Free for academic non-profit institutions. Other users need a Commercial license

Aliases for BCL9 Gene

Aliases for BCL9 Gene

  • B Cell CLL/Lymphoma 9 2 3 5
  • B-Cell Lymphoma 9 Protein 3 4
  • Protein Legless Homolog 3 4
  • Bcl-9 3 4
  • B-Cell CLL/Lymphoma 9 Protein 3
  • LGS 3

External Ids for BCL9 Gene

Previous GeneCards Identifiers for BCL9 Gene

  • GC01P145227
  • GC01P143738
  • GC01P144357
  • GC01P144520
  • GC01P144237
  • GC01P145479
  • GC01P147013
  • GC01P120426

Summaries for BCL9 Gene

Entrez Gene Summary for BCL9 Gene

  • 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for BCL9 Gene

BCL9 (B Cell CLL/Lymphoma 9) is a Protein Coding gene. Diseases associated with BCL9 include Lymphoblastic Leukemia and Lymphoma. Among its related pathways are Signaling by Wnt and Wnt Signaling Pathway Netpath. Gene Ontology (GO) annotations related to this gene include beta-catenin binding. An important paralog of this gene is BCL9L.

UniProtKB/Swiss-Prot for BCL9 Gene

  • Involved in signal transduction through the Wnt pathway. Promotes beta-catenins transcriptional activity (By similarity).

Gene Wiki entry for BCL9 Gene

Additional gene information for BCL9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BCL9 Gene

Genomics for BCL9 Gene

GeneHancer (GH) Regulatory Elements for BCL9 Gene

Promoters and enhancers for BCL9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J147538 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 684.1 -0.4 -391 5.8 PKNOX1 FOXA2 ARNT NEUROD1 SIN3A FEZF1 ZNF2 YY1 ZNF213 ZNF416 BCL9 LOC647481 GPR89B LOC101927468 ACP6 OR13Z3P OR13Z2P OR13Z1P LOC100130018 ENSG00000235988
GH01J148262 Promoter/Enhancer 1.6 Ensembl ENCODE 31.4 +722.7 722691 2.7 HNRNPUL1 PKNOX1 SMAD1 ARNT SIN3A FEZF1 ZNF2 YY1 POLR2B ZNF213 RNU1-120P TRQ-CTG4-1 LOC647481 GPR89B BCL9 ACP6 ENSG00000227700 LOC101927468 LINC01731
GH01J147165 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 14.2 -371.3 -371294 8.3 CLOCK FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 ZNF263 SP3 SSRP1 PRKAB2 GPR89B CHD1L FMO5 BCL9 ACP6 ENSG00000237188 ENSG00000273071 GC01P147160
GH01J147083 Enhancer 1.3 Ensembl ENCODE 24.3 -456.7 -456683 1.8 HNRNPUL1 PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A ZNF2 IRF4 YY1 GC01M147086 LOC441904 RNVU1-8 GPR89B BCL9 LOC644060 PDE4DIPP1 ACP6 PFN1P8
GH01J147598 Promoter/Enhancer 1.5 Ensembl ENCODE 20.8 +58.4 58427 2.9 ZNF493 SIN3A GLI4 ZNF2 ZBTB7B ZNF48 YY1 GLIS2 ZFP91 FOS GPR89B LOC647481 BCL9 LOC101927468 ACP6 GC01P147574
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BCL9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BCL9 gene promoter:
  • PPAR-gamma2
  • PPAR-gamma1
  • GATA-1
  • CUTL1
  • NF-1
  • NF-1/L
  • STAT1
  • GR-beta
  • GR-alpha

Genomic Locations for BCL9 Gene

Genomic Locations for BCL9 Gene
84,819 bases
Plus strand
84,836 bases
Plus strand

Genomic View for BCL9 Gene

Genes around BCL9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BCL9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BCL9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BCL9 Gene

Proteins for BCL9 Gene

  • Protein details for BCL9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    B-cell CLL/lymphoma 9 protein
    Protein Accession:
    Secondary Accessions:
    • Q5T489

    Protein attributes for BCL9 Gene

    1426 amino acids
    Molecular mass:
    149290 Da
    Quaternary structure:
    • Binds to beta-catenin (CTNNB1), PYGO1 and PYGO2; the interaction with PYGO1 increases PYGO1 affinity to histone H3 methylated at Lys 4.
    • Sequence=CAA73942.1; Type=Frameshift; Positions=1391; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for BCL9 Gene

neXtProt entry for BCL9 Gene

Post-translational modifications for BCL9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BCL9 Gene

No data available for DME Specific Peptides for BCL9 Gene

Domains & Families for BCL9 Gene

Gene Families for BCL9 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for BCL9 Gene

Suggested Antigen Peptide Sequences for BCL9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the BCL9 family.
  • Belongs to the BCL9 family.
genes like me logo Genes that share domains with BCL9: view

Function for BCL9 Gene

Molecular function for BCL9 Gene

UniProtKB/Swiss-Prot Function:
Involved in signal transduction through the Wnt pathway. Promotes beta-catenins transcriptional activity (By similarity).
GENATLAS Biochemistry:
gene coding for a large proline-rich protein with two transcripts,expressed in all tissues and a third expressed only in thymus,spleen,small intestine,involved in translocation t(1;14) and t(1;22)

Phenotypes From GWAS Catalog for BCL9 Gene

Gene Ontology (GO) - Molecular Function for BCL9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IEA --
GO:0005515 protein binding IPI 11955446
GO:0008013 beta-catenin binding IEA --
genes like me logo Genes that share ontologies with BCL9: view
genes like me logo Genes that share phenotypes with BCL9: view

Clone Products

  • Addgene plasmids for BCL9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BCL9 Gene

Localization for BCL9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BCL9 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BCL9 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BCL9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005801 cis-Golgi network IDA 23386608
genes like me logo Genes that share ontologies with BCL9: view

Pathways & Interactions for BCL9 Gene

genes like me logo Genes that share pathways with BCL9: view

SIGNOR curated interactions for BCL9 Gene


Gene Ontology (GO) - Biological Process for BCL9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0014908 myotube differentiation involved in skeletal muscle regeneration IEA --
GO:0016055 Wnt signaling pathway IEA --
GO:0017015 NOT regulation of transforming growth factor beta receptor signaling pathway IMP 19328798
GO:0035019 somatic stem cell population maintenance IEA --
GO:0035914 skeletal muscle cell differentiation IEA --
genes like me logo Genes that share ontologies with BCL9: view

Drugs & Compounds for BCL9 Gene

No Compound Related Data Available

Transcripts for BCL9 Gene

Unigene Clusters for BCL9 Gene

B-cell CLL/lymphoma 9:
Representative Sequences:

Clone Products

  • Addgene plasmids for BCL9

Alternative Splicing Database (ASD) splice patterns (SP) for BCL9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1: -
SP3: -

Relevant External Links for BCL9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BCL9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BCL9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for BCL9 Gene

This gene is overexpressed in Fetal Brain (33.3) and Heart (28.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for BCL9 Gene

Protein tissue co-expression partners for BCL9 Gene

NURSA nuclear receptor signaling pathways regulating expression of BCL9 Gene:


SOURCE GeneReport for Unigene cluster for BCL9 Gene:


mRNA Expression by UniProt/SwissProt for BCL9 Gene:

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

Evidence on tissue expression from TISSUES for BCL9 Gene

  • Nervous system(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with BCL9: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for BCL9 Gene

Orthologs for BCL9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for BCL9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BCL9 34 33
  • 99.84 (n)
(Canis familiaris)
Mammalia BCL9 34 33
  • 94.55 (n)
(Bos Taurus)
Mammalia BCL9 34 33
  • 94.18 (n)
(Rattus norvegicus)
Mammalia Bcl9 33
  • 93.08 (n)
(Mus musculus)
Mammalia Bcl9 16 34 33
  • 92.89 (n)
(Monodelphis domestica)
Mammalia BCL9 34
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia BCL9 34
  • 82 (a)
(Gallus gallus)
Aves BCL9 34 33
  • 81.79 (n)
(Anolis carolinensis)
Reptilia BCL9 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bcl9 33
  • 71.8 (n)
Str.18727 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.2426 33
(Danio rerio)
Actinopterygii bcl9 34 33
  • 64.15 (n)
Species where no ortholog for BCL9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for BCL9 Gene

Gene Tree for BCL9 (if available)
Gene Tree for BCL9 (if available)
Evolutionary constrained regions (ECRs) for BCL9: view image

Paralogs for BCL9 Gene

Paralogs for BCL9 Gene Pseudogenes for BCL9 Gene

genes like me logo Genes that share paralogs with BCL9: view

Variants for BCL9 Gene

Sequence variations from dbSNP and Humsavar for BCL9 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000044846 -- 147,543,826(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000113498 -- 147,580,975(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000230405 -- 147,625,937(+) C/T 3_prime_UTR_variant
rs1000239110 -- 147,606,267(+) A/G intron_variant
rs1000257891 -- 147,562,166(+) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BCL9 Gene

Variant ID Type Subtype PubMed ID
dgv183n106 CNV deletion 24896259
dgv327n100 CNV gain 25217958
dgv66e199 CNV deletion 23128226
esv2663751 CNV deletion 23128226
esv2761299 CNV gain+loss 21179565
esv3587441 CNV loss 21293372
esv3587442 CNV loss 21293372
esv3587443 CNV loss 21293372
nsv1003688 CNV gain 25217958
nsv1005055 CNV loss 25217958
nsv1076796 CNV deletion 25765185
nsv1077661 CNV deletion 25765185
nsv1132304 CNV duplication 24896259
nsv1136033 CNV deletion 24896259
nsv509457 CNV insertion 20534489
nsv510962 OTHER complex 20534489
nsv831414 CNV gain 17160897
nsv831426 CNV loss 17160897
nsv951831 CNV duplication 24416366

Variation tolerance for BCL9 Gene

Residual Variation Intolerance Score: 12.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.39; 85.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BCL9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BCL9 Gene

Disorders for BCL9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for BCL9 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lymphoblastic leukemia
  • acute lymphocytic leukemia
  • lymphoid cancer
- elite association - COSMIC cancer census association via MalaCards
Search BCL9 in MalaCards View complete list of genes associated with diseases


  • Note=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. {ECO:0000269 PubMed:9490669}.

Genatlas disease for BCL9 Gene

B-cell CLL ,chronic lymphocytic leukemia with translocation t(1;14)(q21;q32),t(1;22)(q21;q11)

Additional Disease Information for BCL9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BCL9: view

Publications for BCL9 Gene

  1. Molecular cloning of translocation t(1;14)(q21;q32) defines a novel gene (BCL9) at chromosome 1q21. (PMID: 9490669) Willis TG … Dyer MJ (Blood 1998) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. (PMID: 18498752) Fiedler M … Bienz M (Molecular cell 2008) 3 4 58
  5. Cell-type-specific function of BCL9 involves a transcriptional activation domain that synergizes with beta-catenin. (PMID: 18347063) Sustmann C … Grosschedl R (Molecular and cellular biology 2008) 3 22 58

Products for BCL9 Gene

Sources for BCL9 Gene

Loading form....