BCL9

gene
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Summary

BCL9 (BCL9 transcription coactivator, HGNC:1008) is a protein-coding gene on chromosome 1q21.2, encoding B-cell CLL/lymphoma 9 protein (O00512). Involved in signal transduction through the Wnt pathway. It is a selective cancer dependency (DepMap: 12.1% of cell lines).

BCL9 is associated with B-cell acute lymphoblastic leukemia. It may be a target of translocation in B-cell malignancies with abnormalities of 1q21. Its function is unknown. The overexpression of BCL9 may be of pathogenic significance in B-cell malignancies.

Source: NCBI Gene 607 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): congenital heart disease (Limited, ClinGen)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 263 total — 4 pathogenic
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 3 cancer types
  • Cancer dependency (DepMap): dependent in 12.1% of screened cell lines
  • MANE Select transcript: NM_004326

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1008
Approved symbolBCL9
NameBCL9 transcription coactivator
Location1q21.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000116128
Ensembl biotypeprotein_coding
OMIM602597
Entrez607

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000234739, ENST00000497938, ENST00000683836, ENST00000684121

RefSeq mRNA: 1 — MANE Select: NM_004326 NM_004326

CCDS: CCDS30833

Canonical transcript exons

ENST00000234739 — 10 exons

ExonStartEnd
ENSE00000787543147618816147621057
ENSE00000824226147612883147613199
ENSE00000903093147622271147622531
ENSE00001156122147623842147626216
ENSE00001156130147611578147611889
ENSE00001344643147606784147606866
ENSE00001344647147604777147604911
ENSE00001344656147541501147541674
ENSE00003673699147615803147615902
ENSE00003684403147614427147614616

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 93.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7099 / max 328.5775, expressed in 1659 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
49796.15741159
49823.79221516
49831.1200646
49800.3682181
49810.2722129

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534393.24gold quality
ganglionic eminenceUBERON:000402391.10gold quality
ventricular zoneUBERON:000305390.83gold quality
islet of LangerhansUBERON:000000686.11gold quality
right uterine tubeUBERON:000130285.17gold quality
smooth muscle tissueUBERON:000113584.85gold quality
left uterine tubeUBERON:000130384.15gold quality
body of uterusUBERON:000985384.04gold quality
lower esophagus muscularis layerUBERON:003583383.17gold quality
lower esophagusUBERON:001347383.13gold quality
embryoUBERON:000092282.88gold quality
esophagogastric junction muscularis propriaUBERON:003584182.06gold quality
vena cavaUBERON:000408781.55gold quality
fallopian tubeUBERON:000388981.40gold quality
cerebellar cortexUBERON:000212981.30gold quality
cerebellar hemisphereUBERON:000224581.29gold quality
cardia of stomachUBERON:000116281.14silver quality
right hemisphere of cerebellumUBERON:001489080.98gold quality
popliteal arteryUBERON:000225080.93gold quality
tibial arteryUBERON:000761080.90gold quality
endocervixUBERON:000045880.64gold quality
ventral tegmental areaUBERON:000269180.63silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.62gold quality
muscle layer of sigmoid colonUBERON:003580580.58gold quality
rectumUBERON:000105280.43gold quality
right ovaryUBERON:000211880.37gold quality
cerebellumUBERON:000203780.23gold quality
aortaUBERON:000094780.21gold quality
mucosa of stomachUBERON:000119980.19gold quality
saphenous veinUBERON:000731880.15silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.89

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1, ESR2, PAX6

miRNA regulators (miRDB)

189 targeting BCL9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-188-3P100.0068.761240
HSA-MIR-3646100.0073.565283
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4533100.0069.482758
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-428299.9975.366408
HSA-MIR-477599.9875.006394
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-6825-5P99.9669.813431

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • crystallographic analysis of how beta-catenin, BCL9, BCL9-2 and Tcf4 interact (PMID:17052462)
  • BCL9 itself contains a transcriptional activation domain in the C terminus, which functionally synergizes in lymphoid cells with the C-terminal transactivation domain of beta-catenin. (PMID:18347063)
  • Data show that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me). (PMID:18498752)
  • Overexpression and altered subcellular localization of ATG16L1 protein in human oral squamous-cell carcinoma: correlation with lymphovascular invasion and lymph-node metastasis are reported. (PMID:18789482)
  • The amino-terminus of the BCL9 peptide is critical for maintaining the wild-type binding affinity of the BCL9 peptide to beta-catenin. (PMID:19715304)
  • Findings suggest that deregulation of BCL9 is an important contributing factor to tumor progression in multiple myeloma and colon neoplasms. (PMID:19738061)
  • Pygo2 PHD is the only known PHD finger that is capable of interacting simultaneously with two functional ligands, B9L and BCL9 (PMID:20637214)
  • These findings indicate that common variations in the BCL9 gene confer risk of schizophrenia and may also be associated with bipolar disorder and major depressive disorder in the Chinese Han population. (PMID:21383261)
  • growth factor induced proliferation mediates a neutralizing response by significantly increasing miR-30c-2* which reduces BCL9 expression and cell proliferation in SKOV-3 and OVCAR-3 cells (PMID:22024689)
  • Inhibition of the BCL9-beta-catenin interaction and selectively suppresses oncogenic Wnt transcription. (PMID:22914623)
  • we detected five SNPs in the first two genes/loci - BCL9 and C9orf5 - strongly associated with negative symptoms of schizophrenia (PMID:23382809)
  • By beta-catenin’s association with LEF1 and BCL9-2/B9L. (PMID:24419084)
  • MiR-30-5p downregulation occurs as a result of interaction between multiple myeloma cells and bone marrow stromal cells, which in turn enhances expression of BCL9. (PMID:24599134)
  • PCDH10 antagonized MM cell proliferation via the downregulation of Wnt/beta-catenin/BCL-9 signaling, whereas PCDH10 repressed the expression of AKT to promote the expression of GSK3beta and then to restrain the activation of beta-catenin (PMID:26081897)
  • BCL9 is a molecular driver of DCIS invasive progression. (PMID:26384318)
  • findings indicate that BCL9 most likely does not harbor a common genetic variant that can increase the risk for schizophrenia in the Japanese population (PMID:26494551)
  • BCL9/9L-beta-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer (PMID:26844272)
  • results from this study demonstrated that hypoxia induced BCL-9 expression in human CRC cells mainly through HIF-1alpha, which could be an important underlying mechanism for increased BCL-9 expression in CRC. (PMID:27121066)
  • it was demonstrated that miR218 modulated a novel molecular target and the present study provided novel insights into potential mechanisms of RCC oncogenesis. (PMID:27314976)
  • MEF2D-BCL9-positive patients had B-cell precursor immunophenotype and were characterized as being older in age, being resistant to chemotherapy, having very early relapse, and having leukemic blasts that mimic morphologically mature B-cell leukemia with markedly high expression of HDAC9. (PMID:27507882)
  • Specific regulation of BCL9 expression by HIF-1alpha may prove to be an underlying crosstalk between Wnt/beta-catenin signaling and hypoxia signaling pathways. (PMID:28074862)
  • The authors used CRISPR/Cas9 genome engineering of Drosophila legless (lgs) and human BCL9 and B9L to show that the C-terminus downstream of their adaptor elements is crucial for Wnt responses. (PMID:28296634)
  • miR-30a acts as a tumor suppressor by double-targeting COX-2 and BCL9, and significantly affects the development of H. pylori-induced gastric cancer, shedding new light on the mechanisms underlying H. pylori-associated gastric cancer. (PMID:28769030)
  • SOX7 inhibits oncogenic beta-catenin-mediated transcription by disrupting the beta-catenin/BCL9 interaction. (PMID:29271667)
  • The gene BCL9 is overexpressed in malignant adrenocortical tumors and promotes clonal ACC cell growth. These findings suggest that BCL9 overexpression may serve as an alternative driver of constitutive Wnt/beta-Catenin activation in ACC and could represent a potential molecular and diagnostic marker of tumor malignancy. (PMID:29428231)
  • High BCL9 expression is associated with cisplatin-resistance in non-small cell lung cancer. (PMID:30009824)
  • Results find that BCL9 is upregulated in osteosarcoma (OS) tissues and promotes OS proliferation, migration and invasion. BCL9 is a downstream target of miR-1301 in OS cells. In addition, BCL9 restoration could reversed the functional effects of miR-1301 overexpression on OS cell proliferation, migration and invasion. These results revealed the important role of BCL9 in OS tumor progression. (PMID:30172867)
  • results revealed a novel role of BCL9 in controlling mitotic Wnt signalling to promote cell division and growth. (PMID:30217955)
  • We found that miR-532 was significantly upregulated in patients with intervertebral disc degeneration and plays a pro-apoptotic role in human intervertebral disc nucleus pulposus cells. Further, Bcl-9 was confirmed to be a direct target of miR-532 and might be a potential target for disc degeneration therapy. (PMID:30472057)
  • SNHG16 promotes BCL9 expression by sponging miR-1301 to facilitate the proliferation, migration and invasion of OS cells. (PMID:30909141)
  • MiR-30c exerts tumor suppressive functions in colorectal carcinoma by directly targeting BCL9. (PMID:31081087)
  • Investigated targeting the protein interactions of catenin beta 1 and B-cell lymphoma 9 protein (BCL9) binding using peptides designed by peptidomimetic drug design. (PMID:31088961)
  • In response to spontaneous calcium transients or cellular stress, BCL9 is recruited adjacent to the interchromosomal regions, where it stabilizes the mRNA of calcium signaling and neural associated genes by interacting with paraspeckle proteins. (PMID:31911584)
  • BCL9/BCL9L promotes tumorigenicity through immune-dependent and independent mechanisms in triple negative breast cancer. (PMID:33767438)
  • miR-140-3p inhibits colorectal cancer progression and its liver metastasis by targeting BCL9 and BCL2. (PMID:33838016)
  • Evidence for frequent concurrent DCUN1D1, FGFR1, BCL9 gene copy number amplification in squamous cell lung cancer. (PMID:33862557)
  • LncRNA NCK1-AS1 exerts oncogenic property in gastric cancer by targeting the miR-22-3p/BCL9 axis to activate the Wnt/beta-catenin signaling. (PMID:33974352)
  • The interactions of Bcl9/Bcl9L with beta-catenin and Pygopus promote breast cancer growth, invasion, and metastasis. (PMID:34545187)
  • Hypoxia-inducible factor 1alpha induces osteo/odontoblast differentiation of human dental pulp stem cells via Wnt/beta-catenin transcriptional cofactor BCL9. (PMID:35027586)
  • Prognostic and survival impact of BCL9 and RPS6KB1 copy number variation detected from circulating free DNA in hepatocellular carcinoma. (PMID:36803362)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobcl9ENSDARG00000036687
mus_musculusBcl9ENSMUSG00000038256
rattus_norvegicusBcl9ENSRNOG00000017516

Paralogs (1): BCL9L (ENSG00000186174)

Protein

Protein identifiers

B-cell CLL/lymphoma 9 proteinO00512 (reviewed: O00512)

Alternative names: Protein legless homolog

All UniProt accessions (3): O00512, A0A804HI55, A0A804HIV1

UniProt curated annotations — full annotation on UniProt →

Function. Involved in signal transduction through the Wnt pathway. Promotes beta-catenin’s transcriptional activity.

Subunit / interactions. Binds to beta-catenin (CTNNB1), PYGO1 and PYGO2; the interaction with PYGO1 increases PYGO1 affinity to histone H3 methylated at ‘Lys 4’.

Subcellular location. Nucleus.

Tissue specificity. Detected at low levels in thymus, prostate, testis, ovary and small intestine, and at lower levels in spleen, colon and blood.

Disease relevance. A chromosomal aberration involving BCL9 is found in a patient with precursor B-cell acute lymphoblastic leukemia (ALL). Translocation t(1;14)(q21;q32). This translocation leaves the coding region intact, but may have pathogenic effects due to alterations in the expression level of BCL9. Several cases of translocations within the 3’-UTR of BCL9 have been found in B-cell malignancies.

Similarity. Belongs to the BCL9 family.

RefSeq proteins (1): NP_004317* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR015668Bcl-9/Bcl-9lFamily
IPR024670BCL9_beta-catenin-bd_domDomain

Pfam: PF11502

UniProt features (53 total): compositionally biased region 17, modified residue 12, region of interest 10, mutagenesis site 4, sequence conflict 3, sequence variant 2, strand 2, helix 2, chain 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
2VPBX-RAY DIFFRACTION1.59
2VPGX-RAY DIFFRACTION1.6
2VP7X-RAY DIFFRACTION1.65
2VPEX-RAY DIFFRACTION1.7
3SL9X-RAY DIFFRACTION2.2
2GL7X-RAY DIFFRACTION2.6
8Y0PX-RAY DIFFRACTION2.62
2VPDX-RAY DIFFRACTION2.77

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00512-F143.070.03

Functional residue map

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

Post-translational modifications (12): 104, 157, 172, 315, 318, 352, 687, 689, 801, 844, 907, 917

Mutagenesis-validated functional residues (4):

PositionPhenotype
358abolishes interaction with ctnnb1.
359abolishes interaction with ctnnb1.
366abolishes interaction with ctnnb1; when associated with a-369.
369abolishes interaction with ctnnb1; when associated with a-366.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-201722Formation of the beta-catenin:TCF transactivating complex
R-HSA-3769402Deactivation of the beta-catenin transactivating complex
R-HSA-162582Signal Transduction
R-HSA-195721Signaling by WNT
R-HSA-201681TCF dependent signaling in response to WNT

MSigDB gene sets: 304 (showing top): RNGTGGGC_UNKNOWN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, FREAC2_01, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_SOMATIC_STEM_CELL_POPULATION_MAINTENANCE, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GGTGTGT_MIR329, GOBP_SKELETAL_MUSCLE_TISSUE_REGENERATION, TGCGCANK_UNKNOWN, RORA1_01, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, MAZ_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_GROWTH

GO Biological Process (9): transcription by RNA polymerase II (GO:0006366), myotube differentiation involved in skeletal muscle regeneration (GO:0014908), somatic stem cell population maintenance (GO:0035019), skeletal muscle cell differentiation (GO:0035914), myoblast differentiation (GO:0045445), positive regulation of transcription by RNA polymerase II (GO:0045944), canonical Wnt signaling pathway (GO:0060070), Wnt signaling pathway (GO:0016055), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): transcription coactivator activity (GO:0003713), beta-catenin binding (GO:0008013), protein binding (GO:0005515)

GO Cellular Component (7): nucleoplasm (GO:0005654), cis-Golgi network (GO:0005801), sarcoplasm (GO:0016528), beta-catenin-TCF complex (GO:1990907), nucleus (GO:0005634), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
TCF dependent signaling in response to WNT2
Signal Transduction1
Signaling by WNT1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membrane-bounded organelle3
DNA-templated transcription2
cell differentiation2
positive regulation of DNA-templated transcription2
cellular anatomical structure2
cytoplasm2
myotube differentiation1
skeletal muscle tissue regeneration1
stem cell population maintenance1
skeletal muscle tissue development1
muscle structure development1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
Wnt signaling pathway1
cell surface receptor signaling pathway1
regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
transcription coregulator activity1
protein binding1
binding1
nuclear lumen1
Golgi apparatus1
RNA polymerase II transcription regulator complex1
intracellular anatomical structure1
endomembrane system1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BCL9CTNNB1P35222996
BCL9PYGO1Q9Y3Y4984
BCL9PYGO2Q9BRQ0981
BCL9HNF4AP41235979
BCL9LEF1Q9UJU2810
BCL9FCRL5Q96RD9721
BCL9FCRL4Q96PJ5709
BCL9CDC73Q6P1J9704
BCL9AXIN1O15169669
BCL9MYCP01106649
BCL9TCF7L1Q9HCS4589
BCL9BTRCQ9Y297588
BCL9ACP6Q9NPH0575
BCL9BCL9LQ86UU0556
BCL9TERTO14746540

IntAct

75 interactions, top by confidence:

ABTypeScore
BCL9CTNNB1psi-mi:“MI:0915”(physical association)0.720
CTNNB1BCL9psi-mi:“MI:0915”(physical association)0.720
CTNNB1BCL9psi-mi:“MI:0407”(direct interaction)0.720
PYGO1BCL9psi-mi:“MI:0914”(association)0.700
PYGO1BCL9psi-mi:“MI:0407”(direct interaction)0.700
BCL9PYGO1psi-mi:“MI:0407”(direct interaction)0.700
BCL9PYGO1psi-mi:“MI:0915”(physical association)0.700
PYGO1BCL9psi-mi:“MI:0915”(physical association)0.700
BCL9PYGO2psi-mi:“MI:0915”(physical association)0.690
PYGO2BCL9psi-mi:“MI:0914”(association)0.690
PYGO2BCL9psi-mi:“MI:0915”(physical association)0.690
CDC73BCL9psi-mi:“MI:0915”(physical association)0.560
CDC73BCL9psi-mi:“MI:0914”(association)0.560
armBCL9psi-mi:“MI:0915”(physical association)0.550
BCL9armpsi-mi:“MI:0915”(physical association)0.550
FOSMYO1Cpsi-mi:“MI:2364”(proximity)0.480
MAP1LC3ABCL9psi-mi:“MI:0407”(direct interaction)0.440
BCL9psi-mi:“MI:0407”(direct interaction)0.440
TCF4BCL9psi-mi:“MI:0915”(physical association)0.400
Ctnnb1BCL9psi-mi:“MI:0915”(physical association)0.370
BCL9pygopsi-mi:“MI:0915”(physical association)0.370
pygoBCL9psi-mi:“MI:0915”(physical association)0.370
CTNNA1BCL9psi-mi:“MI:0914”(association)0.350

BioGRID (114): CTNNB1 (Affinity Capture-Western), BCL9 (Proximity Label-MS), BCL9 (Affinity Capture-MS), BCL9 (Reconstituted Complex), BCL9 (Proximity Label-MS), BCL9 (Affinity Capture-RNA), HSPA8 (Affinity Capture-MS), HSPA1B (Affinity Capture-MS), KIF11 (Affinity Capture-MS), PYGO2 (Affinity Capture-MS), CTNNB1 (Affinity Capture-MS), USP9X (Affinity Capture-MS), PYGO1 (Affinity Capture-MS), PLEC (Affinity Capture-MS), EPPK1 (Affinity Capture-MS)

ESM2 similar proteins: A1YFU7, A2AJK6, A2BH40, B2RWS6, D3YWE6, E9Q4N7, M9NEY8, O00512, O14497, O35126, O42368, O43365, O57401, P02831, P02833, P22810, P23441, P23512, P25822, P32182, P34545, P35582, P35583, P43698, P43699, P50220, P50901, P54258, P54259, P54269, P55317, Q06A37, Q08DG7, Q08E31, Q09472, Q0VCT9, Q10571, Q1KKX7, Q24248, Q24645

Diamond homologs: O00512, Q67FY2, Q67FY3, Q86UU0, Q95KQ6, Q9D219

SIGNOR signaling

3 interactions.

AEffectBMechanism
BCL9up-regulatesCTNNB1binding
BCL9up-regulatesPYGO1binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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:

PathwayPartnersFoldFDR
Formation of the nephric duct573.8×7e-07
Deactivation of the beta-catenin transactivating complex737.9×1e-07
Gastrulation530.2×3e-05
TCF dependent signaling in response to WNT616.4×7e-05
Formation of the beta-catenin:TCF transactivating complex514.0×7e-04
Signaling by WNT513.0×8e-04

GO biological processes:

GO termPartnersFoldFDR
neuron fate specification672.6×3e-08
branching involved in ureteric bud morphogenesis531.6×3e-05
neuroblast proliferation531.6×3e-05
positive regulation of miRNA transcription630.1×4e-06
inner ear morphogenesis525.9×6e-05
retina development in camera-type eye522.0×1e-04
anatomical structure morphogenesis921.6×4e-08
somatic stem cell population maintenance521.4×1e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 3 cancer types — COAD, COADREAD, STAD.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic0
Uncertain significance228
Likely benign10
Benign3

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1703635GRCh37/hg19 1q21.1-21.2(chr1:146043713-147830830)Pathogenic
2498453GRCh37/hg19 1q21.1-21.2(chr1:146405854-147597284)x1Pathogenic
2506525GRCh37/hg19 1q21.1-21.2(chr1:146465878-147416212)Pathogenic
980944GRCh37/hg19 1q21.1-21.2(chr1:146112080-147819815)x3Pathogenic

SpliceAI

2080 predictions. Top by Δscore:

VariantEffectΔscore
1:147614425:A:AGacceptor_gain1.0000
1:147614426:G:GGacceptor_gain1.0000
1:147614426:GAAT:Gacceptor_gain1.0000
1:147614582:GTGGT:Gdonor_gain1.0000
1:147614609:GCCAA:Gdonor_gain1.0000
1:147614613:A:AGdonor_gain1.0000
1:147614617:G:GGdonor_gain1.0000
1:147615801:A:AGacceptor_gain1.0000
1:147615802:G:GGacceptor_gain1.0000
1:147618815:GAAC:Gacceptor_gain1.0000
1:147604908:AAAG:Adonor_loss0.9900
1:147604909:AAGGT:Adonor_loss0.9900
1:147604910:AG:Adonor_loss0.9900
1:147604911:GG:Gdonor_loss0.9900
1:147604912:G:GAdonor_loss0.9900
1:147604913:T:Adonor_loss0.9900
1:147614422:TTTA:Tacceptor_loss0.9900
1:147614424:TA:Tacceptor_loss0.9900
1:147614425:AGAAT:Aacceptor_gain0.9900
1:147614426:GA:Gacceptor_gain0.9900
1:147614426:GAATG:Gacceptor_gain0.9900
1:147614612:AATAA:Adonor_gain0.9900
1:147614614:TAA:Tdonor_gain0.9900
1:147614614:TAAGT:Tdonor_loss0.9900
1:147614615:AAGTA:Adonor_loss0.9900
1:147614616:AG:Adonor_loss0.9900
1:147614618:T:Adonor_loss0.9900
1:147614619:A:AGdonor_loss0.9900
1:147615800:CAG:Cacceptor_gain0.9900
1:147615801:AGA:Aacceptor_gain0.9900

AlphaMissense

9384 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:147614595:T:CF180S1.000
1:147614609:G:CA185P1.000
1:147614610:C:AA185D1.000
1:147615804:G:CA188P1.000
1:147615805:C:AA188D1.000
1:147615807:G:CA189P1.000
1:147615817:T:AV192D1.000
1:147619222:T:CL356P1.000
1:147619228:A:CH358P1.000
1:147619231:G:CR359P1.000
1:147619237:G:CR361P1.000
1:147619239:T:CS362P1.000
1:147619240:C:TS362F1.000
1:147619243:T:CL363S1.000
1:147619246:A:CQ364P1.000
1:147619252:T:AL366H1.000
1:147619252:T:CL366P1.000
1:147619258:A:CD368A1.000
1:147619258:A:GD368G1.000
1:147619258:A:TD368V1.000
1:147619261:T:AI369N1.000
1:147619261:T:CI369T1.000
1:147619261:T:GI369S1.000
1:147619264:A:CQ370P1.000
1:147619267:G:CR371P1.000
1:147619273:T:CL373P1.000
1:147619569:T:AW472R1.000
1:147619569:T:CW472R1.000
1:147619570:G:CW472S1.000
1:147619571:G:CW472C1.000

dbSNP variants (sampled 300 via entrez): RS1000044846 (1:147543826 C>T), RS1000113498 (1:147580975 C>T), RS1000230405 (1:147625937 C>T), RS1000239110 (1:147606267 A>G,T), RS1000257891 (1:147562166 T>C), RS1000365030 (1:147568015 G>A), RS1000453961 (1:147612757 G>A), RS1000606170 (1:147593361 C>T), RS1000666453 (1:147555216 A>G), RS1000698638 (1:147600293 C>A,T), RS1000779020 (1:147554939 C>G), RS1000805569 (1:147574323 G>A), RS1000847825 (1:147580014 A>G,T), RS1001050889 (1:147542194 G>A), RS1001218608 (1:147587418 T>C)

Disease associations

OMIM: gene MIM:602597 | disease phenotypes: MIM:612475, MIM:192500

GenCC curated gene-disease

DiseaseClassificationInheritance
congenital heart diseaseLimitedAutosomal dominant

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
congenital heart diseaseLimitedAD

Mondo (3): chromosome 1q21.1 duplication syndrome (MONDO:0012915), familial long QT syndrome (MONDO:0019171), congenital heart disease (MONDO:0005453)

Orphanet (3): 1q21.1 microduplication syndrome (Orphanet:250994), Romano-Ward syndrome (Orphanet:101016), Congenital long QT syndrome (Orphanet:768)

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001836_2Schizophrenia (negative symptoms)6.000000e-07
GCST002178_8Adverse response to chemotherapy in breast cancer (alopecia) (cyclophosphamide+doxorubicin+/-5FU)6.000000e-07
GCST002806_16Type 2 diabetes6.000000e-06
GCST004766_1Triglyceride change in response to fenofibrate in statin-treated type 2 diabetes3.000000e-08
GCST010988_253Adult body size2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007681triglyceride change measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D006330Heart Defects, CongenitalC14.240.400; C14.280.400; C16.131.240.400
C567290Chromosome 1q21.1 Duplication Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3712821 (SINGLE PROTEIN), CHEMBL3885525 (PROTEIN COMPLEX)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 74,559 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL50QUERCETIN374,559

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

Binding affinities (BindingDB)

6 measured of 6 human assays (6 total across all organisms); most potent 6 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
4-(3-((S)-3-Ethyl-4-(4’-fluoro-6- (((S)-pyrrolidin-1-ium-3-yl)oxy)- [1,1’-biphenyl]-3-carbonyl) piperazine-1-carbonyl)-5- fluorophenyl)piperazin-1-ium chlorideKI10000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders
(S)-1-(3-Fluoro-5-(4-(4-(pyrrolidin- 3-yloxy)-3-(4-(trifluoromethyl) cyclohexyl)benzoyl)piperazine-1- carbonyl)phenyl)piperazin-2-one hydrochlorideKI14000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders
4-(3-Fluoro-5-((5)-4-(4’-fluoro-6- (((S)-pyrrolidin-1-ium-3-yl)oxy)- [1,1’-biphenyl]-3-carbonyl)-3- isobutylpiperazine-1-carbonyl) phenyl)piperazin-1-ium chlorideKI22000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders
(S)-1-(3-(4-(3-Cyclohexyl-4- (pyrrolidin-3-yloxy)benzoyl) piperazine-1-carbonyl)-5- fluorophenyl)piperazin-2-one hydrochlorideKI39000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders
4-(3-Fluoro-5-((5)-4-(4’-fluoro-6- (((S)-pyrrolidin-1-ium-3-yl)oxy)- [1,1’-biphenyl]-3-carbonyl)-3- isopropylpiperazine-1-carbonyl) phenyl)piperazin-1-ium chlorideKI45000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders
4-(3-Fluoro-5-((S)-4-(4’-fluoro-6- (((S)-pyrrolidin-1-ium-3-yl)oxy)-[1,1’- biphenyl]-3-carbonyl)-3- methylpiperazine-1-carbonyl) phenyl)piperazin-1-ium chlorideKI110000 nMUS-11634409: Compounds for the treatment of BRAF-associated diseases and disorders

ChEMBL bioactivities

282 potent at pChembl≥5 of 495 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.33Ki470nMCHEMBL4762534
6.33Ki470nMCHEMBL4462309
6.19IC50650nMCHEMBL5398967
6.16IC50690nMCHEMBL5398967
6.14IC50720nMCHEMBL5416539
6.12Ki760nMCHEMBL4846565
6.11Kd770nMCHEMBL4871137
6.09IC50820nMCHEMBL5416539
6.07Ki850nMCHEMBL5190873
6.06IC50870nMCHEMBL4846565
6.05IC50890nMCHEMBL5404409
6.04IC50910nMCHEMBL5413417
6.03IC50940nMCHEMBL5413417
6.02IC50960nMCHEMBL5190873
6.02Ki960nMCHEMBL5280053
6.00Ki1000nMCHEMBL4462309
6.00IC501000nMCHEMBL5422967
5.96IC501100nMCHEMBL5399058
5.96IC501100nMCHEMBL5440529
5.95IC501130nMCHEMBL5398170
5.93IC501180nMCHEMBL5440529
5.93IC501180nMCHEMBL5400908
5.93IC501180nMCHEMBL5574223
5.92IC501200nMCHEMBL4583576
5.92IC501200nMCHEMBL4846565
5.92Ki1200nMCHEMBL5208427
5.92IC501200nMCHEMBL5280053
5.92Ki1200nMCHEMBL5280053
5.92IC501190nMCHEMBL5422967
5.90IC501270nMCHEMBL5398170
5.89Ki1300nMCHEMBL4549859
5.89Ki1300nMCHEMBL4583576
5.88IC501310nMCHEMBL5418296
5.88IC501330nMCHEMBL5397851
5.87IC501360nMCHEMBL5400908
5.87IC501350nMCHEMBL5570851
5.86IC501380nMCHEMBL5399058
5.85IC501400nMCHEMBL5208427
5.85IC501420nMCHEMBL5573872
5.83IC501490nMCHEMBL5420343
5.82Ki1500nMCHEMBL4074243
5.82IC501500nMCHEMBL5280053
5.80Kd1590nMCHEMBL4074243
5.80Ki1600nMCHEMBL4783692
5.80IC501580nMCHEMBL5406240
5.79IC501640nMCHEMBL5571557
5.79IC501610nMCHEMBL5570927
5.78IC501650nMCHEMBL5572538
5.75Ki1800nMCHEMBL5187855
5.74IC501830nMCHEMBL5573731

PubChem BioAssay actives

256 with measured affinity, of 588 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
3-(3,4-difluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxy-N-[4-[(3S)-pyrrolidin-3-yl]oxy-3-[3-(2H-tetrazol-5-yl)phenyl]phenyl]benzamide;dihydrochloride1966236: Inhibition of beta-catenin (unknown origin)/BCL9 (unknown origin) protein-protein interaction assessed as inhibition constant by AlphaScreen assayki0.4700uM
3-(3,4-difluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxy-N-[4-[(3R)-pyrrolidin-3-yl]oxy-3-[3-(2H-tetrazol-5-yl)phenyl]phenyl]benzamide;dihydrochloride1686801: Inhibition of protein interaction between C-terminal 6x-histidine tagged full-length beta-catenin (1 to 781 residues) (unknown origin)/N-terminal biotinylated human BCL9 ( 350 to 375 residues) incubated for 1 hr by Alpha-screen competitive inhibition assayki0.4700uM
2-methyl-2-[3-[(3R)-1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-[4-(trifluoromethyl)phenyl]sulfonylpropanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic500.6500uM
2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-[4-(trifluoromethyl)phenyl]sulfonylpropanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic500.7200uM
(3R)-N-cyclopropyl-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrazol-4-yl)phenyl]methyl]piperidine-3-carboxamide;hydrochloride1781263: Inhibition of C-terminal 6-His-tagged beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki0.7600uM
(3R)-N-[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethyl]-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrazol-4-yl)phenyl]methyl]piperidine-3-carboxamide1781265: Competitive binding affinity to C-terminal 6-His-tagged beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)- N-terminal biotinylated human BCL9 (350 to 375 residues) assessed as apparent dissociation constant incubated for 2 hrs by AlphaScreen assaykd0.7700uM
(3R)-N-cyclopropyl-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)phenyl]methyl]piperidine-3-carboxamide;hydrochloride1910851: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki0.8500uM
N-(4-acetamidophenyl)sulfonyl-2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic500.8900uM
2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-thiophen-2-ylsulfonylpropanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic500.9100uM
2-[1-[3-(4-tert-butylcyclohexyl)-4-[(3S)-pyrrolidin-3-yl]oxybenzoyl]piperidin-4-yl]oxy-4-piperazin-1-ylbenzonitrile;dihydrochloride1925278: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)/N-terminal biotinylated human BCL9 HD2 (350 to 375 residues) protein-protein interaction assessed as inhibition constant incubated for 1 hr by Alphascreen assayki0.9600uM
2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-[4-(trifluoromethoxy)phenyl]sulfonylpropanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic501.0000uM
2-methyl-2-[3-[(3S)-1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-[4-(trifluoromethyl)phenyl]sulfonylpropanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic501.1000uM
N-(benzenesulfonyl)-2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanamide1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic501.1000uM
N-(3-cyanophenyl)sulfonyl-2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanamide1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic501.1300uM
N-[2-chloro-4-(trifluoromethyl)phenyl]sulfonyl-2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanamide1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic501.1800uM
N-[2-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-2-oxoethyl]-2-[3-[(3R)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.1800uM
3-(1-benzothiophen-6-yl)-N-[3-(4-fluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1686813: Inhibition of protein interaction between beta-catenin (unknown origin)/BCL9 in human SW480 cells transfected with beta-catenin assessed as reduction in Wnt/beta-catenin transactivation incubated for 24 hrs by Wnt-responsive TOP-Flash luciferase reporter assayic501.2000uM
(3R)-N-cyclopropyl-N-[[4-(1H-indol-3-yl)phenyl]methyl]-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]piperidine-3-carboxamide;hydrochloride1910851: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki1.2000uM
3-(6-fluoronaphthalen-2-yl)-N-[3-(4-fluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1686801: Inhibition of protein interaction between C-terminal 6x-histidine tagged full-length beta-catenin (1 to 781 residues) (unknown origin)/N-terminal biotinylated human BCL9 ( 350 to 375 residues) incubated for 1 hr by Alpha-screen competitive inhibition assayki1.3000uM
2-[3-[1-[3-(4-tert-butylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-2-methylpropanoic acid1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic501.3100uM
2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]-N-[3-(trifluoromethyl)phenyl]sulfonylpropanamide1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic501.3300uM
methyl 2-[[2-[3-[(3R)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanoyl]amino]acetate2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.3500uM
N-[2-[(2S)-2-(aminomethyl)pyrrolidin-1-yl]-2-oxoethyl]-2-[3-[(3S)-3-[[cyclopropyl-[[6-(1H-pyrazol-4-yl)-3-pyridinyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.4200uM
N-(4-cyanophenyl)sulfonyl-2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanamide1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic501.4900uM
3-(3,4-difluorophenyl)-N-[3-(4-fluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1686801: Inhibition of protein interaction between C-terminal 6x-histidine tagged full-length beta-catenin (1 to 781 residues) (unknown origin)/N-terminal biotinylated human BCL9 ( 350 to 375 residues) incubated for 1 hr by Alpha-screen competitive inhibition assayki1.5000uM
2-methyl-2-[3-[1-[3-(4-propan-2-ylphenyl)phenyl]sulfonylpiperidin-3-yl]phenoxy]propanoic acid1966238: Inhibition of N-terminal His6-tagged full-length recombinant beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 DE3/N-terminal FAM tagged BCL9 HD2(350 to 375 residues) (unknown origin) protein-protein interaction assessed as inhibition constant incubated for 3 hrs by competitive fluorescence polarization assayic501.5800uM
3-(1-benzothiophen-6-yl)-4-[(3S)-pyrrolidin-3-yl]oxy-N-[4-[(3R)-pyrrolidin-3-yl]oxy-3-[3-(2H-tetrazol-5-yl)phenyl]phenyl]benzamide;dihydrochloride1686801: Inhibition of protein interaction between C-terminal 6x-histidine tagged full-length beta-catenin (1 to 781 residues) (unknown origin)/N-terminal biotinylated human BCL9 ( 350 to 375 residues) incubated for 1 hr by Alpha-screen competitive inhibition assayki1.6000uM
2-[3-[(3S)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-N-[2-[(3S)-3-hydroxypyrrolidin-1-yl]-2-oxoethyl]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.6100uM
N-[2-[(2S)-2-(aminomethyl)piperidin-1-yl]-2-oxoethyl]-2-[3-[(3R)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.6400uM
2-[3-[(3S)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-N-[2-[(3S)-3-(dimethylamino)pyrrolidin-1-yl]-2-oxoethyl]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.6500uM
(3R)-N-cyclopropyl-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl]methyl]piperidine-3-carboxamide;hydrochloride1910851: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki1.8000uM
2-[3-[(3S)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-N-[2-[(2S)-2-[(dimethylamino)methyl]pyrrolidin-1-yl]-2-oxoethyl]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.8200uM
N-(2-aminoethyl)-2-[3-[(3S)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic501.8300uM
(3R)-N-(2-ethoxyethyl)-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrazol-4-yl)phenyl]methyl]piperidine-3-carboxamide;hydrochloride1781263: Inhibition of C-terminal 6-His-tagged beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki1.9000uM
3-(3,4-difluorophenyl)-N-[3-(4-fluoro-2-methylphenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1686813: Inhibition of protein interaction between beta-catenin (unknown origin)/BCL9 in human SW480 cells transfected with beta-catenin assessed as reduction in Wnt/beta-catenin transactivation incubated for 24 hrs by Wnt-responsive TOP-Flash luciferase reporter assayic502.0000uM
(3R)-N-cyclopropyl-N-[[4-(1H-indazol-4-yl)phenyl]methyl]-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]piperidine-3-carboxamide;hydrochloride1910851: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki2.0000uM
N-[2-[2-(2-aminoethyl)pyrrolidin-1-yl]-2-oxoethyl]-2-[3-[(3S)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic502.0600uM
3-(3,4-difluorophenyl)-N-[3-(4-fluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide1979699: Inhibition of His6-tagged human beta-Catenin (138 to 686 residues)/biotinylated human BCL9 (350 to 375 residues) protein-protein interaction assessed as inhibition constant by AlphaScreen competitive assayki2.1000uM
3-(3,4-difluorophenyl)-N-[3-(4-fluorophenyl)-4-pyrrolidin-3-yloxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1308849: Competitive inhibition of wild type beta-catenin (unknown origin) expressed in Escherichia coli BL21 DE3 interaction with N-terminally biotinylated human BCL9 (350 to 375 residues) by alpha screen assayki2.1000uM
3-(3,4-difluorophenyl)-N-[3-(4-fluorophenyl)-4-[(3R)-pyrrolidin-3-yl]oxyphenyl]-4-[(3S)-pyrrolidin-3-yl]oxybenzamide;dihydrochloride1966235: Inhibition of beta-catenin (unknown origin)/human BCL9 (350 to 375 residues) protein-protein interaction assessed as inhibition constant by AlphaScreen assayki2.1000uM
(3R)-N-ethyl-1-[3-(2-methyl-1-oxo-1-piperazin-1-ylpropan-2-yl)oxyphenyl]-N-[[4-(1H-pyrazol-4-yl)phenyl]methyl]piperidine-3-carboxamide;hydrochloride1781263: Inhibition of C-terminal 6-His-tagged beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki2.1000uM
(4-nitrophenyl) butanoate2109717: Inhibition of beta-catenin (unknown origin)/BCL9 (unknown origin) protein-protein interactionki2.1000uM
6-(3,4-difluorophenyl)-3-[3-(4-fluorophenyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-7-[(3S)-pyrrolidin-3-yl]oxyquinoline;dihydrochloride1686801: Inhibition of protein interaction between C-terminal 6x-histidine tagged full-length beta-catenin (1 to 781 residues) (unknown origin)/N-terminal biotinylated human BCL9 ( 350 to 375 residues) incubated for 1 hr by Alpha-screen competitive inhibition assayki2.2000uM
[3-(4-tert-butylcyclohexyl)-4-[(3S)-pyrrolidin-3-yl]oxyphenyl]-[4-(2-chloro-5-piperazin-1-ylphenoxy)piperidin-1-yl]methanone;dihydrochloride1925278: Inhibition of full length beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)/N-terminal biotinylated human BCL9 HD2 (350 to 375 residues) protein-protein interaction assessed as inhibition constant incubated for 1 hr by Alphascreen assayki2.2000uM
N-[2-[(2S)-2-(aminomethyl)pyrrolidin-1-yl]-2-oxoethyl]-2-[3-[(3R)-3-[[cyclopropyl-[[6-(1H-pyrazol-4-yl)-3-pyridinyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic502.2100uM
2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-8-(4-methylphenyl)chromen-4-one2005038: Inhibition of full length beta-catenin (unknown origin)/FAM labeled BCL9 (350 to 375 residues) (unknown origin) protein-protein interaction by competitive FP assayic502.2500uM
(3S)-N-cyclopropyl-1-[3-[1-[(3-methoxyphenyl)sulfonylamino]-2-methyl-1-oxopropan-2-yl]oxyphenyl]-N-[(4-thiophen-2-ylphenyl)methyl]piperidine-3-carboxamide1765112: Inhibition of full length C-terminal 6-His-tagged beta-catenin (1 to 781 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3)-N-terminal biotinylated human BCL9 (350 to 375 residues) protein-protein interaction incubated for 1 hr by Alphascreen assayki2.3000uM
2-(3,4-dihydroxyphenyl)-8-(4-fluorophenyl)-3,5,7-trihydroxychromen-4-one2005038: Inhibition of full length beta-catenin (unknown origin)/FAM labeled BCL9 (350 to 375 residues) (unknown origin) protein-protein interaction by competitive FP assayic502.3500uM
N-(3-aminopropyl)-2-[3-[(3R)-3-[[cyclopropyl-[[4-(1H-pyrazol-4-yl)phenyl]methyl]carbamoyl]amino]piperidin-1-yl]phenoxy]-2-methylpropanamide2109718: Inhibition of full length his-tagged human beta-catenin (1 to 781 residues) expressed in Escherichia coli DE3/N-terminal FAM-tagged human BCL9 (350 to 375 residues) protein-protein interaction incubated for 2 hrs by fluorescence polarization assayic502.5900uM
(6S,9aS)-N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-(naphthalen-1-ylmethyl)-4,7-dioxo-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide1966239: Inhibition of beta-catenin/BCL9 protein-protein interaction in Wnt-dependent human HCT-116 cells assessed as reduction in Axin2 expression level by qRT-PCR assayic502.6900uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation2
Aflatoxin B1increases methylation2
GSK-J4decreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases methylation1
dicrotophosincreases expression1
bufotalindecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
arseniteaffects binding, decreases reaction1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)increases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
nickel sulfateincreases expression1
chromium hexavalent ionincreases expression1
CGP 52608affects binding, increases reaction1
PKF115-584increases expression1
Irinotecanincreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Matrinesdecreases expression, decreases reaction, increases cleavage, increases expression1
Arsenicincreases expression, affects cotreatment, increases abundance1
Atrazineincreases expression1
Cadmiumdecreases expression, increases abundance1
Caffeineaffects phosphorylation1
Cannabidiolincreases expression1
Coumestrolaffects cotreatment, decreases expression1
Doxorubicindecreases expression1

ChEMBL screening assays

125 unique, capped per target: 125 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4419383BindingBinding affinity to human BCL9 (350 to 375 residues) by ITC methodSubstituted n-([1,1’’-biphenyl]-3-yl)-[1,1’’-biphenyl]-3-carboxamide analogs as inhibitors for beta-catenin/b-cell lymphoma 9 interactions

Cellosaurus cell lines

7 cell lines: 7 cancer cell line

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

CellosaurusNameCategorySex
CVCL_9489CEMO-1Cancer cell lineMale
CVCL_A083YCUB-4Cancer cell lineMale
CVCL_A084YCUB-4RCancer cell lineMale
CVCL_D3ZJKCB9Cancer cell lineFemale
CVCL_D4AFM4A1-M2B9Cancer cell lineMale
CVCL_SF05HAP1 BCL9 (-) 1Cancer cell lineMale
CVCL_SF06HAP1 BCL9 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00668824PHASE4UNKNOWNImproved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705PHASE4COMPLETEDNitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982PHASE4COMPLETEDPre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679PHASE4WITHDRAWNTranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811PHASE4UNKNOWNUlinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700PHASE4COMPLETEDFibrinogen Concentrate vs Cryoprecipitate
NCT03408340PHASE4TERMINATEDParavertebral Nerve Blocks in Neonates
NCT03630796PHASE4UNKNOWNEffect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703PHASE4COMPLETEDStress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761PHASE4UNKNOWNThiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389PHASE4RECRUITINGSodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154PHASE4NOT_YET_RECRUITINGPerioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT02513940PHASE4COMPLETEDInfluence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883PHASE4COMPLETEDReducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100PHASE4UNKNOWNNovel Form of Acquired Long QT Syndrome
NCT04675788PHASE4COMPLETEDNovel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT00000470PHASE3COMPLETEDInfant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494PHASE3COMPLETEDManagement of Patent Ductus in Premature Infants
NCT01134302PHASE3UNKNOWNHybrid Versus Norwood Management Strategies in Infants Undergoing Single Ventricle Palliation
NCT01607983PHASE3WITHDRAWNEffects of Pulmonary Vasodilation Upon VA Coupling in Fontan Patients
NCT01662011PHASE3UNKNOWNApplication of Neurally Adjusted Ventilatory Assist to Children After Congenital Cardiac Surgery
NCT02320669PHASE3COMPLETEDPhase 3 Triiodothyronine Supplementation for Infants After Cardiopulmonary Bypass
NCT02615262PHASE3COMPLETEDIntraoperative Dexamethasone in Pediatric Cardiac Surgery
NCT03153137PHASE3COMPLETEDClinical Study Assessing the Efficacy and Safety of Macitentan in Fontan-palliated Subjects
NCT03154476PHASE3COMPLETEDRole of Sildenafil for Fontan Associated Liver Disease (SiFALD) Study
NCT04536194PHASE3COMPLETEDDopamine Versus Norepinephrine Under General Anesthesia
NCT04702373PHASE3ACTIVE_NOT_RECRUITINGTraining in Exercise Activities and Motion for Growth (TEAM 4 Growth) RCT
NCT05049590PHASE3COMPLETEDAcute Normovolemic Hemodilution in Complex Cardiac Surgery
NCT06406517PHASE3UNKNOWNComparative Effectiveness of Gadopiclenol for Evaluation of Adult Congenital Heart Anatomy and Hemodynamics
NCT06693674PHASE3RECRUITINGEffect of Sacubitril-Valsartan on Cardiac Structure and Function
NCT06955260PHASE3NOT_YET_RECRUITINGSGLT2 Inhibition With Empagliflozin in Fontan Circulatory Failure
NCT00115375PHASE2COMPLETEDPlatelet Aggregation Inhibition in Children on Clopidogrel (PICOLO)
NCT00350220PHASE2COMPLETEDTransfusion Strategies in Pediatric Cardiothoracic Surgery
NCT00374088PHASE2COMPLETEDN-Acetylcysteine in Neonatal Congenital Heart Surgery (INACT Study)
NCT00538785PHASE2COMPLETEDA Study to Evaluate MEDI-524 In Children With Hemodynamically Significant Congenital Heart Disease
NCT00770705PHASE2WITHDRAWNParenteral Phenoxybenzamine During Congenital Heart Disease Surgery
NCT00919945PHASE2TERMINATEDImpact of Early Enteral Feeding on Splanchnic Blood Flow After Surgery for Critical Heart Disease in the Newborn
NCT01063712PHASE2COMPLETEDSafety and Effectiveness of the Device Nit-Occlud® PDA-R
NCT01069510PHASE2COMPLETEDSpironolactone in Adult Congenital Heart Disease
NCT01189981PHASE2COMPLETEDEffect of eHealth Encouragements to Intensive Exercise in Adolescents With Congenital Heart Disease