BEX1

gene
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Summary

BEX1 (brain expressed X-linked 1, HGNC:1036) is a protein-coding gene on chromosome Xq22.1, encoding Protein BEX1 (Q9HBH7). Signaling adapter molecule involved in p75NTR/NGFR signaling.

Enables RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in positive regulation of DNA-binding transcription factor activity and positive regulation of transcription by RNA polymerase II. Part of transcription regulator complex.

Source: NCBI Gene 55859 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 31 total — 2 pathogenic
  • MANE Select transcript: NM_018476

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1036
Approved symbolBEX1
Namebrain expressed X-linked 1
LocationXq22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000133169
Ensembl biotypeprotein_coding
OMIM300690
Entrez55859

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 protein_coding

ENST00000372728, ENST00000885580, ENST00000885581, ENST00000885582, ENST00000885583, ENST00000885584, ENST00000933949, ENST00000933950, ENST00000933951, ENST00000933952, ENST00000933953, ENST00000933954, ENST00000933955, ENST00000953426

RefSeq mRNA: 1 — MANE Select: NM_018476 NM_018476

CCDS: CCDS35354

Canonical transcript exons

ENST00000372728 — 3 exons

ExonStartEnd
ENSE00001105455103063642103063731
ENSE00001105457103064096103064171
ENSE00001458479103062651103063279

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 99.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 139.5323 / max 7115.6011, expressed in 1095 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
199979138.87851094
1999780.6538206

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011599.96gold quality
Brodmann (1909) area 23UBERON:001355499.90gold quality
middle temporal gyrusUBERON:000277199.89gold quality
orbitofrontal cortexUBERON:000416799.72gold quality
primary visual cortexUBERON:000243699.62gold quality
dorsolateral prefrontal cortexUBERON:000983499.57gold quality
superior frontal gyrusUBERON:000266199.56gold quality
prefrontal cortexUBERON:000045199.54gold quality
occipital lobeUBERON:000202199.54gold quality
Brodmann (1909) area 9UBERON:001354099.54gold quality
frontal cortexUBERON:000187099.53gold quality
pituitary glandUBERON:000000799.52gold quality
adenohypophysisUBERON:000219699.51gold quality
hypothalamusUBERON:000189899.48gold quality
right frontal lobeUBERON:000281099.48gold quality
CA1 field of hippocampusUBERON:000388199.48gold quality
entorhinal cortexUBERON:000272899.47gold quality
cerebral cortexUBERON:000095699.45gold quality
neocortexUBERON:000195099.45gold quality
Brodmann (1909) area 46UBERON:000648399.45gold quality
temporal lobeUBERON:000187199.41gold quality
superior vestibular nucleusUBERON:000722799.41gold quality
nucleus accumbensUBERON:000188299.40gold quality
cerebellar vermisUBERON:000472099.39gold quality
parietal lobeUBERON:000187299.38gold quality
ponsUBERON:000098899.37gold quality
postcentral gyrusUBERON:000258199.36gold quality
amygdalaUBERON:000187699.35gold quality
type B pancreatic cellCL:000016999.34gold quality
forebrainUBERON:000189099.34gold quality

Single-cell (SCXA)

Detected in 24 experiment(s), a significant marker in 17.

ExperimentMarker?Max mean expression
E-GEOD-134144yes2949.50
E-GEOD-124263yes2483.50
E-MTAB-8271yes976.11
E-MTAB-9435yes686.01
E-MTAB-10662yes539.19
E-MTAB-9906yes531.79
E-MTAB-8381yes451.43
E-HCAD-10yes385.92
E-HCAD-35yes48.19
E-HCAD-5yes42.99
E-MTAB-7316yes42.20
E-GEOD-84465yes23.34
E-GEOD-81547yes21.45
E-MTAB-5061yes10.75
E-HCAD-25yes9.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting BEX1, 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-5584-5P99.4968.222814
HSA-MIR-542-3P99.3467.581270
HSA-MIR-18A-5P99.2971.05806
HSA-MIR-18B-5P99.2971.05806
HSA-MIR-133A-5P99.2869.13941
HSA-MIR-4735-3P99.1469.85777
HSA-MIR-1213598.9970.261814
HSA-MIR-607498.8969.642187
HSA-MIR-806098.6166.931187
HSA-MIR-299-5P98.5671.141140
HSA-MIR-5581-3P98.5570.311161
HSA-MIR-6837-3P98.4266.711149
HSA-MIR-320E97.4965.96865
HSA-MIR-6872-3P97.0866.99750
HSA-MIR-60097.0766.731259
HSA-MIR-10A-3P93.5764.43451
HSA-MIR-66290.6462.72148

Literature-anchored findings (GeneRIF, showing 15)

  • This new human gene is mapped to the X chromosome and has an expression pattern of a spermatogenesis-related gene. (PMID:11989783)
  • Two novel brain expressed genes, BEX1 and BEX2 are identified; they are silenced in all glioma specimens and exhibit extensive promoter hypermethylation. (PMID:16818640)
  • expression of hBex1 in leukemic cells is a novel mechanism by which chemoresistance is achieved and suggests that hBex1 is a potential molecular target for the development of novel leukemia treatments (PMID:19028701)
  • Silencing of BEX1 and LDOC1 by promoter hypermethylation might represent a critical event in the molecular pathogenesis of oral squamous cell carcinoma (OSCC) and the male predominance of OSCC occurrence. (PMID:23362108)
  • Epigenetic inactivation of BEX1 supports its role as a candidate tumour suppressor gene in intracranial ependymoma (PMID:24333734)
  • Our results revealed an interaction between BEX1 and BCL-2 and a novel mechanism of imatinib resistance mediated by the BEX1/BCL-2 pathway. (PMID:24626299)
  • Bex family members play important roles in the formation of protein network hubs. (PMID:25612294)
  • loss of BEX1 expression in FLT3-ITD driven AML potentiates oncogenic signaling and leads to decreased overall survival (PMID:26046670)
  • BEX1 functions as an mRNA-dependent effector that augments pathology-promoting gene expression during heart failure. (PMID:29192139)
  • BEX1 was downregulated in esophageal squamous cell cancer (ESCC) tissues compared to adjacent normal tissues, and low BEX1 expression was significantly associated with larger tumor volume, advanced clinical, and poor survival in patients with ESCC. (PMID:30132532)
  • BEX1 Is Differentially Expressed in Aldosterone-Producing Adenomas and Protects Human Adrenocortical Cells From Ferroptosis. (PMID:33745298)
  • DNMT1-mediated methylation of BEX1 regulates stemness and tumorigenicity in liver cancer. (PMID:34217777)
  • BEX1 and BEX4 Induce GBM Progression through Regulation of Actin Polymerization and Activation of YAP/TAZ Signaling. (PMID:34576008)
  • BEX1 mediates sorafenib resistance in hepatocellular carcinoma by regulating AKT signaling. (PMID:37209973)
  • BEX1 supports the stemness of hepatoblastoma by facilitating Warburg effect in a PPARgamma/PDK1 dependent manner. (PMID:37715024)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusBex2ENSMUSG00000042750
mus_musculusBex1ENSMUSG00000050071
rattus_norvegicusBex2ENSRNOG00000032729
rattus_norvegicusLOC100912195ENSRNOG00000033844
rattus_norvegicusENSRNOG00000082512

Paralogs (3): BEX2 (ENSG00000133134), BEX3 (ENSG00000166681), BEX5 (ENSG00000184515)

Protein

Protein identifiers

Protein BEX1Q9HBH7 (reviewed: Q9HBH7)

Alternative names: Brain-expressed X-linked protein 1

All UniProt accessions (1): Q9HBH7

UniProt curated annotations — full annotation on UniProt →

Function. Signaling adapter molecule involved in p75NTR/NGFR signaling. Plays a role in cell cycle progression and neuronal differentiation. Inhibits neuronal differentiation in response to nerve growth factor (NGF). May act as a link between the cell cycle and neurotrophic factor signaling, possibly by functioning as an upstream modulator of receptor signaling, coordinating biological responses to external signals with internal cellular states. In absence of reductive stress, acts as a pseudosubstrate for the CRL2(FEM1B) complex: associates with FEM1B via zinc, thereby preventing association between FEM1B and its substrates.

Subunit / interactions. Interacts with neurotrophin receptor p75NTR/NGFR. Interacts with OMP.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed in central nervous system, with high level in pituitary, cerebellum and temporal lobe. Expressed in lung, skeletal muscle, peripheral blood leukocyte, stomach, lymph node, trachea and bone marrow. Highly expressed in acute myeloid leukemia.

Post-translational modifications. Phosphorylated. Phosphorylation of Ser-102 protects it from the proteasome. Ubiquitinated. Degraded by the proteasome.

Domain organisation. The histidine cluster (His cluster) and Cys-122 mediate zinc-binding.

Similarity. Belongs to the BEX family.

RefSeq proteins (1): NP_060946* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007623BEXFamily
IPR021156TF_A-like/BEXFamily

Pfam: PF04538

UniProt features (17 total): sequence variant 7, region of interest 3, sequence conflict 3, chain 1, compositionally biased region 1, binding site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HBH7-F168.100.10

Functional residue map

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

Ligand- & substrate-binding residues (1): 122

Post-translational modifications (1): 102

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 220 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, MODULE_151, LA_MEN1_TARGETS, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, BORLAK_LIVER_CANCER_EGF_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, KHETCHOUMIAN_TRIM24_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, CAIRO_HEPATOBLASTOMA_UP, AFFAR_YY1_TARGETS_UP, PID_P75_NTR_PATHWAY

GO Biological Process (5): signal transduction (GO:0007165), nervous system development (GO:0007399), cell differentiation (GO:0030154), negative regulation of protein ubiquitination (GO:0031397), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (6): transcription coactivator binding (GO:0001223), signaling receptor binding (GO:0005102), signaling adaptor activity (GO:0035591), metal ion binding (GO:0046872), molecular function inhibitor activity (GO:0140678), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), transcription regulator complex (GO:0005667), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
system development1
cellular developmental process1
protein ubiquitination1
regulation of protein ubiquitination1
negative regulation of protein modification by small protein conjugation or removal1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
transcription coregulator binding1
protein binding1
protein-macromolecule adaptor activity1
cation binding1
molecular function regulator activity1
binding1
intracellular membrane-bounded organelle1
protein-containing complex1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

848 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BEX1LMO2P25791895
BEX1LDB2O43679875
BEX1LDB1Q86U70868
BEX1NHLH2Q02577833
BEX1CALML6Q8TD86748
BEX1CALML3P27482748
BEX1CALML4Q96GE6748
BEX1CALML5Q9NZT1748
BEX1CALM1P02593667
BEX1TCEAL5Q5H9L2644
BEX1TCEAL3Q969E4641
BEX1OMPP47874583
BEX1NGFRP08138516
BEX1NGFP01138506
BEX1GPRASP1Q5JY77493

IntAct

57 interactions, top by confidence:

ABTypeScore
BEX1MDFIpsi-mi:“MI:0915”(physical association)0.720
MDFIBEX1psi-mi:“MI:0915”(physical association)0.720
TEX11BEX1psi-mi:“MI:0915”(physical association)0.560
BEX1TEX11psi-mi:“MI:0915”(physical association)0.560
CNOT2BEX1psi-mi:“MI:0915”(physical association)0.560
CTAG1ABEX1psi-mi:“MI:0915”(physical association)0.560
BEX1PICK1psi-mi:“MI:0915”(physical association)0.560
KRT34BEX1psi-mi:“MI:0915”(physical association)0.560
CYSRT1BEX1psi-mi:“MI:0915”(physical association)0.560
MAGEA2BEX1psi-mi:“MI:0915”(physical association)0.560
MEOX2BEX1psi-mi:“MI:0915”(physical association)0.560
OTPBEX1psi-mi:“MI:0915”(physical association)0.560
KLHL20BEX1psi-mi:“MI:0915”(physical association)0.560
BEX1CNOT2psi-mi:“MI:0915”(physical association)0.560
KRT31BEX1psi-mi:“MI:0915”(physical association)0.560
BEX1PTPN11psi-mi:“MI:0915”(physical association)0.370
GSK3BBEX1psi-mi:“MI:0915”(physical association)0.370
BEX1BAG4psi-mi:“MI:0915”(physical association)0.370
BCAR3BEX1psi-mi:“MI:0915”(physical association)0.370
BEX1CASP8psi-mi:“MI:0915”(physical association)0.370
CDH1BEX1psi-mi:“MI:0915”(physical association)0.370
CHEK2BEX1psi-mi:“MI:0915”(physical association)0.370
BEX1FBXW7psi-mi:“MI:0915”(physical association)0.370
FGFR2BEX1psi-mi:“MI:0915”(physical association)0.370
PAX2BEX1psi-mi:“MI:0915”(physical association)0.370
PIK3CABEX1psi-mi:“MI:0915”(physical association)0.370

BioGRID (55): BEX1 (Two-hybrid), TEX11 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid), BEX1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVZ2, A0A2B4SJZ1, A3KGA4, B0BK70, D3ZT37, O55527, O74982, P03246, P03247, P03407, P04602, P04862, P05860, P05909, P06747, P0C569, P0C783, P12479, P14253, P15829, P16286, P19032, P20885, P22385, P22745, P24103, P31278, P69479, P69480, P69738, Q0GBX8, Q2PG52, Q2TBV0, Q38036, Q4VKV7, Q6I7R5, Q6W0C5, Q82855, Q873B8, Q89868

Diamond homologs: Q00994, Q2PG52, Q2TBV0, Q3MKP9, Q3MKQ1, Q3MKQ2, Q3ZBJ6, Q3ZBJ9, Q5H9J7, Q5R590, Q6PDU5, Q9BXY8, Q9CWT2, Q9HBH7, Q9NWD9, Q9R224, Q9WTZ8, Q9WTZ9, Q3TZW7

SIGNOR signaling

1 interactions.

AEffectBMechanism
AKT“up-regulates quantity by stabilization”BEX1phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance21
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
686068GRCh37/hg19 Xq22.1(chrX:100868897-102422345)x1Pathogenic
691848GRCh37/hg19 Xq22.1-22.3(chrX:102066350-105409822)x1Pathogenic

SpliceAI

176 predictions. Top by Δscore:

VariantEffectΔscore
X:103063275:TACTC:Tacceptor_gain1.0000
X:103063277:CTC:Cacceptor_gain1.0000
X:103063278:TCC:Tacceptor_loss1.0000
X:103063280:C:CCacceptor_gain1.0000
X:103063281:T:Cacceptor_loss1.0000
X:103064090:CCTTA:Cdonor_loss1.0000
X:103064091:CTTA:Cdonor_loss1.0000
X:103064092:TTA:Tdonor_loss1.0000
X:103064093:TA:Tdonor_loss1.0000
X:103064094:A:ATdonor_loss1.0000
X:103064095:C:Adonor_loss1.0000
X:103063278:TC:Tacceptor_gain0.9900
X:103063279:CC:Cacceptor_gain0.9900
X:103063288:C:CTacceptor_gain0.9900
X:103063639:GACCT:Gdonor_loss0.9900
X:103063289:A:Tacceptor_gain0.9800
X:103063650:AT:Adonor_gain0.9800
X:103063728:AGGG:Aacceptor_gain0.9800
X:103063651:T:TAdonor_gain0.9700
X:103063729:GGG:Gacceptor_gain0.9700
X:103063727:AAGGG:Aacceptor_gain0.9600
X:103063730:GG:Gacceptor_gain0.9600
X:103063640:A:ACdonor_gain0.9500
X:103063641:C:CCdonor_gain0.9500
X:103063873:T:TAdonor_gain0.9500
X:103064094:A:ACdonor_gain0.9500
X:103064095:C:CCdonor_gain0.9500
X:103063665:T:TAdonor_gain0.9400
X:103063280:C:Tacceptor_gain0.9300
X:103063728:AGGGC:Aacceptor_loss0.9200

AlphaMissense

847 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:103062912:A:CF121L0.994
X:103062912:A:TF121L0.994
X:103062914:A:GF121L0.994
X:103062901:G:TP125H0.962
X:103062913:A:CF121C0.962
X:103062913:A:GF121S0.961
X:103062904:A:GM124T0.948
X:103062948:G:CS109R0.945
X:103062948:G:TS109R0.945
X:103062950:T:GS109R0.945
X:103062902:G:AP125S0.944
X:103062901:G:CP125R0.940
X:103062907:A:GL123P0.937
X:103063000:A:GL92P0.937
X:103062907:A:TL123H0.935
X:103062911:A:GC122R0.932
X:103062909:G:CC122W0.928
X:103062902:G:TP125T0.927
X:103062988:A:GL96P0.925
X:103062963:A:CS104R0.924
X:103062963:A:TS104R0.924
X:103062965:T:GS104R0.924
X:103062901:G:AP125L0.906
X:103062952:A:TV108D0.899
X:103062914:A:CF121V0.889
X:103062914:A:TF121I0.866
X:103062903:C:AM124I0.865
X:103062903:C:GM124I0.865
X:103062903:C:TM124I0.865
X:103062907:A:CL123R0.854

dbSNP variants (sampled 300 via entrez): RS1002587678 (X:103065226 A>G), RS1003066320 (X:103064931 A>C,G), RS1003210186 (X:103065487 C>G), RS1005166888 (X:103063762 C>A,T), RS1005835002 (X:103064815 A>C), RS1005890355 (X:103064272 C>A,T), RS1007055909 (X:103066071 G>A,C,T), RS1007109761 (X:103065914 C>T), RS1007383678 (X:103064168 G>A,C), RS1007443501 (X:103063922 G>C), RS1007658046 (X:103062193 C>A), RS1009762775 (X:103062502 T>G), RS1010403971 (X:103065272 C>T), RS1010737624 (X:103063591 G>T), RS1011400905 (X:103065432 C>A)

Disease associations

OMIM: gene MIM:300690 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
bisphenol Adecreases expression, affects cotreatment3
Benzo(a)pyreneaffects methylation, increases expression, decreases reaction3
Ethanolaffects cotreatment, decreases expression, increases abundance2
Phenylmercuric Acetatedecreases expression, affects cotreatment2
Cyclosporinedecreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
bisphenol Faffects cotreatment, decreases expression1
dicrotophosdecreases expression1
chlorophyllindecreases reaction, increases expression1
2,5,2’,5’-tetrachlorobiphenyldecreases expression1
sodium arsenitedecreases expression1
butyraldehydeincreases expression1
nickel sulfatedecreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
bisphenol Sdecreases expression, affects cotreatment1
NSC 689534decreases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Carbamazepineaffects expression1
Dexamethasonedecreases expression, affects cotreatment1
Doxorubicinincreases expression1
Folic Aciddecreases expression, affects cotreatment1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Hydrogen Peroxideaffects expression1
Indomethacinaffects cotreatment, decreases expression1
Mustard Gasincreases 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.