KBTBD4

gene
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Also known as FLJ10450HSPC252

Summary

KBTBD4 (kelch repeat and BTB domain containing 4, HGNC:23761) is a protein-coding gene on chromosome 11p11.2, encoding Kelch repeat and BTB domain-containing protein 4 (Q9NVX7). Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex which targets CoREST corepressor complex components RCOR1, KDM1A/LSD1 and HDAC2 for proteasomal degradation.

At a glance

  • GWAS associations: 17
  • Clinical variants (ClinVar): 78 total
  • MANE Select transcript: NM_018095

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23761
Approved symbolKBTBD4
Namekelch repeat and BTB domain containing 4
Location11p11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10450, HSPC252
Ensembl geneENSG00000123444
Ensembl biotypeprotein_coding
OMIM617645
Entrez55709

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 nonsense_mediated_decay

ENST00000395288, ENST00000430070, ENST00000525720, ENST00000526005, ENST00000529499, ENST00000529946, ENST00000530668, ENST00000531067, ENST00000533290, ENST00000534239, ENST00000915129, ENST00000962990

RefSeq mRNA: 12 — MANE Select: NM_018095 NM_001318716, NM_001318717, NM_001318718, NM_001318719, NM_001318720, NM_001318721, NM_001318722, NM_001318723, NM_001318724, NM_001318725, NM_016506, NM_018095

CCDS: CCDS44594, CCDS7940, CCDS81566

Canonical transcript exons

ENST00000430070 — 4 exons

ExonStartEnd
ENSE000009892104757559347575699
ENSE000015212244757219747573790
ENSE000022506474757893347578970
ENSE000035391584757741147578028

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.4133 / max 33.9493, expressed in 1633 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1196404.41331633

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
islet of LangerhansUBERON:000000691.04gold quality
cortical plateUBERON:000534389.54gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.59gold quality
muscle of legUBERON:000138386.53gold quality
gastrocnemiusUBERON:000138886.42gold quality
ganglionic eminenceUBERON:000402385.62gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.22gold quality
hindlimb stylopod muscleUBERON:000425284.86gold quality
skeletal muscle tissueUBERON:000113484.75gold quality
ventricular zoneUBERON:000305384.59gold quality
prefrontal cortexUBERON:000045184.07gold quality
smooth muscle tissueUBERON:000113583.89gold quality
stromal cell of endometriumCL:000225583.51gold quality
olfactory segment of nasal mucosaUBERON:000538683.32gold quality
fallopian tubeUBERON:000388982.94gold quality
bone marrowUBERON:000237182.76gold quality
cerebellumUBERON:000203782.43gold quality
cerebellar cortexUBERON:000212982.31gold quality
superior frontal gyrusUBERON:000266182.31gold quality
cerebellar hemisphereUBERON:000224582.30gold quality
right adrenal glandUBERON:000123382.26gold quality
frontal cortexUBERON:000187082.26gold quality
bloodUBERON:000017882.24gold quality
right adrenal gland cortexUBERON:003582782.21gold quality
calcaneal tendonUBERON:000370182.14gold quality
right hemisphere of cerebellumUBERON:001489082.07gold quality
lymph nodeUBERON:000002981.94gold quality
muscle tissueUBERON:000238581.78gold quality
left adrenal glandUBERON:000123481.74gold quality
bone marrow cellCL:000209281.68gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-CURD-10no62.27
E-ANND-3no2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting KBTBD4, 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-190A-3P100.0080.355520
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3134100.0066.43777
HSA-MIR-1252-5P100.0069.802774
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-4482-3P99.9872.503147
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-570-3P99.9672.414910
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-544A99.8468.661965
HSA-MIR-684499.8270.692423
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-366099.6867.331149
HSA-MIR-452699.6867.071136

Literature-anchored findings (GeneRIF, showing 3)

  • Our findings suggest that KBTBD4 mutations are uncommon in Brazilian MBGRP3 and MBGRP4 medulloblastomas subgroups. (PMID:31403685)
  • Role of proliferative marker index and KBTBD4 mutation in the pathological diagnosis of pineal parenchymal tumors. (PMID:35000018)
  • Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation. (PMID:35379950)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriokbtbd4ENSDARG00000069271
mus_musculusKbtbd4ENSMUSG00000005505
rattus_norvegicusKbtbd4ENSRNOG00000009397
drosophila_melanogasterBTBD9FBGN0030228
drosophila_melanogasterCG17068FBGN0031098
drosophila_melanogasterluteFBGN0262871
caenorhabditis_elegansWBGENE00015463

Paralogs (11): BTBD1 (ENSG00000064726), ABTB1 (ENSG00000114626), SPOP (ENSG00000121067), BTBD3 (ENSG00000132640), BTBD2 (ENSG00000133243), SPOPL (ENSG00000144228), ABTB3 (ENSG00000151136), ABTB2 (ENSG00000166016), KLHL11 (ENSG00000178502), BTBD9 (ENSG00000183826), BTBD6 (ENSG00000184887)

Protein

Protein identifiers

Kelch repeat and BTB domain-containing protein 4Q9NVX7 (reviewed: Q9NVX7)

Alternative names: BTB and kelch domain-containing protein 4

All UniProt accessions (7): E9PJ66, E9PJY1, E9PL18, E9PM58, Q9NVX7, E9PQ38, E9PSA4

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex which targets CoREST corepressor complex components RCOR1, KDM1A/LSD1 and HDAC2 for proteasomal degradation. RCOR1 is likely to be the primary target while degradation of KDM1A and HDAC2 is likely due to their association with RCOR1. Also targets RCOR3, MIER2 and MIER3 for proteasomal degradation as well as associated proteins ZNF217 and RREB1. Degradation is dependent on the presence of an ELM2 domain in the target proteins.

Subunit / interactions. Component of the BCR(KBTBD4) E3 ubiquitin ligase complex, at least composed of CUL3, KBTBD4 and RBX1.

Miscellaneous. As part of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex, mediates the effects of the small molecule UM171 in enhancing hematopoietic stem and progenitor cell expansion ex vivo by specifically targeting the CoREST repressor complex for proteasomal degradation.

Isoforms (3)

UniProt IDNamesCanonical?
Q9NVX7-21yes
Q9NVX7-12
Q9NVX7-33

RefSeq proteins (12): NP_001305645, NP_001305646, NP_001305647, NP_001305648, NP_001305649, NP_001305650, NP_001305651, NP_001305652, NP_001305653, NP_001305654, NP_057590, NP_060565* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011498Kelch_2Repeat
IPR011705BACKDomain
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR017096BTB-kelch_proteinFamily
IPR042884KBTBD4Family
IPR042949KBTBD4_BTB_POZDomain
IPR042950KBTBD4_BACKDomain

Pfam: PF00651, PF07646, PF07707

UniProt features (83 total): strand 36, helix 18, turn 11, sequence conflict 6, repeat 5, domain 2, splice variant 2, chain 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
9GGMELECTRON MICROSCOPY2.71
9DTQELECTRON MICROSCOPY2.87
9GGNELECTRON MICROSCOPY2.9
9GGLELECTRON MICROSCOPY3.13
8VPQELECTRON MICROSCOPY3.3
9I2CELECTRON MICROSCOPY3.3
8VRTELECTRON MICROSCOPY3.42
8VOJELECTRON MICROSCOPY3.77
9DTGELECTRON MICROSCOPY3.83
2EQXSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NVX7-F178.200.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, CACCAGC_MIR138, WANG_LMO4_TARGETS_DN, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GTCAGGA_MIR378, GOBP_PROTEIN_CATABOLIC_PROCESS, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOCC_TRANSFERASE_COMPLEX, GAL_LEUKEMIC_STEM_CELL_UP, LIU_SOX4_TARGETS_UP, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_CUL3_RING_UBIQUITIN_LIGASE_COMPLEX, MGGAAGTG_GABP_B

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1

Protein interactions and networks

STRING

568 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KBTBD4PRDM6Q9NQX0622
KBTBD4ZMYM3Q14202513
KBTBD4SNCAIPQ9Y6H5464
KBTBD4PTPMT1Q8WUK0461
KBTBD4MBLAC1A4D2B0456
KBTBD4RBM26Q5T8P6449
KBTBD4MTCH2Q9Y6C9440
KBTBD4ZC3H6P61129425
KBTBD4GFI1BQ5VTD9418
KBTBD4ATOSAQ32MH5415
KBTBD4NDUFS3O75489388
KBTBD4GFI1Q99684367
KBTBD4ISG20L2Q9H9L3363
KBTBD4KDM6AO15550349
KBTBD4NDUFAF3Q9BU61342

IntAct

20 interactions, top by confidence:

ABTypeScore
CUL3RHOBTB1psi-mi:“MI:0914”(association)0.530
KBTBD4KPNA5psi-mi:“MI:0914”(association)0.530
CUL3ZSWIM8psi-mi:“MI:0914”(association)0.530
BCL6CUL1psi-mi:“MI:0914”(association)0.530
HSP90AB1KBTBD4psi-mi:“MI:0915”(physical association)0.400
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
MPGELP1psi-mi:“MI:0914”(association)0.350
FUCA1psi-mi:“MI:0914”(association)0.350
CUL3ZBTB24psi-mi:“MI:0914”(association)0.350
FBXL17ENC1psi-mi:“MI:0914”(association)0.350
KLHL14ARHGAP32psi-mi:“MI:0914”(association)0.350
MPP3KBTBD4psi-mi:“MI:0915”(physical association)0.000

BioGRID (353): KBTBD4 (Affinity Capture-MS), KBTBD4 (Reconstituted Complex), CACUL1 (Affinity Capture-MS), KBTBD4 (Affinity Capture-MS), DDX11 (Affinity Capture-MS), CUL3 (Affinity Capture-MS), PEX6 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), CCT2 (Affinity Capture-MS), PI4K2B (Affinity Capture-MS), KPNA6 (Affinity Capture-MS), KPNA5 (Affinity Capture-MS), LZTR1 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), TCP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B8YAB1, B1H285, B3DIV9, E9QIN8, E9QJ30, F1QEG2, O88879, Q08CL3, Q08CY1, Q0D2A9, Q13939, Q28068, Q3UQV5, Q3ZCT8, Q503R4, Q5F3N5, Q5R4S6, Q5R663, Q5RG82, Q5XHZ6, Q5XI58, Q5ZI33, Q69ZK5, Q6DFF7, Q6DFU2, Q6Q7X9, Q6V595, Q7ZVQ8, Q86V97, Q8BHI4, Q8BUL5, Q8BWA5, Q8CA72, Q8CDE2, Q8CE33, Q8IXQ5, Q8NAB2, Q8NFY9, Q8R179, Q8WVZ9

Diamond homologs: A0A072VIM5, A0A0K0PU92, A2CIR7, E7BQV0, G3LSH3, G8GTN7, Q05823, Q0JJ01, Q2HW56, Q2QXZ2, Q2RAQ5, Q5D0W8, Q5ICL9, Q5R4S6, Q75HA6, Q8L746, Q8R179, Q9FDY4, Q9M1I7, Q9N010, Q9NVX7, Q9ZVC2, S4VGD0, A0JN76, A1L4W5, A2AAX3, B1WBS3, B2RXF5, B7U179, D3YUB6, D3ZA50, O14867, O15062, O43167, P0DMR5, P0DMR6, P41182, P41183, P97303, Q0IJ29

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 19 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.

GO biological processes:

GO termPartnersFoldFDR
protein ubiquitination512.2×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

583 predictions. Top by Δscore:

VariantEffectΔscore
11:47573787:TTTC:Tacceptor_gain1.0000
11:47573787:TTTCC:Tacceptor_loss1.0000
11:47573788:TTCC:Tacceptor_loss1.0000
11:47575587:CCTTA:Cdonor_loss1.0000
11:47575588:CTTA:Cdonor_loss1.0000
11:47575589:TTAC:Tdonor_loss1.0000
11:47575590:TA:Tdonor_loss1.0000
11:47575591:A:ACdonor_gain1.0000
11:47575592:C:CCdonor_gain1.0000
11:47575592:CCTT:Cdonor_gain1.0000
11:47575696:CCAT:Cacceptor_gain1.0000
11:47575697:CAT:Cacceptor_gain1.0000
11:47575697:CATC:Cacceptor_gain1.0000
11:47575698:ATCTG:Aacceptor_loss1.0000
11:47575699:TCTGT:Tacceptor_loss1.0000
11:47575700:C:CCacceptor_gain1.0000
11:47575700:C:CGacceptor_loss1.0000
11:47575710:C:CTacceptor_gain1.0000
11:47575710:C:Tacceptor_gain1.0000
11:47575711:A:Tacceptor_gain1.0000
11:47577406:CTTA:Cdonor_loss1.0000
11:47577408:TA:Tdonor_loss1.0000
11:47577409:A:ACdonor_gain1.0000
11:47577409:AC:Adonor_gain1.0000
11:47577409:ACCCG:Adonor_loss1.0000
11:47577410:C:CCdonor_gain1.0000
11:47577410:CC:Cdonor_gain1.0000
11:47573788:TTC:Tacceptor_gain0.9900
11:47573791:C:CCacceptor_gain0.9900
11:47573792:T:Gacceptor_loss0.9900

AlphaMissense

3491 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:47573415:A:GW358R1.000
11:47573415:A:TW358R1.000
11:47573413:C:AW358C0.999
11:47573413:C:GW358C0.999
11:47573414:C:GW358S0.999
11:47573436:A:CY351D0.999
11:47573490:A:CY333D0.999
11:47573534:C:GR318P0.999
11:47573563:C:AW308C0.999
11:47573563:C:GW308C0.999
11:47573565:A:GW308R0.999
11:47573565:A:TW308R0.999
11:47573615:C:AG291V0.999
11:47573615:C:TG291E0.999
11:47573625:A:CY288D0.999
11:47575655:A:GW212R0.999
11:47575655:A:TW212R0.999
11:47577539:G:TA154E0.999
11:47577540:C:GA154P0.999
11:47577620:A:GL127P0.999
11:47577779:A:GF74S0.999
11:47577791:A:GF70S0.999
11:47577799:G:CS67R0.999
11:47577799:G:TS67R0.999
11:47577801:T:GS67R0.999
11:47577812:A:GL63P0.999
11:47577812:A:TL63H0.999
11:47577821:C:GR60P0.999
11:47573336:C:TG384E0.998
11:47573337:C:AG384W0.998

dbSNP variants (sampled 300 via entrez): RS1000147083 (11:47575986 G>A), RS1000243573 (11:47578514 C>G), RS1000332324 (11:47574850 ATCTC>A,ATC,ATCTCTC), RS1000458989 (11:47578743 G>A), RS1000771608 (11:47574021 C>T), RS1001335529 (11:47575467 A>C), RS1001981342 (11:47573244 A>C,G), RS1002290501 (11:47571968 T>G), RS1002317878 (11:47578999 AGAT>A), RS1002539493 (11:47579856 C>T), RS1002590039 (11:47576589 G>A), RS1002608455 (11:47578738 C>A,G,T), RS1002643822 (11:47576475 C>T), RS1003655609 (11:47574803 G>A), RS1004214589 (11:47579178 T>A,C)

Disease associations

OMIM: gene MIM:617645 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

StudyTraitp-value
GCST005232_56Neuroticism1.000000e-16
GCST006923_11Loneliness1.000000e-07
GCST006924_13Loneliness (MTAG)1.000000e-08
GCST007293_118Body fat distribution (arm fat ratio)3.000000e-08
GCST007293_19Body fat distribution (arm fat ratio)2.000000e-10
GCST007293_45Body fat distribution (arm fat ratio)5.000000e-14
GCST007294_28Body fat distribution (trunk fat ratio)6.000000e-09
GCST007294_9Body fat distribution (trunk fat ratio)4.000000e-06
GCST007295_159Body fat distribution (leg fat ratio)1.000000e-18
GCST007295_24Body fat distribution (leg fat ratio)7.000000e-08
GCST007295_50Body fat distribution (leg fat ratio)2.000000e-12
GCST007559_27Sleep duration (short sleep)4.000000e-08
GCST007825_4Alzheimer’s disease or fasting glucose levels (pleiotropy)3.000000e-16
GCST008103_60Bipolar disorder5.000000e-07
GCST008357_37Mood instability9.000000e-14
GCST010136_2Fruit consumption5.000000e-09
GCST010703_36Brain morphology (MOSTest)8.000000e-09

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement
EFO:0007865loneliness measurement
EFO:0004341body fat distribution
EFO:0008475mood instability measurement
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, decreases methylation7
trichostatin Adecreases expression2
sodium arseniteincreases abundance, increases expression, decreases expression2
Cyclosporinedecreases expression2
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cupric oxideincreases 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
dorsomorphinaffects cotreatment, decreases expression1
Leflunomidedecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Phenylmercuric Acetatedecreases expression1
Quercetindecreases expression1
Aflatoxin B1increases methylation1
Particulate Matterincreases abundance, decreases expression1

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.