RCBTB2

gene
On this page

Summary

RCBTB2 (RCC1 and BTB domain containing protein 2, HGNC:1914) is a protein-coding gene on chromosome 13q14.2, encoding RCC1 and BTB domain-containing protein 2 (O95199).

This gene encodes a protein containing two C-terminal BTB/POZ domains that is related to regulator of chromosome condensation (RCC). The encoded protein may act as a guanine nucleotide exchange factor. This gene is observed to be lost or underexpressed in prostate cancers. There is a pseudogene of this gene on chromosome 10. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 1102 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 80 total
  • MANE Select transcript: NM_001268

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1914
Approved symbolRCBTB2
NameRCC1 and BTB domain containing protein 2
Location13q14.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000136161
Ensembl biotypeprotein_coding
OMIM603524
Entrez1102

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 17 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000344532, ENST00000430805, ENST00000462703, ENST00000481144, ENST00000544492, ENST00000544904, ENST00000611827, ENST00000874757, ENST00000874758, ENST00000874759, ENST00000874760, ENST00000874761, ENST00000874762, ENST00000874763, ENST00000929084, ENST00000959816, ENST00000959817, ENST00000959818, ENST00000959819, ENST00000959820

RefSeq mRNA: 10 — MANE Select: NM_001268 NM_001268, NM_001286830, NM_001286831, NM_001286832, NM_001352424, NM_001352425, NM_001352426, NM_001352427, NM_001352428, NM_001352429

CCDS: CCDS73570, CCDS73571, CCDS73572, CCDS9411

Canonical transcript exons

ENST00000344532 — 15 exons

ExonStartEnd
ENSE000006824324851201648512174
ENSE000008368344851062948510771
ENSE000013866394852465948524757
ENSE000015990884849962148499760
ENSE000016950744850272448502914
ENSE000017706534850174248501868
ENSE000018002974849619148496321
ENSE000019199054853302848533080
ENSE000019261424848896348490251
ENSE000022937504852189848521962
ENSE000035054124851272948512895
ENSE000035062984851520548515355
ENSE000036411704851177048511877
ENSE000036668874852230848522403
ENSE000036915584851558648515741

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2180 / max 133.5083, expressed in 1539 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1372834.55881450
1372841.6692393
1372601.6148290
1372820.5879283
1372580.3373133
1372610.241691
1372590.166689
1372850.041927

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065597.73gold quality
monocyteCL:000057697.46gold quality
mononuclear cellCL:000084297.30gold quality
leukocyteCL:000073897.03gold quality
cranial nerve IIUBERON:000094195.83gold quality
parietal pleuraUBERON:000240095.23gold quality
visceral pleuraUBERON:000240194.81gold quality
pleuraUBERON:000097794.73gold quality
choroid plexus epitheliumUBERON:000391194.29gold quality
pigmented layer of retinaUBERON:000178294.02gold quality
seminal vesicleUBERON:000099893.70gold quality
ganglionic eminenceUBERON:000402392.87gold quality
ventricular zoneUBERON:000305392.83gold quality
granulocyteCL:000009492.68gold quality
parotid glandUBERON:000183191.32gold quality
esophagus squamous epitheliumUBERON:000692091.32gold quality
bloodUBERON:000017891.24gold quality
germinal epithelium of ovaryUBERON:000130491.08gold quality
gingival epitheliumUBERON:000194990.98gold quality
tibiaUBERON:000097990.59gold quality
nephron tubuleUBERON:000123190.58gold quality
gingivaUBERON:000182890.33gold quality
epithelium of esophagusUBERON:000197690.20gold quality
minor salivary glandUBERON:000183090.03gold quality
embryoUBERON:000092290.01gold quality
saliva-secreting glandUBERON:000104490.01gold quality
renal glomerulusUBERON:000007489.59gold quality
mouth mucosaUBERON:000372989.49gold quality
squamous epitheliumUBERON:000691489.44gold quality
metanephrosUBERON:000008189.28gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-111727yes1289.30
E-MTAB-5061yes6.22
E-MTAB-6075no311.98
E-MTAB-7303no47.32
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

99 targeting RCBTB2, 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-6833-3P100.0070.633197
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-1213699.9872.815713
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-512-3P99.9767.351049
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-391099.9571.132227
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-539-5P99.9370.302855
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-311999.9271.342390
HSA-MIR-589-3P99.9169.622088
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-506-3P99.8973.553057
HSA-MIR-124-3P99.8973.743043
HSA-MIR-576-5P99.8470.462582
HSA-MIR-520F-3P99.8271.321216
HSA-MIR-323A-3P99.7970.301739
HSA-MIR-205299.7969.372031
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-320A-3P99.7769.732107
HSA-MIR-320B99.7769.732107
HSA-MIR-320C99.7769.732107
HSA-MIR-320D99.7769.732107

Literature-anchored findings (GeneRIF, showing 2)

  • decreased expression in prostate cancer associated with the difference in frequency of variant isoforms between normal and neoplastic prostate tissues places it in a pivotal role or possibly adjacent to a gene with that role in prostate cancer evolution (PMID:12115502)
  • Expression of CLLD7 and CHC1L Proteins in Oral Epithelial Dysplasia in a Group of Thai Patients. (PMID:38679985)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriorcbtb2ENSDARG00000090687
mus_musculusRcbtb2ENSMUSG00000022106
rattus_norvegicusRcbtb2ENSRNOG00000015054
drosophila_melanogastercaFBGN0000247
drosophila_melanogasterRcc1FBGN0002638
drosophila_melanogasterCG7420FBGN0031344
caenorhabditis_elegansWBGENE00004304

Paralogs (9): ALS2 (ENSG00000003393), HERC1 (ENSG00000103657), SERGEF (ENSG00000129158), RCBTB1 (ENSG00000136144), RPGR (ENSG00000156313), RCCD1 (ENSG00000166965), RCC2 (ENSG00000179051), RCC1 (ENSG00000180198), RCC1L (ENSG00000274523)

Protein

Protein identifiers

RCC1 and BTB domain-containing protein 2O95199 (reviewed: O95199)

Alternative names: Chromosome condensation 1-like, RCC1-like G exchanging factor, Regulator of chromosome condensation and BTB domain-containing protein 2

All UniProt accessions (3): B4DWG0, B4E372, O95199

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome.

Domain organisation. The BTB domain might play a role in targeting to acrosomal vesicles.

Isoforms (2)

UniProt IDNamesCanonical?
O95199-11yes
O95199-22

RefSeq proteins (10): NP_001259, NP_001273759, NP_001273760, NP_001273761, NP_001339353, NP_001339354, NP_001339355, NP_001339356, NP_001339357, NP_001339358 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR000408Reg_chr_condensRepeat
IPR009091RCC1/BLIP-IIHomologous_superfamily
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR051625Signaling_Regulatory_DomainFamily
IPR058923RCC1-like_domDomain

Pfam: PF00651, PF25390

UniProt features (11 total): repeat 6, sequence variant 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95199-F190.450.73

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 263 (showing top): GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, GOCC_SECRETORY_GRANULE, MODULE_45, GOBP_LYMPH_NODE_DEVELOPMENT, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP, GOBP_HEMATOPOIETIC_OR_LYMPHOID_ORGAN_DEVELOPMENT, COATES_MACROPHAGE_M1_VS_M2_UP, BASSO_HAIRY_CELL_LEUKEMIA_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, SCHLOSSER_SERUM_RESPONSE_DN, AACTTT_UNKNOWN

GO Biological Process (5): liver development (GO:0001889), cell population proliferation (GO:0008283), lymph node development (GO:0048535), spleen development (GO:0048536), digestive tract development (GO:0048565)

GO Molecular Function (2): guanyl-nucleotide exchange factor activity (GO:0005085), protein binding (GO:0005515)

GO Cellular Component (3): acrosomal vesicle (GO:0001669), cytoplasm (GO:0005737), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
hematopoietic or lymphoid organ development2
gland development1
hepaticobiliary system development1
cellular process1
tube development1
digestive system development1
GTP binding1
GDP binding1
GTPase regulator activity1
binding1
secretory granule1
intracellular anatomical structure1
cellular anatomical structure1
cytoplasm1
intracellular vesicle1

Protein interactions and networks

STRING

814 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RCBTB2LPAR6P43657641
RCBTB2ITM2BQ9Y287629
RCBTB2FNDC3AQ9Y2H6531
RCBTB2CDADC1Q9BWV3517
RCBTB2CYSLTR2Q9NS75489
RCBTB2TSSK4Q6SA08489
RCBTB2SETDB2Q96T68478
RCBTB2AGTR1P30556470
RCBTB2PHF11Q9UIL8465
RCBTB2AFAP1L1Q8TED9463
RCBTB2MLNRO43193460
RCBTB2GRPEL2Q8TAA5459
RCBTB2ZNF608Q9ULD9446
RCBTB2PRSS55Q6UWB4436
RCBTB2CAB39LQ9H9S4425

IntAct

61 interactions, top by confidence:

ABTypeScore
HDAC3TBL1Xpsi-mi:“MI:0914”(association)0.760
FARS2RCBTB2psi-mi:“MI:0915”(physical association)0.720
RCBTB2FARS2psi-mi:“MI:0915”(physical association)0.720
IGF2BP1IGF2BP3psi-mi:“MI:0914”(association)0.640
PIK3R2IRS4psi-mi:“MI:0914”(association)0.640
RCBTB2UBE2Ipsi-mi:“MI:0915”(physical association)0.560
UBE2IRCBTB2psi-mi:“MI:0915”(physical association)0.560
RCBTB2TAE1psi-mi:“MI:0915”(physical association)0.560
TAE1RCBTB2psi-mi:“MI:0915”(physical association)0.560
RCBTB2MORF4L1psi-mi:“MI:0915”(physical association)0.560
PLA2G6RCBTB2psi-mi:“MI:0915”(physical association)0.560
RBBP9RCBTB2psi-mi:“MI:0915”(physical association)0.560
RCBTB2NUDCD2psi-mi:“MI:0915”(physical association)0.560
RCBTB2RCBTB2psi-mi:“MI:0915”(physical association)0.550
TTKRCBTB2psi-mi:“MI:0915”(physical association)0.400
USP10RCBTB2psi-mi:“MI:0915”(physical association)0.400
VRK3RCBTB2psi-mi:“MI:0915”(physical association)0.400
RUNX3RCBTB2psi-mi:“MI:0915”(physical association)0.400
RCBTB2HSP90AB1psi-mi:“MI:0915”(physical association)0.400
PDE4BRCBTB2psi-mi:“MI:0915”(physical association)0.370
RCBTB2COPS4psi-mi:“MI:0915”(physical association)0.370
ATXN2LMCRIP1psi-mi:“MI:0914”(association)0.350
CAPRIN1EIF3CLpsi-mi:“MI:0914”(association)0.350
CLASP1KIF2Apsi-mi:“MI:0914”(association)0.350
CLASP2TAF5Lpsi-mi:“MI:0914”(association)0.350

BioGRID (69): RCBTB2 (Two-hybrid), UBE2I (Two-hybrid), FARS2 (Two-hybrid), RCBTB2 (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS), COPS4 (Two-hybrid), RCBTB2 (Two-hybrid), RCBTB2 (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS), RCBTB1 (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS), FECH (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS), RCBTB2 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8Q1W5, A2AAX3, A4IF63, A6QQY2, D3ZA50, D3ZQG6, F7H9X2, G3X9X1, O95199, P28575, P57790, Q14145, Q28DE7, Q2T9Z7, Q2WGJ6, Q56A24, Q58CV6, Q59H18, Q5BK60, Q5GIG6, Q5R774, Q5RCZ7, Q5RDY3, Q5U3Y0, Q5U580, Q5ZJU2, Q5ZLD3, Q684M4, Q6AYI2, Q6P798, Q6TFL4, Q6ZPT1, Q7TQP6, Q80TF4, Q80YG3, Q8BRG6, Q8BSF5, Q8IY47, Q8N7A1, Q8VEM9

Diamond homologs: A1L4W5, B7U179, B9DHT4, E9Q4F2, F7ASZ0, G5E8B9, M3XQV7, O22286, O43791, O94889, O95199, O95625, P17789, P28575, P42282, P57790, P58545, Q0IHH9, Q0V9W6, Q0VCW1, Q14145, Q1EBV6, Q2LE78, Q2M2N2, Q54D84, Q5BL35, Q5NVK7, Q5R774, Q5RCZ7, Q5TC79, Q5TZE1, Q684M4, Q6DEL7, Q6IQ16, Q6NRH0, Q6P8B3, Q6YCH2, Q6ZWS8, Q7T330, Q7ZX06

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 57 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
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal514.6×8e-03
EML4 and NUDC in mitotic spindle formation511.6×8e-03
Resolution of Sister Chromatid Cohesion510.8×8e-03
RHO GTPases Activate Formins59.7×8e-03
Mitotic Prometaphase58.7×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance70
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2039 predictions. Top by Δscore:

VariantEffectΔscore
13:48496185:CCTTA:Cdonor_loss1.0000
13:48496186:CTTA:Cdonor_loss1.0000
13:48496187:TTAC:Tdonor_loss1.0000
13:48499623:A:ACdonor_gain1.0000
13:48499623:ACTG:Adonor_gain1.0000
13:48499624:C:CCdonor_gain1.0000
13:48499624:CTGC:Cdonor_gain1.0000
13:48501737:CTT:Cdonor_loss1.0000
13:48501738:TTACC:Tdonor_loss1.0000
13:48501740:A:ACdonor_gain1.0000
13:48501740:ACCGA:Adonor_loss1.0000
13:48501741:C:CCdonor_gain1.0000
13:48501741:C:CGdonor_loss1.0000
13:48501780:T:Adonor_gain1.0000
13:48501864:AGGTT:Aacceptor_gain1.0000
13:48501865:GGTT:Gacceptor_gain1.0000
13:48501866:GTT:Gacceptor_gain1.0000
13:48501867:TT:Tacceptor_gain1.0000
13:48501868:TC:Tacceptor_loss1.0000
13:48501869:C:CCacceptor_gain1.0000
13:48501869:CT:Cacceptor_loss1.0000
13:48502719:CTTA:Cdonor_loss1.0000
13:48502720:TTACC:Tdonor_loss1.0000
13:48502722:A:ACdonor_gain1.0000
13:48502722:AC:Adonor_gain1.0000
13:48502723:C:CCdonor_gain1.0000
13:48502723:CC:Cdonor_gain1.0000
13:48502723:CCCA:Cdonor_gain1.0000
13:48502910:TAATC:Tacceptor_gain1.0000
13:48502916:T:Gacceptor_loss1.0000

AlphaMissense

3603 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:48490234:G:CC511W1.000
13:48496211:C:GA499P1.000
13:48496269:G:CC479W1.000
13:48496306:G:TA467D1.000
13:48496318:A:GL463P1.000
13:48490120:A:CF549L0.999
13:48490120:A:TF549L0.999
13:48490121:A:GF549S0.999
13:48490122:A:GF549L0.999
13:48490139:G:TA543E0.999
13:48490140:C:GA543P0.999
13:48490151:A:GF539S0.999
13:48490222:G:CC515W0.999
13:48490224:A:GC515R0.999
13:48490225:A:CF514L0.999
13:48490225:A:TF514L0.999
13:48490227:A:GF514L0.999
13:48490235:C:TC511Y0.999
13:48490236:A:GC511R0.999
13:48496210:G:TA499E0.999
13:48496219:A:GL496P0.999
13:48496222:A:GL495P0.999
13:48496231:G:TA492D0.999
13:48496258:A:TI483N0.999
13:48496270:C:TC479Y0.999
13:48496271:A:GC479R0.999
13:48496282:A:GL475S0.999
13:48496307:C:GA467P0.999
13:48496309:A:GL466S0.999
13:48496315:A:GL464P0.999

dbSNP variants (sampled 300 via entrez): RS1000097334 (13:48517780 C>G), RS1000186103 (13:48532984 C>A,T), RS1000197989 (13:48536216 G>A), RS1000239366 (13:48504839 G>C), RS1000251667 (13:48534773 T>C,G), RS1000324781 (13:48492411 C>T), RS1000463841 (13:48498652 A>G), RS1000499211 (13:48522557 C>T), RS1000529645 (13:48517410 C>A), RS1000550019 (13:48506298 C>T), RS1000575112 (13:48503357 A>T), RS1000625884 (13:48500410 T>C,G), RS1000658628 (13:48500212 TAAG>T), RS1000687075 (13:48497095 C>T), RS1000751557 (13:48498506 G>A,T)

Disease associations

OMIM: gene MIM:603524 | disease phenotypes: MIM:612073

GenCC curated gene-disease

Mondo (1): mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria (MONDO:0012791)

Orphanet (1): Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria (Orphanet:1933)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009391_118Metabolite levels5.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010354diacylglycerol 36:1 measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C567624Mitochondrial Dna Depletion Syndrome, Encephalomyopathic Form, With Methylmalonic Aciduria, Autosomal Recessive (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression7
bisphenol Aaffects cotreatment, increases methylation, decreases expression, decreases methylation, increases expression3
Tretinoinincreases expression3
methylmercuric chloridedecreases expression2
sodium arseniteaffects expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cyclosporinedecreases expression2
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
sodium bichromatedecreases expression1
potassium chromate(VI)decreases expression1
CGP 52608affects binding, increases reaction1
motexafin gadoliniumaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
belinostatdecreases expression1
abrineincreases expression1
dorsomorphindecreases expression, affects cotreatment1
gardiquimoddecreases reaction, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Zoledronic Acidincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutants, Occupationaldecreases expression1
Cisplatinincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases expression1
Diurondecreases expression1
Drugs, Chinese Herbaldecreases expression1
Ethyl Methanesulfonateincreases expression1
Fluorouracilaffects expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_TI65HAP1 RCBTB2 (-) 1Cancer cell lineMale
CVCL_XS18HAP1 RCBTB2 (-) 2Cancer cell lineMale
CVCL_XS19HAP1 RCBTB2 (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

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