BRIX1

gene
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Also known as BRIXFLJ11100

Summary

BRIX1 (biogenesis of ribosomes BRX1, HGNC:24170) is a protein-coding gene on chromosome 5p13.2, encoding Ribosome biogenesis protein BRX1 homolog (Q8TDN6). Required for biogenesis of the 60S ribosomal subunit. It is a common-essential gene (DepMap: required in 98.8% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in ribosomal large subunit assembly. Located in chromosome and nucleolus.

Source: NCBI Gene 55299 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 70 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 98.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_018321

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24170
Approved symbolBRIX1
Namebiogenesis of ribosomes BRX1
Location5p13.2
Locus typegene with protein product
StatusApproved
AliasesBRIX, FLJ11100
Ensembl geneENSG00000113460
Ensembl biotypeprotein_coding
OMIM618466
Entrez55299

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000336767, ENST00000506023, ENST00000510834, ENST00000510960, ENST00000515798, ENST00000938601, ENST00000938602, ENST00000938603, ENST00000938604, ENST00000938605, ENST00000938606, ENST00000938607, ENST00000938608, ENST00000970234

RefSeq mRNA: 1 — MANE Select: NM_018321 NM_018321

CCDS: CCDS34143

Canonical transcript exons

ENST00000336767 — 10 exons

ExonStartEnd
ENSE000013567363492522634925996
ENSE000020818943491571134915897
ENSE000034762703492269534922768
ENSE000035367053492484734924975
ENSE000035399783491836434918475
ENSE000035512893491984034919883
ENSE000035669333492221734922287
ENSE000035815963492253934922588
ENSE000036395703492313334923234
ENSE000036565983492300134923051

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 92.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.7209 / max 237.8671, expressed in 1803 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
5608624.15981791
560841.9637647
560851.4731769
560830.124352

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370192.15gold quality
ventricular zoneUBERON:000305390.10gold quality
ganglionic eminenceUBERON:000402390.04gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.68gold quality
islet of LangerhansUBERON:000000689.59gold quality
olfactory segment of nasal mucosaUBERON:000538689.57gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.37gold quality
cortical plateUBERON:000534388.81gold quality
adrenal tissueUBERON:001830388.71gold quality
rectumUBERON:000105288.68gold quality
left uterine tubeUBERON:000130388.02gold quality
esophagus mucosaUBERON:000246987.67gold quality
omental fat padUBERON:001041487.66gold quality
C1 segment of cervical spinal cordUBERON:000646987.61gold quality
peritoneumUBERON:000235887.59gold quality
left adrenal gland cortexUBERON:003582587.55gold quality
left adrenal glandUBERON:000123487.43gold quality
ectocervixUBERON:001224987.27gold quality
left ovaryUBERON:000211987.15gold quality
descending thoracic aortaUBERON:000234587.14gold quality
body of uterusUBERON:000985387.08gold quality
popliteal arteryUBERON:000225087.07gold quality
tibial arteryUBERON:000761087.07gold quality
buccal mucosa cellCL:000233687.01gold quality
right adrenal gland cortexUBERON:003582787.00gold quality
right adrenal glandUBERON:000123386.80gold quality
left coronary arteryUBERON:000162686.77gold quality
esophagusUBERON:000104386.70gold quality
endocervixUBERON:000045886.61gold quality
adipose tissue of abdominal regionUBERON:000780886.55gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-7249no481.88
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting BRIX1, 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-548N99.9871.944170
HSA-MIR-477599.9875.006394
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-797899.8666.90856
HSA-MIR-394199.8670.542735
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • BRIX1 promotes ribosome synthesis and enhances glycolysis by selected translation of GLUT1 in colorectal cancer. (PMID:38282151)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriobxdc2ENSDARG00000098935
mus_musculusBrix1ENSMUSG00000022247
rattus_norvegicusBrix1ENSRNOG00000018021
drosophila_melanogasterCG11583FBGN0035524
caenorhabditis_elegansWBGENE00019678

Protein

Protein identifiers

Ribosome biogenesis protein BRX1 homologQ8TDN6 (reviewed: Q8TDN6)

Alternative names: Brix domain-containing protein 2

All UniProt accessions (1): Q8TDN6

UniProt curated annotations — full annotation on UniProt →

Function. Required for biogenesis of the 60S ribosomal subunit.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the BRX1 family.

RefSeq proteins (1): NP_060791* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007109BrixDomain
IPR026532BRX1Family

Pfam: PF04427

UniProt features (13 total): sequence conflict 3, cross-link 3, compositionally biased region 2, modified residue 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
8FKVELECTRON MICROSCOPY2.47
8FKWELECTRON MICROSCOPY2.5
8FKXELECTRON MICROSCOPY2.59
8FKYELECTRON MICROSCOPY2.67
8FKQELECTRON MICROSCOPY2.76
8FKTELECTRON MICROSCOPY2.81
8FKUELECTRON MICROSCOPY2.82
8FKPELECTRON MICROSCOPY2.85
8FKSELECTRON MICROSCOPY2.88
8FKRELECTRON MICROSCOPY2.89

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TDN6-F181.680.53

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 261, 276, 160, 314, 322

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 147 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_RIBOSOME_ASSEMBLY, WEI_MYCN_TARGETS_WITH_E_BOX, MUELLER_PLURINET, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, WCTCNATGGY_UNKNOWN, MODULE_206, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS

GO Biological Process (3): ribosomal large subunit assembly (GO:0000027), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (3): RNA binding (GO:0003723), rRNA binding (GO:0019843), protein binding (GO:0005515)

GO Cellular Component (3): chromosome (GO:0005694), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle2
protein-RNA complex assembly1
ribosome assembly1
ribosomal large subunit biogenesis1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
ribonucleoprotein complex biogenesis1
nucleic acid binding1
RNA binding1
binding1
nuclear lumen1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

3236 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BRIX1WDR12Q9GZL7720
BRIX1DDX18Q9NVP1661
BRIX1ABT1Q9ULW3621
BRIX1NIP7Q9Y221611
BRIX1RPF1Q9H9Y2575
BRIX1BMS1Q14692563
BRIX1PDCD11Q14690554
BRIX1RPF2Q9H7B2543
BRIX1NIFKQ9BYG3540
BRIX1LYARQ9NX58501
BRIX1RRP1BQ14684498
BRIX1PWP1Q13610491
BRIX1DHX32Q7L7V1483
BRIX1RRP1P56182482
BRIX1BOP1Q14137479

IntAct

258 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:0914”(association)0.900
BRIX1EBNA1BP2psi-mi:“MI:0915”(physical association)0.810
EBNA1BP2BRIX1psi-mi:“MI:0915”(physical association)0.810
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
NOP53RRP8psi-mi:“MI:0914”(association)0.640
NPM1NVLpsi-mi:“MI:0914”(association)0.610
BRIX1HNRNPUpsi-mi:“MI:0915”(physical association)0.560
BRIX1RPL13psi-mi:“MI:0915”(physical association)0.560
RPS6IPO7psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
MAGEB10GTPBP10psi-mi:“MI:0914”(association)0.530
H1-6ZNF724psi-mi:“MI:0914”(association)0.530
RBM34NVLpsi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
ILF2IGF2BP3psi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
RPL18ARRP8psi-mi:“MI:0914”(association)0.530
PUM3RRP8psi-mi:“MI:0914”(association)0.530
PDGFBDKC1psi-mi:“MI:0914”(association)0.530

BioGRID (421): BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BRIX1 (Co-fractionation)

ESM2 similar proteins: A0A1D8PF11, G1STW0, O13019, O13672, O57592, O76732, P0DJ14, P0DKK7, P12970, P15125, P15126, P17076, P29453, P32429, P35685, P46223, P49196, P49692, P62424, P62425, P80455, Q02892, Q29375, Q2TBQ5, Q3SZZ0, Q4QQT6, Q4R5C2, Q54PX9, Q54ZD1, Q5ADQ6, Q5ANA1, Q5I7K9, Q5RAN2, Q6FRV0, Q74ZK6, Q8SSG1, Q8TDN6, Q8UVY2, Q90YW2, Q966C6

Diamond homologs: P34524, Q08235, Q3SZZ0, Q4QQT6, Q54JN0, Q5RAN2, Q8TDN6, Q8UVY2, Q9C928, Q9DCA5, Q9HGL6, Q9LE16, Q9VZE6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 207 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
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA2522.3×4e-25
Peptide chain elongation2322.1×4e-23
Viral mRNA Translation2322.1×4e-23
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA2321.9×4e-23
Selenocysteine synthesis2320.9×1e-22
Eukaryotic Translation Termination2320.9×1e-22
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)2320.5×1e-22
SRP-dependent cotranslational protein targeting to membrane2720.5×5e-26

GO biological processes:

GO termPartnersFoldFDR
negative regulation of DNA recombination530.7×5e-05
cytoplasmic translation2525.3×1e-25
chromosome condensation523.0×2e-04
negative regulation of mRNA splicing, via spliceosome520.9×3e-04
ribosomal large subunit biogenesis819.4×2e-06
rRNA processing1813.9×3e-13
translation2312.9×2e-16
ribosomal small subunit biogenesis1012.4×2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

797 predictions. Top by Δscore:

VariantEffectΔscore
5:34915898:GTAG:Gdonor_loss1.0000
5:34918442:GACT:Gdonor_gain1.0000
5:34919838:A:AGacceptor_gain1.0000
5:34919839:G:GGacceptor_gain1.0000
5:34919894:A:Tdonor_gain1.0000
5:34922213:TTAG:Tacceptor_loss1.0000
5:34922215:A:Tacceptor_loss1.0000
5:34922216:G:Aacceptor_loss1.0000
5:34922216:GGTTT:Gacceptor_gain1.0000
5:34922260:C:Gdonor_gain1.0000
5:34922285:GTG:Gdonor_gain1.0000
5:34922285:GTGGT:Gdonor_loss1.0000
5:34922286:TGGTA:Tdonor_loss1.0000
5:34922288:G:GGdonor_gain1.0000
5:34922288:GT:Gdonor_loss1.0000
5:34922289:T:Adonor_loss1.0000
5:34922589:G:GGdonor_gain1.0000
5:34922684:A:AGacceptor_gain1.0000
5:34922693:A:AGacceptor_gain1.0000
5:34922694:G:GTacceptor_gain1.0000
5:34922694:GTT:Gacceptor_gain1.0000
5:34922694:GTTC:Gacceptor_gain1.0000
5:34922694:GTTCA:Gacceptor_gain1.0000
5:34922764:ACCCT:Adonor_gain1.0000
5:34922765:CCCT:Cdonor_gain1.0000
5:34922766:CCT:Cdonor_gain1.0000
5:34922767:CT:Cdonor_gain1.0000
5:34922767:CTGTA:Cdonor_loss1.0000
5:34922768:TGTA:Tdonor_loss1.0000
5:34922769:G:GGdonor_gain1.0000

AlphaMissense

2356 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:34919847:A:CK93N1.000
5:34919847:A:TK93N1.000
5:34922286:T:AW129R1.000
5:34922286:T:CW129R1.000
5:34922725:G:AG156E1.000
5:34923172:T:CF201L1.000
5:34923174:T:AF201L1.000
5:34923174:T:GF201L1.000
5:34923224:G:CR218P1.000
5:34924881:G:AG233E1.000
5:34918392:T:CL63P0.999
5:34918407:G:TR68I0.999
5:34918428:G:CR75T0.999
5:34918429:A:CR75S0.999
5:34918429:A:TR75S0.999
5:34918430:C:GH76D0.999
5:34919845:A:GK93E0.999
5:34919846:A:TK93I0.999
5:34922221:G:AC107Y0.999
5:34922222:T:GC107W0.999
5:34922237:T:GC112W0.999
5:34922244:T:CC115R0.999
5:34922558:G:AG136R0.999
5:34922558:G:CG136R0.999
5:34922559:G:AG136E0.999
5:34922568:C:AA139D0.999
5:34922580:T:AV143D0.999
5:34922713:T:CL152P0.999
5:34922729:C:AN157K0.999
5:34922729:C:GN157K0.999

dbSNP variants (sampled 300 via entrez): RS1000154959 (5:34916318 G>A,C), RS1000450483 (5:34916667 A>C,T), RS1000994229 (5:34921861 C>G,T), RS1001205374 (5:34920461 C>T), RS1001336712 (5:34922155 A>G), RS1001426201 (5:34920830 TG>T), RS1001577269 (5:34916337 G>A), RS1001629751 (5:34916128 G>A), RS1001808508 (5:34914542 C>A,T), RS1002583428 (5:34915257 C>A,T), RS1002635613 (5:34915057 A>C,T), RS1002827133 (5:34921632 G>A), RS1003096879 (5:34919301 G>A,C,T), RS1003431751 (5:34917470 A>G), RS1003621702 (5:34917228 T>A)

Disease associations

OMIM: gene MIM:618466 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009391_1913Metabolite levels1.000000e-20

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010464beta-aminoisobutyric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066494 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.86Kd1383nMCHEMBL5653589
5.86ED501383nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2147958: Binding affinity to human BRIX1 incubated for 45 mins by Kinobead based pull down assaykd1.3829uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, affects cotreatment, increases expression4
trichostatin Aaffects expression, decreases reaction2
(+)-JQ1 compounddecreases expression2
Estradiolaffects expression, increases expression2
Aflatoxin B1decreases expression, increases expression, affects cotreatment2
afuresertibdecreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
coumarinincreases phosphorylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
bisphenol Sincreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
Atrazineincreases expression1
Calcitrioldecreases expression, affects cotreatment1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Fluorouracildecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Nickelaffects expression, decreases reaction1
Progesteronedecreases expression1
Ribonucleotidesaffects binding1
Rotenoneincreases expression1
Silicon Dioxideincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651000BindingBinding affinity to human BRIX1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.