BTBD2

gene
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Summary

BTBD2 (BTB domain containing 2, HGNC:15504) is a protein-coding gene on chromosome 19p13.3, encoding BTB/POZ domain-containing protein 2 (Q9BX70).

The C-terminus of the protein encoded by this gene binds topoisomerase I. The N-terminus contains a proline-rich region and a BTB/POZ domain (broad-complex, Tramtrack and bric a brac/Pox virus and Zinc finger), both of which are typically involved in protein-protein interactions. Subcellularly, the protein localizes to cytoplasmic bodies.

Source: NCBI Gene 55643 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 114 total
  • MANE Select transcript: NM_017797

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15504
Approved symbolBTBD2
NameBTB domain containing 2
Location19p13.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000133243
Ensembl biotypeprotein_coding
OMIM608531
Entrez55643

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000255608, ENST00000587225, ENST00000587742, ENST00000587825, ENST00000588395, ENST00000589200, ENST00000589685, ENST00000590646, ENST00000592082, ENST00000592895, ENST00000611545, ENST00000936983

RefSeq mRNA: 1 — MANE Select: NM_017797 NM_017797

CCDS: CCDS12078

Canonical transcript exons

ENST00000255608 — 9 exons

ExonStartEnd
ENSE0000105589720152972015714
ENSE0000346864719900041990201
ENSE0000348173319868301986976
ENSE0000350852619907171990822
ENSE0000354707719854481986649
ENSE0000356230519930201993176
ENSE0000356647719875001987692
ENSE0000363624219871661987253
ENSE0000363720819973441997463

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 98.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.5797 / max 126.1598, expressed in 1788 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
17809820.85191786
1780970.5742371
1780990.153688

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right frontal lobeUBERON:000281098.03gold quality
right hemisphere of cerebellumUBERON:001489098.02gold quality
cerebellar hemisphereUBERON:000224597.63gold quality
cerebellar cortexUBERON:000212997.53gold quality
cingulate cortexUBERON:000302797.52gold quality
anterior cingulate cortexUBERON:000983597.52gold quality
stromal cell of endometriumCL:000225597.13gold quality
right uterine tubeUBERON:000130296.98gold quality
amygdalaUBERON:000187696.95gold quality
lower esophagus mucosaUBERON:003583496.68gold quality
right ovaryUBERON:000211896.56gold quality
ventricular zoneUBERON:000305396.46gold quality
cortical plateUBERON:000534396.44gold quality
apex of heartUBERON:000209896.39gold quality
left ovaryUBERON:000211996.33gold quality
cerebellumUBERON:000203796.17gold quality
ganglionic eminenceUBERON:000402396.10gold quality
prefrontal cortexUBERON:000045195.64gold quality
right lobe of thyroid glandUBERON:000111995.53gold quality
Brodmann (1909) area 9UBERON:001354095.49gold quality
nucleus accumbensUBERON:000188295.46gold quality
endocervixUBERON:000045895.32gold quality
body of uterusUBERON:000985395.31gold quality
dorsolateral prefrontal cortexUBERON:000983495.29gold quality
granulocyteCL:000009495.22gold quality
left uterine tubeUBERON:000130395.22gold quality
adenohypophysisUBERON:000219695.19gold quality
muscle layer of sigmoid colonUBERON:003580595.09gold quality
ectocervixUBERON:001224995.07gold quality
hindlimb stylopod muscleUBERON:000425295.06gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting BTBD2, 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-548C-3P99.9974.017587
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-1255A99.7468.09744
HSA-MIR-1255B-5P99.7468.16741
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-128-2-5P99.3360.83311
HSA-MIR-504-3P99.3067.181745
HSA-MIR-143-5P98.9868.87946
HSA-MIR-6829-5P98.8665.121480
HSA-MIR-873-5P98.8466.901348
HSA-MIR-6838-3P98.4065.88559
HSA-MIR-63797.9164.051517
HSA-MIR-296-5P97.6164.02851
HSA-MIR-122-5P97.2364.921024
HSA-MIR-6815-5P96.0565.55662
HSA-MIR-6865-5P96.0565.58675
HSA-MIR-3622B-5P94.6264.58835
HSA-MIR-4743-5P88.0864.3191
HSA-MIR-1247-5P85.9261.0765

Literature-anchored findings (GeneRIF, showing 3)

  • subcellular colocalization of BTBD1 and BTBD2 to cytoplasmic bodies; TRIM5delta colocalized with BTBD1/2 and appeared to serve as a scaffold for the assembly of endogenous BTBD1/2 proteins (PMID:12878161)
  • Polymorphisms in the LIG4, BTBD2, HMGA2, and RTEL1 genes, which are involved in the double-strand break repair pathway, are associated with glioblastoma multiforme survival. (PMID:20368557)
  • Interaction of BTBD1 and BTBD2 with TOP1 requires TOP1 residues 236 and 237, the same residues required to enhance the infectivity of progeny virions when TOP1 is expressed in African Green Monkey producer cells. (PMID:21092135)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriobtbd2aENSDARG00000042091
danio_reriobtbd2bENSDARG00000104653
mus_musculusBtbd2ENSMUSG00000003344
rattus_norvegicusBtbd2ENSRNOG00000018788
drosophila_melanogasterBTBD9FBGN0030228
drosophila_melanogasterCG17068FBGN0031098
drosophila_melanogasterluteFBGN0262871
caenorhabditis_elegansWBGENE00015463

Paralogs (11): BTBD1 (ENSG00000064726), ABTB1 (ENSG00000114626), SPOP (ENSG00000121067), KBTBD4 (ENSG00000123444), BTBD3 (ENSG00000132640), SPOPL (ENSG00000144228), ABTB3 (ENSG00000151136), ABTB2 (ENSG00000166016), KLHL11 (ENSG00000178502), BTBD9 (ENSG00000183826), BTBD6 (ENSG00000184887)

Protein

Protein identifiers

BTB/POZ domain-containing protein 2Q9BX70 (reviewed: Q9BX70)

All UniProt accessions (7): A0A087WUX2, A0A087WXN3, A0A087WY57, A0A087X147, Q9BX70, K7EMW9, K7ENV9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with topoisomerase 1 and with TRIM5 isoform Delta.

Subcellular location. Cytoplasm.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BX70-11yes
Q9BX70-22

RefSeq proteins (1): NP_060267* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011705BACKDomain
IPR012983PHRDomain
IPR038648PHR_sfHomologous_superfamily

Pfam: PF00651, PF07707, PF08005

UniProt features (25 total): strand 14, compositionally biased region 4, turn 2, chain 1, domain 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3NO8X-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BX70-F184.820.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GSE45365_NK_CELL_VS_CD11B_DC_UP, AAGCCAT_MIR135A_MIR135B, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOBP_NEUROGENESIS, BROWNE_HCMV_INFECTION_48HR_DN, RICKMAN_METASTASIS_DN, CAATGCA_MIR33, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SENESE_HDAC3_TARGETS_DN, GOCC_RIBONUCLEOPROTEIN_GRANULE, chr19p13, MORF_ACTG1, VERHAAK_GLIOBLASTOMA_CLASSICAL, GOCC_P_BODY

GO Biological Process (1): neurogenesis (GO:0022008)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): P-body (GO:0000932), cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
nervous system development1
cell differentiation1
binding1
cytoplasmic ribonucleoprotein granule1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

646 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BTBD2TRIM5Q9C035942
BTBD2TOP1P11387811
BTBD2UBE2D2P51669613
BTBD2CUL3Q13618598
BTBD2RBX1P62877543
BTBD2WDSUB1Q8N9V3539
BTBD2HESX1Q9UBX0518
BTBD2SIAH1Q8IUQ4506
BTBD2TRIM34Q9BYJ4494
BTBD2TRIM6Q9C030492
BTBD2LONP2Q86WA8489
BTBD2TOB1P50616482
BTBD2LMBRD2Q68DH5466
BTBD2TOPORSQ9NS56462
BTBD2CHD3Q12873439

IntAct

127 interactions, top by confidence:

ABTypeScore
CUL3KLHL12psi-mi:“MI:0914”(association)0.920
COPS5COPS2psi-mi:“MI:0914”(association)0.910
COPS2GPS1psi-mi:“MI:0914”(association)0.860
COPS8COPS2psi-mi:“MI:0914”(association)0.850
COPS5CUL4Apsi-mi:“MI:0914”(association)0.840
CUL3BTBD2psi-mi:“MI:0915”(physical association)0.800
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
BTBD1BTBD2psi-mi:“MI:0403”(colocalization)0.620
BTBD2BTBD1psi-mi:“MI:0403”(colocalization)0.620
PSMD5BTBD2psi-mi:“MI:0915”(physical association)0.560
MLH1BTBD2psi-mi:“MI:0915”(physical association)0.560
BTBD2OSGIN1psi-mi:“MI:0915”(physical association)0.560
CCNCBTBD2psi-mi:“MI:0915”(physical association)0.560
BTBD2NGBpsi-mi:“MI:0915”(physical association)0.560
CINPBTBD2psi-mi:“MI:0915”(physical association)0.560
NTAQ1BTBD2psi-mi:“MI:0915”(physical association)0.560
COPS5KLHL18psi-mi:“MI:0914”(association)0.530
CUL3RHOBTB1psi-mi:“MI:0914”(association)0.530
BTBD1TRAPPC10psi-mi:“MI:0914”(association)0.530
COPS3HBBpsi-mi:“MI:0914”(association)0.530

BioGRID (102): BTBD2 (Affinity Capture-Western), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS), BTBD2 (Affinity Capture-MS)

ESM2 similar proteins: A0A072VIM5, A2AQW0, B5X561, F4JSE7, O04615, O35099, O81916, O82343, O94955, P58544, Q0IY07, Q0JC27, Q10MI4, Q2HW56, Q53NI2, Q5ZJ87, Q66J91, Q6E7H0, Q6PNC0, Q6ZN16, Q7ZX59, Q80WG7, Q84UI6, Q8CFE5, Q8LPQ5, Q8NEA9, Q8S8F2, Q8VYP9, Q8VZF6, Q8W032, Q8W519, Q94BM7, Q99683, Q9BX70, Q9CAJ9, Q9CTN4, Q9FLR0, Q9FNP1, Q9FPW6, Q9FYF9

Diamond homologs: A0A2R8Q1W5, A4IFG2, A9JRD8, B7U179, F1RD40, F7ASZ0, G3X9X1, M3XQV7, O75592, P57790, P58544, P58545, Q0V9W6, Q14145, Q17551, Q2LE78, Q5R774, Q5TZE1, Q684M4, Q7TPH6, Q8BHI4, Q8IY47, Q8K2J9, Q96KE9, Q96Q07, Q9BX70, Q9H0C5, Q9W2S3, Q9Y2F9, Q9Z2X8, A6NED2, D3ZGQ5, O95199, O95714, P0C5Y8, P18754, P23800, P25171, P25183, Q15034

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 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
DNA Damage Recognition in GG-NER1052.9×9e-13
Formation of TC-NER Pre-Incision Complex1039.2×1e-11
Cargo recognition for clathrin-mediated endocytosis917.5×2e-07
Neddylation1210.5×2e-07

GO biological processes:

GO termPartnersFoldFDR
regulation of protein neddylation897.3×2e-12
protein neddylation763.8×2e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance89
Likely benign9
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1282 predictions. Top by Δscore:

VariantEffectΔscore
19:1986645:GGGCC:Gacceptor_gain1.0000
19:1986646:GGCC:Gacceptor_gain1.0000
19:1986647:GCC:Gacceptor_gain1.0000
19:1986648:CC:Cacceptor_gain1.0000
19:1986648:CCC:Cacceptor_gain1.0000
19:1986649:CCTG:Cacceptor_gain1.0000
19:1986650:C:CCacceptor_gain1.0000
19:1986650:CTGTA:Cacceptor_loss1.0000
19:1986651:T:Cacceptor_loss1.0000
19:1986826:GCAC:Gdonor_loss1.0000
19:1986827:CACC:Cdonor_loss1.0000
19:1986972:ATAAT:Aacceptor_gain1.0000
19:1986973:TAAT:Tacceptor_gain1.0000
19:1986974:AAT:Aacceptor_gain1.0000
19:1986974:AATC:Aacceptor_loss1.0000
19:1986975:AT:Aacceptor_gain1.0000
19:1986976:TC:Tacceptor_loss1.0000
19:1986977:C:CAacceptor_loss1.0000
19:1986977:C:CCacceptor_gain1.0000
19:1986978:T:Gacceptor_loss1.0000
19:1987162:GTAC:Gdonor_loss1.0000
19:1987163:TA:Tdonor_loss1.0000
19:1987164:A:Cdonor_loss1.0000
19:1987165:C:Adonor_loss1.0000
19:1987252:ACCT:Aacceptor_loss1.0000
19:1987254:C:Aacceptor_loss1.0000
19:1987499:C:CAdonor_loss1.0000
19:1987692:CCT:Cacceptor_loss1.0000
19:1987693:C:CCacceptor_gain1.0000
19:1987693:C:CGacceptor_loss1.0000

AlphaMissense

3413 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:1986510:G:CP519R1.000
19:1986510:G:TP519H1.000
19:1986513:A:CI518S1.000
19:1986513:A:GI518T1.000
19:1986513:A:TI518N1.000
19:1986515:C:AQ517H1.000
19:1986515:C:GQ517H1.000
19:1986516:T:CQ517R1.000
19:1986519:C:AG516V1.000
19:1986519:C:GG516A1.000
19:1986519:C:TG516D1.000
19:1986520:C:AG516C1.000
19:1986520:C:GG516R1.000
19:1986520:C:TG516S1.000
19:1986521:G:CD515E1.000
19:1986521:G:TD515E1.000
19:1986522:T:AD515V1.000
19:1986522:T:GD515A1.000
19:1986523:C:AD515Y1.000
19:1986523:C:GD515H1.000
19:1986525:T:AE514V1.000
19:1986526:C:TE514K1.000
19:1986531:G:AS512F1.000
19:1986531:G:TS512Y1.000
19:1986532:A:GS512P1.000
19:1986534:G:AT511I1.000
19:1986534:G:CT511R1.000
19:1986534:G:TT511K1.000
19:1986535:T:CT511A1.000
19:1986537:C:AG510V1.000

dbSNP variants (sampled 300 via entrez): RS1000225194 (19:2009316 A>G), RS1000316997 (19:1985037 C>T), RS1000334046 (19:2004684 G>A), RS1000495959 (19:2009160 A>G), RS1000498033 (19:1996622 G>A), RS1000615184 (19:2003854 A>T), RS1000654965 (19:1996910 C>T), RS1000658560 (19:1986428 A>C,T), RS1000667777 (19:2012485 G>A), RS1000767633 (19:2000155 G>A), RS1000935831 (19:2012283 G>A), RS1001047967 (19:2004063 T>TCAATG), RS1001100328 (19:2007664 A>C), RS1001146848 (19:2012662 C>T), RS1001155417 (19:2016228 A>C)

Disease associations

OMIM: gene MIM:608531 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004603_189Platelet count8.000000e-09
GCST007396_2Mitochondrial DNA copy number (white blood cells)5.000000e-08
GCST90002400_257Plateletcrit1.000000e-09
GCST90002401_569Platelet distribution width6.000000e-18
GCST90002402_607Platelet count4.000000e-15

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004309platelet count
EFO:0006312mitochondrial DNA measurement
EFO:0007985platelet crit
EFO:0007984platelet component distribution width

MeSH disease descriptors (1)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, decreases methylation3
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
aristolochic acid Idecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
cupric chloridedecreases expression1
nickel sulfateincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
abrinedecreases expression1
bisphenol AFdecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation, increases methylation1
Carcinogensdecreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Quercetinincreases expression1
Smokedecreases expression1
Dronabinolincreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
Zincaffects expression1
Cyclosporinedecreases methylation1
Okadaic Aciddecreases expression1
tert-Butylhydroperoxidedecreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): breast ductal adenocarcinoma