BCL6B

gene
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Also known as ZBTB28BAZF

Summary

BCL6B (BCL6B transcription repressor, HGNC:1002) is a protein-coding gene on chromosome 17p13.1, encoding B-cell CLL/lymphoma 6 member B protein (Q8N143). Acts as a sequence-specific transcriptional repressor in association with BCL6.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of inflammatory response; and type 2 immune response. Predicted to be located in nucleus. Predicted to be active in nucleoplasm.

Source: NCBI Gene 255877 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 29 total
  • Druggable target: yes
  • MANE Select transcript: NM_181844

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1002
Approved symbolBCL6B
NameBCL6B transcription repressor
Location17p13.1
Locus typegene with protein product
StatusApproved
AliasesZBTB28, BAZF
Ensembl geneENSG00000161940
Ensembl biotypeprotein_coding
OMIM608992
Entrez255877

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000293805, ENST00000537931, ENST00000571729, ENST00000572216, ENST00000573503, ENST00000576705, ENST00000896964, ENST00000896967

RefSeq mRNA: 1 — MANE Select: NM_181844 NM_181844

CCDS: CCDS42248

Canonical transcript exons

ENST00000293805 — 9 exons

ExonStartEnd
ENSE0000106153970250767025200
ENSE0000106154370264577026621
ENSE0000120385870244017024763
ENSE0000128654570275037029644
ENSE0000233717870269507027087
ENSE0000242913770267057026835
ENSE0000263545470230507023099
ENSE0000367596170236607023850
ENSE0000378978470240837024304

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 88.30.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6894 / max 81.1628, expressed in 353 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1590992.4867328
1591000.2027136

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
epithelial cell of pancreasCL:000008388.30silver quality
upper lobe of left lungUBERON:000895287.84gold quality
upper lobe of lungUBERON:000894887.49gold quality
apex of heartUBERON:000209887.21gold quality
right lungUBERON:000216785.87gold quality
omental fat padUBERON:001041485.63gold quality
peritoneumUBERON:000235885.59gold quality
kidney epitheliumUBERON:000481985.47gold quality
adipose tissue of abdominal regionUBERON:000780885.24gold quality
lungUBERON:000204884.86gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.64gold quality
gall bladderUBERON:000211084.07gold quality
pancreatic ductal cellCL:000207984.04silver quality
adipose tissueUBERON:000101382.65gold quality
subcutaneous adipose tissueUBERON:000219082.49gold quality
tendon of biceps brachiiUBERON:000818882.25gold quality
heart left ventricleUBERON:000208481.94gold quality
cardiac ventricleUBERON:000208281.79gold quality
lower lobe of lungUBERON:000894981.20gold quality
left lobe of thyroid glandUBERON:000112080.19gold quality
thyroid glandUBERON:000204679.78gold quality
vena cavaUBERON:000408779.70silver quality
heartUBERON:000094879.58gold quality
spleenUBERON:000210679.43gold quality
smooth muscle tissueUBERON:000113579.35gold quality
tibialis anteriorUBERON:000138579.27silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.04gold quality
left ventricle myocardiumUBERON:000656679.04gold quality
cardiac muscle of right atriumUBERON:000337978.79gold quality
right lobe of thyroid glandUBERON:000111978.53gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.72
E-MTAB-8271no263.40
E-MTAB-6678no2.43

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

TargetRegulation
CD8A
GDNF
IL2
IL4Activation

miRNA regulators (miRDB)

99 targeting BCL6B, 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-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-4481100.0066.421669
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-607799.9968.042299
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-545-3P99.9570.742783
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-539-5P99.9370.302855
HSA-MIR-314399.9371.963104
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394

Literature-anchored findings (GeneRIF, showing 15)

  • BCL6B plays a pivotal role as a potential tumour suppressor in GC. Detection of methylated BCL6B may serve as an independent biomarker for the prognosis of GC. (PMID:21917650)
  • BCL6B methylation may serve as a novel potential non-invasive plasma biomarker for the detection of gastric cancer (PMID:24191714)
  • Patients with three or more methylated CpG sites in the BCL6B promoter were significantly associated with poor survival. (PMID:25008234)
  • BCL6B functions as a tumor suppressor that inhibits HCC metastases in vitro and in vivo. (PMID:25218345)
  • Epigenetic silencing of BCL6B inactivates p53 signaling and causes human hepatocellular carcinoma cells to become resistant to 5-FU. (PMID:25909168)
  • BCL6B plays a pivotal role as a prognostic biomarker for HCC. (PMID:25970780)
  • BCL6B suppressed the proliferation and migration of colorectal carcinoma cells cells indirectly, via inhibition of PI3K. (PMID:29393377)
  • Tumor suppressive BTB/POZ zinc-finger protein ZBTB28 inhibits oncogenic BCL6/ZBTB27 signaling to maintain p53 transcription in multiple carcinogenesis. (PMID:31754389)
  • BTB/POZ zinc finger protein ZBTB16 inhibits breast cancer proliferation and metastasis through upregulating ZBTB28 and antagonizing BCL6/ZBTB27. (PMID:32517789)
  • ZBTB28 induces autophagy by regulation of FIP200 and Bcl-XL facilitating cervical cancer cell apoptosis. (PMID:33931087)
  • BCL6B hypermethylation predicts metastasis and poor prognosis in early-stage hepatocellular carcinoma after thermal ablation. (PMID:34269294)
  • ZBTB28 inhibits breast cancer by activating IFNAR and dual blocking CD24 and CD47 to enhance macrophages phagocytosis. (PMID:35048182)
  • CircTFF1 Promotes Proliferation, Migration and Invasion of Lung Cancer Cells by Facilitating Methylation of BCL6B Promoter via miR-29c-3p/DNMT3A Axis. (PMID:36376550)
  • BCL6B Contributes to Ocular Vascular Diseases via Notch Signal Silencing. (PMID:37078291)
  • BCL6B-dependent suppression of ETV2 hampers endothelial cell differentiation. (PMID:39075623)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobcl6bENSDARG00000069335
mus_musculusBcl6bENSMUSG00000000317
rattus_norvegicusBcl6bENSRNOG00000059956

Paralogs (28): ZNF280C (ENSG00000056277), ZBTB25 (ENSG00000089775), PRDM13 (ENSG00000112238), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), NACC2 (ENSG00000148411), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF280A (ENSG00000169548), ZNF581 (ENSG00000171425), ZNF524 (ENSG00000171443), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

B-cell CLL/lymphoma 6 member B proteinQ8N143 (reviewed: Q8N143)

Alternative names: Bcl6-associated zinc finger protein, Zinc finger protein 62

All UniProt accessions (4): Q8N143, H0YGW0, I3L304, I3L396

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a sequence-specific transcriptional repressor in association with BCL6. May function in a narrow stage or be related to some events in the early B-cell development.

Subunit / interactions. Associates with BCL6 through the BTB domain.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed with higher expression found in heart and placenta.

RefSeq proteins (1): NP_862827* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050457ZnFinger_BTB_dom_containFamily

Pfam: PF00096, PF00651

UniProt features (14 total): zinc finger region 5, compositionally biased region 3, sequence conflict 2, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N143-F155.790.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): CREL_01, GOBP_INFLAMMATORY_RESPONSE, SP3_Q3, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, SP1_Q2_01, LA_MEN1_TARGETS, SREBP1_02, CCANNAGRKGGC_UNKNOWN, GROSS_HYPOXIA_VIA_ELK3_UP, GOBP_CYTOKINE_PRODUCTION, GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GGGNNTTTCC_NFKB_Q6_01, GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN

GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of cytokine production (GO:0001817), regulation of immune system process (GO:0002682), type 2 immune response (GO:0042092), regulation of cell population proliferation (GO:0042127), regulation of cell differentiation (GO:0045595), regulation of inflammatory response (GO:0050727)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of cellular process2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
cytokine production1
regulation of gene expression1
regulation of multicellular organismal process1
immune system process1
regulation of biological process1
immune response1
cell population proliferation1
cell differentiation1
regulation of developmental process1
inflammatory response1
regulation of defense response1
regulation of response to external stimulus1
cis-regulatory region sequence-specific DNA binding1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
transition metal ion binding1
double-stranded DNA binding1
sequence-specific DNA binding1
transcription cis-regulatory region binding1
nucleic acid binding1
binding1
cation binding1
nuclear lumen1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

986 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BCL6BBCL6P41182848
BCL6BETV5P41161712
BCL6BSTRA8Q7Z7C7680
BCL6BSOHLH1Q5JUK2641
BCL6BGFRA1P56159635
BCL6BNANOS2P60321618
BCL6BLHX1P48742616
BCL6BID4P47928559
BCL6BACTL6BO94805546
BCL6BRBPJQ06330544
BCL6BGDNFP39905542
BCL6BZBTB16Q05516511
BCL6BSOHLH2Q9NX45510
BCL6BARID1BQ8NFD5503
BCL6BBCL11BQ9C0K0502

IntAct

4 interactions, top by confidence:

ABTypeScore
BCL6BSULT4A1psi-mi:“MI:0915”(physical association)0.560
BCL6BNOTCH2NLApsi-mi:“MI:0915”(physical association)0.370
BCL6BTUBA3Cpsi-mi:“MI:0914”(association)0.350

BioGRID (38): BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), BCL6B (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), SULT4A1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNJ4, A2APT9, A6NEL2, A6NP61, B1ASB6, B1WBS3, B2RXF5, F6WEQ6, O15015, O43918, O88282, O88286, O95785, P98168, P98169, Q2M3G4, Q2MHN3, Q2QGD7, Q3U1J1, Q3U381, Q497V6, Q5SW24, Q5SXM2, Q6YND2, Q6ZMQ8, Q6ZMY3, Q7TN08, Q7TSX9, Q80SU3, Q80YE4, Q811H0, Q8BG26, Q8BZW2, Q8C8V1, Q8IX07, Q8IY92, Q8N143, Q8N1G0, Q8NC74, Q8TBE0

Diamond homologs: A0A0A6YY25, B2RXH4, E0CZ16, E1B932, E7F6F9, F1LZ52, F1LZF0, F1MBP6, O88282, O93567, O95198, P10074, P17789, P42282, P42283, P42284, Q01295, Q1H9T6, Q24174, Q24206, Q3B7M1, Q52KG4, Q53G59, Q53HC5, Q5R633, Q5REP9, Q5U374, Q66HD2, Q6NRH0, Q7KQZ4, Q7KRI2, Q867Z4, Q86B87, Q8BGY4, Q8BZM0, Q8CA72, Q8IN81, Q8JZP3, Q8K0L9, Q8N143

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1359 predictions. Top by Δscore:

VariantEffectΔscore
17:7023848:CAGG:Cdonor_loss1.0000
17:7023849:AG:Adonor_loss1.0000
17:7023850:GGTTC:Gdonor_loss1.0000
17:7023851:GTTCG:Gdonor_loss1.0000
17:7024081:A:AGacceptor_gain1.0000
17:7024082:G:GGacceptor_gain1.0000
17:7024300:GCCAG:Gdonor_gain1.0000
17:7024302:CAGG:Cdonor_loss1.0000
17:7024304:GGTGA:Gdonor_loss1.0000
17:7024305:G:GGdonor_gain1.0000
17:7024305:GT:Gdonor_loss1.0000
17:7024306:T:Gdonor_loss1.0000
17:7025074:A:AGacceptor_gain1.0000
17:7025075:G:GGacceptor_gain1.0000
17:7025199:GG:Gdonor_gain1.0000
17:7025200:GG:Gdonor_gain1.0000
17:7025201:G:GGdonor_gain1.0000
17:7026456:GGAA:Gacceptor_gain1.0000
17:7026696:T:TAacceptor_gain1.0000
17:7026701:CCA:Cacceptor_loss1.0000
17:7026703:A:AGacceptor_gain1.0000
17:7026703:AG:Aacceptor_gain1.0000
17:7026703:AGG:Aacceptor_gain1.0000
17:7026703:AGGG:Aacceptor_gain1.0000
17:7026704:G:GTacceptor_gain1.0000
17:7026704:GG:Gacceptor_gain1.0000
17:7026704:GGG:Gacceptor_gain1.0000
17:7026704:GGGG:Gacceptor_gain1.0000
17:7026704:GGGGA:Gacceptor_gain1.0000
17:7026833:CAGGT:Cdonor_loss1.0000

AlphaMissense

3084 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:7026576:T:CF337L1.000
17:7026578:C:AF337L1.000
17:7026578:C:GF337L1.000
17:7026722:T:CC358R1.000
17:7026731:T:CC361R1.000
17:7026732:G:AC361Y1.000
17:7026743:T:CF365L1.000
17:7026744:T:CF365S1.000
17:7026745:T:AF365L1.000
17:7026745:T:GF365L1.000
17:7026806:T:CC386R1.000
17:7026827:T:CF393L1.000
17:7026829:T:AF393L1.000
17:7026829:T:GF393L1.000
17:7027025:T:CF421L1.000
17:7027027:C:AF421L1.000
17:7027027:C:GF421L1.000
17:7026555:T:CC330R0.999
17:7026577:T:CF337S0.999
17:7026603:C:GH346D0.999
17:7026605:T:AH346Q0.999
17:7026605:T:GH346Q0.999
17:7026723:G:AC358Y0.999
17:7026724:C:GC358W0.999
17:7026731:T:AC361S0.999
17:7026732:G:CC361S0.999
17:7026733:C:GC361W0.999
17:7026762:T:CL371P0.999
17:7026770:C:AH374N0.999
17:7026770:C:GH374D0.999

dbSNP variants (sampled 300 via entrez): RS1000145965 (17:7024003 C>T), RS1000880100 (17:7028267 C>A), RS1000944195 (17:7022245 G>A,T), RS1000978265 (17:7022055 T>G), RS1001311702 (17:7023242 C>T), RS1001448415 (17:7029198 G>C,T), RS1001610278 (17:7030142 A>C,G), RS1002492888 (17:7029778 T>C), RS1002547570 (17:7025850 A>C), RS1002845184 (17:7024145 C>T), RS1002947908 (17:7024997 G>A), RS1002980522 (17:7024428 C>A,G,T), RS1002997655 (17:7026110 C>CGAGGTT), RS1003590744 (17:7026024 C>T), RS1004004427 (17:7024539 C>A,G,T)

Disease associations

OMIM: gene MIM:608992 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008839_85Height9.000000e-18
GCST90002401_579Platelet distribution width6.000000e-13

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5291528 (SINGLE PROTEIN)

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

ChEMBL bioactivities

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

pChemblTypeValueUnitMolecule
5.43Kd3683nMCHEMBL4755229

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, decreases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Valproic Acidaffects expression, decreases expression2
sodium arseniteincreases expression1
avobenzonedecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphindecreases expression, affects cotreatment1
Resveratroldecreases expression, affects cotreatment1
Air Pollutantsincreases abundance, decreases expression1
Cadmiumincreases abundance, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Folic Aciddecreases expression1
Nickeldecreases expression1
Niclosamideincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Thimerosaldecreases expression1
Cyclosporineincreases methylation1
Cadmium Chlorideincreases abundance, decreases expression1
Particulate Matterdecreases expression, increases abundance1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5226232BindingBinding affinity to BAZF (unknown origin) assessed as fold changeDiscovery of OICR12694: A Novel, Potent, Selective, and Orally Bioavailable BCL6 BTB Inhibitor. — ACS Med Chem Lett

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_XV63HEK293 eGFP-BCL6BTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.