumb
HP:0011462	Young adult onset
HP:0011463	Childhood onset
HP:0200021	Down-sloping shoulders

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004630_203	Mean corpuscular hemoglobin	4.000000e-13
GCST90000025_95	Appendicular lean mass	2.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0004980	appendicular lean mass

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D015470	Leukemia, Myeloid, Acute	C04.557.337.539.275; C15.378.508.539.275

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL1615386 (SINGLE PROTEIN), CHEMBL2093862 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 6,816 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL3187985	APOMORPHINE HYDROCHLORIDE	4	5,278
CHEMBL1232461	MOLIBRESIB	2	1,538

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

Binding affinities (BindingDB)

34 measured of 34 human assays (34 total across all organisms); most potent 34 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
4,6-dichloro-2-pyridin-2-yl-1H-benzimidazole	IC50	700 nM	US-8748618: Inhibitors of inv(16) leukemia
4-chloro-2-pyridin-2-yl-6-(trifluoromethyl)-1H-benzimidazole	IC50	760 nM	US-8748618: Inhibitors of inv(16) leukemia
2-pyridin-2-yl-6-(trifluoromethoxy)-1H-benzimidazole	IC50	1000 nM	US-8748618: Inhibitors of inv(16) leukemia
4-(2-pyridin-2-yl-3H-benzimidazol-5-yl)morpholine	IC50	1000 nM	US-8748618: Inhibitors of inv(16) leukemia
[2-(4-methoxy-2-pyridinyl)-3H-benzimidazol-5-yl]methanol	IC50	1000 nM	US-8748618: Inhibitors of inv(16) leukemia
2-pyridin-2-yl-6-(trifluoromethyl)-1H-benzimidazole	IC50	1100 nM	US-8748618: Inhibitors of inv(16) leukemia
(4,6-difluoro-2-pyridin-2-yl-1H-benzimidazol-5-yl)methanol	IC50	1300 nM	US-8748618: Inhibitors of inv(16) leukemia
(6-chloro-2-pyridin-2-yl-3H-benzimidazol-5-yl)methanol	IC50	1300 nM	US-8748618: Inhibitors of inv(16) leukemia
6-propan-2-yloxy-2-pyridin-2-yl-1H-benzimidazole	IC50	1400 nM	US-8748618: Inhibitors of inv(16) leukemia
4,5,6-trifluoro-2-pyridin-2-yl-1H-benzimidazole	IC50	1400 nM	US-8748618: Inhibitors of inv(16) leukemia
6-ethoxy-2-pyridin-2-yl-1H-benzimidazole	IC50	1500 nM	US-8748618: Inhibitors of inv(16) leukemia
(2-pyridin-2-yl-3H-benzimidazol-5-yl)methanethiol	IC50	1800 nM	US-8748618: Inhibitors of inv(16) leukemia
2-pyridin-2-yl-4-pyridin-3-yl-6-(trifluoromethoxy)-1H-benzimidazole	IC50	2000 nM	US-8748618: Inhibitors of inv(16) leukemia
[2-(4-methoxy-2-pyridinyl)-3H-benzimidazol-5-yl] formate	IC50	2000 nM	US-8748618: Inhibitors of inv(16) leukemia
5,6-dimethyl-2-pyridin-2-yl-1H-benzimidazole	IC50	2000 nM	US-8748618: Inhibitors of inv(16) leukemia
[2-[5-(2-methoxyethoxy)-2-pyridinyl]-3H-benzimidazol-5-yl]methanol	IC50	2300 nM	US-8748618: Inhibitors of inv(16) leukemia
2-[5-(2-methoxyethoxy)-2-pyridinyl]-6-(trifluoromethoxy)-1H-benzimidazole	IC50	2300 nM	US-8748618: Inhibitors of inv(16) leukemia
6-chloro-2-pyridin-2-yl-1H-benzimidazole	IC50	2300 nM	US-8748618: Inhibitors of inv(16) leukemia
US8748618, AI-10-61	IC50	2500 nM	US-8748618: Inhibitors of inv(16) leukemia
5,6-difluoro-2-pyridin-2-yl-1H-benzimidazole	IC50	2500 nM	US-8748618: Inhibitors of inv(16) leukemia
[2-(5-methoxy-2-pyridinyl)-3H-benzimidazol-5-yl]methanol	IC50	2500 nM	US-8748618: Inhibitors of inv(16) leukemia
6-fluoro-2-pyridin-2-yl-1H-benzimidazole	IC50	2500 nM	US-8748618: Inhibitors of inv(16) leukemia
5-methyl-2-(pyridin-2-yl)-1H-benzo[d]imidazole	IC50	2900 nM	US-8748618: Inhibitors of inv(16) leukemia
[2-(3-methoxy-2-pyridinyl)-3H-benzimidazol-5-yl]methanol	IC50	3000 nM	US-8748618: Inhibitors of inv(16) leukemia
6-methylsulfonyl-2-pyridin-2-yl-1H-benzimidazole	IC50	3300 nM	US-8748618: Inhibitors of inv(16) leukemia
6-imidazol-1-yl-2-pyridin-2-yl-1H-benzimidazole	IC50	3400 nM	US-8748618: Inhibitors of inv(16) leukemia
4-ethoxy-2-pyridin-2-yl-1H-benzimidazole	IC50	4200 nM	US-8748618: Inhibitors of inv(16) leukemia
4,5-dimethyl-2-pyridin-2-yl-1H-benzimidazole	IC50	4300 nM	US-8748618: Inhibitors of inv(16) leukemia
[6-(hydroxymethyl)-2-pyridin-2-yl-3H-benzimidazol-5-yl]methanol	IC50	4600 nM	US-8748618: Inhibitors of inv(16) leukemia
4-methyl-2-pyridin-2-yl-1H-benzimidazole	IC50	5300 nM	US-8748618: Inhibitors of inv(16) leukemia
4-methoxy-2-pyridin-2-yl-1H-benzimidazole	IC50	5500 nM	US-8748618: Inhibitors of inv(16) leukemia
(2-pyridin-2-yl-3H-benzimidazol-5-yl)methanol	IC50	16000 nM	US-8748618: Inhibitors of inv(16) leukemia
2-(3-fluoro-2-pyridinyl)-6-(trifluoromethoxy)-1H-benzimidazole	IC50	22000 nM	US-8748618: Inhibitors of inv(16) leukemia
(2-pyridin-2-yl-3H-benzimidazol-5-yl) formate	IC50	40000 nM	US-8748618: Inhibitors of inv(16) leukemia

ChEMBL bioactivities

90 potent at pChembl≥5 of 162 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.59	IC50	257	nM	CHEMBL1487114
6.47	IC50	340	nM	CHEMBL1548014
6.43	IC50	372	nM	CHEMBL1492213
6.41	IC50	393	nM	CHEMBL1555914
6.37	IC50	429	nM	CHEMBL1998294
6.32	IC50	475	nM	CHEMBL1360981
6.20	IC50	629	nM	CHEMBL1299795
6.19	IC50	643	nM	CHEMBL1331901
6.16	IC50	700	nM	CHEMBL3675784
6.15	IC50	713.4	nM	CHEMBL1372231
6.12	IC50	760	nM	CHEMBL3675786
6.06	IC50	865	nM	CHEMBL1486938
6.00	IC50	1000	nM	CHEMBL3675778
6.00	IC50	1000	nM	CHEMBL3675787
6.00	IC50	1000	nM	CHEMBL3675795
5.98	IC50	1040	nM	CHEMBL427876
5.96	IC50	1100	nM	CHEMBL3675785
5.92	IC50	1190	nM	CHEMBL1429988
5.89	IC50	1300	nM	CHEMBL3675782
5.89	IC50	1300	nM	CHEMBL3675783
5.88	IC50	1330	nM	CHEMBL1424123
5.87	IC50	1350	nM	CHEMBL1333600
5.85	IC50	1400	nM	CHEMBL3675773
5.85	IC50	1400	nM	CHEMBL3675781
5.82	IC50	1500	nM	CHEMBL3675771
5.80	IC50	1600	nM	CHEMBL1372231
5.78	IC50	1670	nM	CHEMBL1987092
5.75	IC50	1800	nM	CHEMBL3675776
5.73	IC50	1860	nM	CHEMBL1505563
5.73	IC50	1865	nM	CHEMBL1323994
5.70	IC50	2000	nM	CHEMBL3675770
5.70	IC50	2000	nM	CHEMBL371956
5.70	IC50	2000	nM	CHEMBL3675789
5.70	IC50	2000	nM	CHEMBL3675796
5.70	IC50	2000	nM	CHEMBL1499658
5.69	IC50	2040	nM	CHEMBL1303198
5.67	IC50	2140	nM	CHEMBL1328822
5.65	IC50	2220	nM	CHEMBL1339329
5.64	IC50	2300	nM	CHEMBL166127
5.64	IC50	2300	nM	CHEMBL3675791
5.64	IC50	2300	nM	CHEMBL3675792
5.63	IC50	2340	nM	CHEMBL1529346
5.62	IC50	2370	nM	CHEMBL3196628
5.60	IC50	2500	nM	CHEMBL3675774
5.60	IC50	2500	nM	CHEMBL199982
5.60	IC50	2500	nM	CHEMBL3675780
5.60	IC50	2500	nM	CHEMBL3675790
5.58	IC50	2600	nM	CHEMBL3675770
5.57	IC50	2710	nM	CHEMBL1410686
5.54	IC50	2900	nM	CHEMBL352049

PubChem BioAssay actives

1 with measured affinity, of 6 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178610: Inhibition of CBFB (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	4.1000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
entinostat	decreases expression, affects cotreatment	2
Resveratrol	affects cotreatment, increases expression	2
Acetaminophen	increases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Aflatoxin B1	affects expression, increases expression	2
FR900359	increases phosphorylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects methylation	1
geraniol	decreases expression	1
trichostatin A	affects expression	1
arsenite	affects binding, decreases reaction	1
cobaltous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
motexafin gadolinium	affects cotreatment, affects expression, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Arsenic	affects methylation	1
Cannabidiol	decreases expression	1
Coumestrol	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Malathion	increases expression	1

ChEMBL screening assays

15 unique, capped per target: 12 binding, 3 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3705193	Binding	FRET Assay: We have developed effective assays to monitor the inhibition of CBFβ-SMMHC binding to the Runt domain (as well as for CBFβ binding to the Runt domain). We fused the green fluorescent protein derivative Cerulean to the N-terminus	Inhibitors of inv(16) leukemia
CHEMBL1737904	Functional	PubChem BioAssay. qHTS Assay for Compounds Blocking the Interaction Between CBF-beta and RUNX1 for the Treatment of Acute Myeloid Leukemia: Hit Validation with Orthogonal Assay. (Class of assay: confirmatory)	PubChem BioAssay data set

Cellosaurus cell lines

29 cell lines: 26 cancer cell line, 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_0131	A-172	Cancer cell line	Male
CVCL_1820	HPB-ALL	Cancer cell line	Male
CVCL_2110	ME-1 [Human leukemia]	Cancer cell line	Male
CVCL_5735	D-54MG	Cancer cell line	Male
CVCL_7959	HPB-MLT	Cancer cell line	Male
CVCL_A0K7	SEES3-1V human CBFB, clone1	Embryonic stem cell	Male
CVCL_A0K8	SEES3-1V human CBFB, clone2	Embryonic stem cell	Male
CVCL_A0K9	SEES3-1V human CBFB, clone3	Embryonic stem cell	Male
CVCL_B1BV	Abcam A-431 CBFB KO	Cancer cell line	Female
CVCL_D5ZN	A172/TMZ	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00199147	PHASE4	UNKNOWN	Efficacy of G-CSF-Priming in Elderly AML Patients
NCT00304447	PHASE4	COMPLETED	Study Evaluating the Effect of Corticosteroids on Mylotarg® Infusion-Related Adverse Events in Patients With Leukemia
NCT00464217	PHASE4	COMPLETED	Treatment of the Acute Myeloblastic Leukaemia in Patients Over 65 Years
NCT00487448	PHASE4	COMPLETED	SMD_FLAG-IDA_98: FLAG-IDA in Induction Treatment of High Risk Myelodysplastic Syndromes or Secondary Acute Myeloblastic Leukemia
NCT00488709	PHASE4	COMPLETED	Fludarabine, Cytarabine, Topotecan in Treating Patients With Relapsed or Refractory Acute Myeloid Leukemia
NCT00686543	PHASE4	COMPLETED	Oral Posaconazole in High Risk Patients With Gastrointestinal Dysfunction (Study P05115)
NCT01041040	PHASE4	COMPLETED	LAM07: Study to Analyze the Efficacy of a Risk Adapted Treatment Strategy, Including Gemtuzumab Ozogamicin (GO) During Consolidation, for Patients With Acute Myeloid Leukemia (AML)
NCT01198054	PHASE4	TERMINATED	LENA-LMA-5:Lenalidomide in Acute Myeloid Leukemia (AML)
NCT01200355	PHASE4	COMPLETED	Posaconazole Versus Micafungin for Prophylaxis Against Invasive Fungal Infections During Neutropenia in Patients Undergoing Chemotherapy for Acute Myelogenous Leukemia, Acute Lymphocytic Leukemia or Myelodysplastic Syndrome
NCT01347996	PHASE4	COMPLETED	Maintenance Therapy With Ceplene® (Histamine) and IL-2 on Immune Response and MRD in Acute Myeloid Leukemia
NCT01587430	PHASE4	UNKNOWN	3 Anthracyclines, 2 Types of Consolidation With Different ARA-C Doses and Maintenance in Adult Acute Myeloid Leukemia
NCT01819792	PHASE4	COMPLETED	Respiratory Viral Infections During Acute Myeloid Leukemia (AML)Chemotherapy Related Aplasia
NCT02024308	PHASE4	UNKNOWN	AML1-ETO Acute Myeloid Leukemia With Fludarabine and Cytarabine Chemotherapy
NCT02027064	PHASE4	UNKNOWN	Interferon for the Intervention of Molecular Relapse in t (8; 21) AML After Allo-HSCT
NCT02277847	PHASE4	UNKNOWN	Idarubicin at Different Dosages as Induction Therapy for Newly Diagnosed Acute Myeloid Leukaemia
NCT02386800	PHASE4	ACTIVE_NOT_RECRUITING	CINC424A2X01B Rollover Protocol
NCT02926586	PHASE4	COMPLETED	Fludarabine and Cytarabine Versus High-dose Cytarabine for CBF-AML
NCT02933333	PHASE4	UNKNOWN	G-CSF Alone or Combination With GM-CSF on Prevention and Treatment of Infection in Children With Malignant Tumor
NCT03026842	PHASE4	UNKNOWN	Decitabine Versus Conventional Chemotherapy for Maintenance Therapy of Acute Myeloid Leukemia With t(8;21)
NCT03150134	PHASE4	UNKNOWN	Early Tapering of Immunosuppressive Agents to Immunomodulation to Improve Survival of AML Patients
NCT05144243	PHASE4	ACTIVE_NOT_RECRUITING	Study to Assess Adverse Events and Change in Disease State of Oral Venetoclax in Combination With Subcutaneous (SC) Azacitidine in Newly Diagnosed Adult Participants With Acute Myeloid Leukemia (AML) Who Are Ineligible for Intensive Chemotherapy in China
NCT06370000	PHASE4	RECRUITING	Oral Azacitidine in Transplant-Eligible Patients With Acute Myeloid Leukemia (AML) Suffering From Health-Inequality
NCT06571825	PHASE4	RECRUITING	RIC Allo-HSCT vs. Venetoclax-Based Consolidation in Elderly AML Patients After First CR
NCT07016165	PHASE4	RECRUITING	Ciprofloxacin vs Ceftazidime for Empirical Treatment of High-Risk Neutropenic Fever in Children With Hematologic Malignancies
NCT07044687	PHASE4	RECRUITING	Study to Assess Adverse Events and Change in Disease Activity of Oral Venetoclax in Combination With Subcutaneous (SC) or Intravenous (IV) Azacitidine in Newly Diagnosed Adult Participants With Acute Myeloid Leukemia (AML) Who Are Ineligible for Standard Induction Therapy in India
NCT07486713	PHASE4	RECRUITING	Olutasidenib DDI Study in Patients With IDH1 Mutation Positive Malignancies
NCT07561892	PHASE4	RECRUITING	Study of the Effectiveness and Safety of Daunorubicin /Idarubicin ± Silibinin in Treating Newly Diagnosed AML (Non-M3).
NCT00000589	PHASE3	COMPLETED	Trial to Reduce Alloimmunization to Platelets (TRAP)
NCT00044486	PHASE3	COMPLETED	Prophylaxis Trial of Posaconazole Versus Standard Azole Therapy for Neutropenic Patients (Study P01899)
NCT00093990	PHASE3	COMPLETED	Tipifarnib Versus Best Supportive Care in the Treatment of Newly Diagnosed Acute Myeloid Leukemia (AML)
NCT00125606	PHASE3	TERMINATED	Phase 3 Trial for AML Patients in CR2 Comparing 8Gy TBI /Fludarabine to Conditioning With TBI 12Gy/Cyclophosphamide
NCT00136084	PHASE3	COMPLETED	Treatment of Patients With Newly Diagnosed Acute Myeloid Leukemia or Myelodysplasia
NCT00146120	PHASE3	COMPLETED	Risk-Adapted Therapy of Acute Myeloid Leukemia of Adults (18-60 Years) According to the Cytogenetic Result
NCT00150878	PHASE3	TERMINATED	Standard vs. Reduced-Intensity Conditioning in Patients With Acute Myeloid Leukemia in First Remission
NCT00151255	PHASE3	COMPLETED	All-Trans Retinoic Acid in Combination With Standard Induction and Consolidation Therapy in Older Patients With Newly Diagnosed Acute Myeloid Leukemia
NCT00152139	PHASE3	COMPLETED	Stem Cell Transplantation for Patients With Hematologic Malignancies
NCT00152594	PHASE3	TERMINATED	Voriconazole or Placebo in the Prophylaxis of Lung Infiltrates in Patients Undergoing Induction Chemotherapy for Acute Myelogenous Leukemia
NCT00186966	PHASE3	COMPLETED	Treatment of Children and Adolescents With Refractory or Relapsed Acute Myeloid Leukemia
NCT00226512	PHASE3	WITHDRAWN	To Determine the Role of Adding Campath-1H or ATG Given In-vivo in Addition to Fludarabine and Low Dose Busulfex on Outcome in Patients Treated With Reduced Intensity Conditioning
NCT00260832	PHASE3	COMPLETED	Trial of Decitabine in Patients With Acute Myeloid Leukemia