BEX5

Summary

BEX5 (brain expressed X-linked 5, HGNC:27990) is a protein-coding gene on chromosome Xq22.1, encoding Protein BEX5 (Q5H9J7).

Predicted to enable signaling receptor binding activity. Predicted to be involved in signal transduction. Predicted to be active in cytoplasm.

Source: NCBI Gene 340542 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001012978

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27990
Approved symbol	BEX5
Name	brain expressed X-linked 5
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184515
Ensembl biotype	protein_coding
OMIM	300693
Entrez	340542

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000333643, ENST00000484837, ENST00000543160, ENST00000883041, ENST00000883042, ENST00000883043, ENST00000932979, ENST00000932980, ENST00000932981, ENST00000932982, ENST00000932983, ENST00000932984, ENST00000946235

RefSeq mRNA: 2 — MANE Select: NM_001012978 NM_001012978, NM_001159560

CCDS: CCDS35350

Canonical transcript exons

ENST00000333643 — 3 exons

Exon	Start	End
ENSE00001310955	102153712	102154302
ENSE00001348416	102154744	102154810
ENSE00001348436	102155859	102155977

Expression profiles

Bgee: expression breadth ubiquitous, 227 present calls, max score 99.75.

FANTOM5 (CAGE): breadth broad, TPM avg 14.6568 / max 5956.7499, expressed in 728 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199971	14.6568	728

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	99.75	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.34	gold quality
middle temporal gyrus	UBERON:0002771	99.07	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.38	gold quality
primary visual cortex	UBERON:0002436	98.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.16	gold quality
pancreatic ductal cell	CL:0002079	98.15	gold quality
occipital lobe	UBERON:0002021	97.98	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.86	gold quality
pons	UBERON:0000988	97.75	gold quality
right frontal lobe	UBERON:0002810	97.75	gold quality
prefrontal cortex	UBERON:0000451	97.72	gold quality
hypothalamus	UBERON:0001898	97.71	gold quality
frontal cortex	UBERON:0001870	97.69	gold quality
epithelial cell of pancreas	CL:0000083	97.66	gold quality
anterior cingulate cortex	UBERON:0009835	97.53	gold quality
neocortex	UBERON:0001950	97.36	gold quality
superior frontal gyrus	UBERON:0002661	97.32	gold quality
pituitary gland	UBERON:0000007	97.27	gold quality
superior vestibular nucleus	UBERON:0007227	97.24	gold quality
cerebral cortex	UBERON:0000956	97.18	gold quality
adenohypophysis	UBERON:0002196	97.17	gold quality
amygdala	UBERON:0001876	97.04	gold quality
substantia nigra pars compacta	UBERON:0001965	96.93	gold quality
temporal lobe	UBERON:0001871	96.85	gold quality
nucleus accumbens	UBERON:0001882	96.70	gold quality
entorhinal cortex	UBERON:0002728	96.60	gold quality
parietal lobe	UBERON:0001872	96.53	gold quality
forebrain	UBERON:0001890	96.53	gold quality
Ammon’s horn	UBERON:0001954	96.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	14.60
E-ANND-3	yes	10.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting BEX5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-12135	98.99	70.26	1814
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-302F	98.44	69.02	1776
HSA-MIR-4733-3P	98.35	65.20	994

Cross-species orthologs

0 orthologs

Paralogs (3): BEX2 (ENSG00000133134), BEX1 (ENSG00000133169), BEX3 (ENSG00000166681)

Protein

Protein identifiers

Protein BEX5 — Q5H9J7 (reviewed: Q5H9J7)

Alternative names: Brain-expressed X-linked protein 5, NGFRAP1-like protein 1, Nerve growth factor receptor-associated protein 2

All UniProt accessions (1): Q5H9J7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Post-translational modifications. Ubiquitinated. Degraded by the proteasome.

Miscellaneous. The mouse orthologous protein does not seem to exist. A publication described a sequence that they named Bex5, but it probably represents a pseudogene.

Similarity. Belongs to the BEX family.

RefSeq proteins (2): NP_001012996, NP_001153032 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007623	BEX	Family
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (7 total): region of interest 2, sequence conflict 2, chain 1, compositionally biased region 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H9J7-F1	64.96	0.15

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): 108

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): VECCHI_GASTRIC_CANCER_EARLY_DN, GOMF_SIGNALING_RECEPTOR_BINDING, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP, chrXq22, MIR23A_3P_MIR23B_3P, MIR23C, GSE11864_CSF1_VS_CSF1_IFNG_IN_MAC_DN, MIR3660, MIR4526, MIR4733_3P, MANNO_MIDBRAIN_NEUROTYPES_HDA, MANNO_MIDBRAIN_NEUROTYPES_HDA1, MANNO_MIDBRAIN_NEUROTYPES_HDA2, MANNO_MIDBRAIN_NEUROTYPES_HSERT

GO Biological Process (1): signal transduction (GO:0007165)

GO Molecular Function (3): signaling receptor binding (GO:0005102), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
protein binding	1
cation binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BEX5	TCEAL3	Q969E4	682
BEX5	TCEAL5	Q5H9L2	588
BEX5	SAXO2	Q658L1	579
BEX5	TCEAL2	Q9H3H9	575
BEX5	XPO1	O14980	523
BEX5	PDZRN4	Q6ZMN7	459
BEX5	TCP11	Q8WWU5	459
BEX5	BEX1	Q9HBH7	441
BEX5	MORF4L2	Q15014	441
BEX5	TCEAL4	Q96EI5	433
BEX5	RAB40A	Q8WXH6	431
BEX5	RAB40AL	P0C0E4	410
BEX5	GLA	P06280	405
BEX5	TCEAL7	Q9BRU2	402
BEX5	RBM18	Q96H35	397

IntAct

85 interactions, top by confidence:

A	B	Type	Score
BEX5	MAGEA8	psi-mi:“MI:0915”(physical association)	0.760
MAGEA8	BEX5	psi-mi:“MI:0915”(physical association)	0.760
BEX5	EMILIN1	psi-mi:“MI:0915”(physical association)	0.670
EMILIN1	BEX5	psi-mi:“MI:0915”(physical association)	0.670
BEX5	GOLGA8F	psi-mi:“MI:0915”(physical association)	0.560
GOLGA8F	BEX5	psi-mi:“MI:0915”(physical association)	0.560
BEX5	COPS7B	psi-mi:“MI:0915”(physical association)	0.560
BEX5	GNG13	psi-mi:“MI:0915”(physical association)	0.560
BEX5	MORF4L1	psi-mi:“MI:0915”(physical association)	0.560
BFSP2	BEX5	psi-mi:“MI:0915”(physical association)	0.560
BEX5	PACRGL	psi-mi:“MI:0915”(physical association)	0.560
BEX5	FOXD4L3	psi-mi:“MI:0915”(physical association)	0.560
NDUFAB1	BEX5	psi-mi:“MI:0915”(physical association)	0.560
ING3	BEX5	psi-mi:“MI:0915”(physical association)	0.560
FARS2	BEX5	psi-mi:“MI:0915”(physical association)	0.560
MORF4L2	BEX5	psi-mi:“MI:0915”(physical association)	0.560
LSM1	BEX5	psi-mi:“MI:0915”(physical association)	0.560
BEX5	DMWD	psi-mi:“MI:0915”(physical association)	0.560
ELAVL4	BEX5	psi-mi:“MI:0915”(physical association)	0.560
BEX5	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
BEX5	FKBP1A	psi-mi:“MI:0915”(physical association)	0.560
BEX5	GSN	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (28): BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), GOLGA8F (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Affinity Capture-MS), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid), BEX5 (Two-hybrid)

ESM2 similar proteins: A0JP43, A1YEW9, A2D4U8, A2D5N1, A2D671, A2T6K9, A8T6P4, B8AE37, F6QRE9, G3V9A7, O60238, P48785, P79149, Q0IIJ3, Q0P6D6, Q15170, Q15361, Q15390, Q2KIJ9, Q3T013, Q3ULM0, Q3ZBJ9, Q4V7L5, Q5H9J7, Q5NVG8, Q5PPP3, Q5PR69, Q5RFN3, Q5W0A0, Q66HD8, Q67XL4, Q6K678, Q86X53, Q8BP27, Q8BPM6, Q8C627, Q8N4S0, Q8R5H6, Q91W45, Q921P9

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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 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 term	Partners	Fold	FDR
regulation of apoptotic process	5	16.7×	8e-04
regulation of cell cycle	5	14.9×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

497 predictions. Top by Δscore:

Variant	Effect	Δscore
X:102155594:T:TA	donor_gain	1.0000
X:102155595:C:A	donor_gain	1.0000
X:102155627:T:TA	donor_gain	1.0000
X:102154299:CTTC:C	acceptor_gain	0.9900
X:102154302:CCTA:C	acceptor_loss	0.9900
X:102154303:C:CA	acceptor_loss	0.9900
X:102154303:C:CC	acceptor_gain	0.9900
X:102154304:T:C	acceptor_loss	0.9900
X:102154300:TTC:T	acceptor_gain	0.9700
X:102154310:A:AC	acceptor_gain	0.9600
X:102154310:A:C	acceptor_gain	0.9600
X:102154301:TC:T	acceptor_gain	0.9500
X:102154302:CC:C	acceptor_gain	0.9500
X:102155591:ACCTC:A	donor_gain	0.9500
X:102155592:CCTCC:C	donor_gain	0.9500
X:102155610:G:A	donor_gain	0.9500
X:102155587:CTGTA:C	donor_loss	0.9400
X:102155588:TGTAC:T	donor_loss	0.9400
X:102155589:GTA:G	donor_loss	0.9400
X:102155590:TA:T	donor_loss	0.9400
X:102155591:A:AC	donor_loss	0.9400
X:102155592:C:CT	donor_loss	0.9400
X:102155602:GCGGA:G	donor_loss	0.9300
X:102155603:CGGAC:C	donor_loss	0.9300
X:102155604:GGACC:G	donor_loss	0.9300
X:102155605:GACC:G	donor_loss	0.9300
X:102155606:ACCT:A	donor_loss	0.9300
X:102155607:C:G	donor_loss	0.9300
X:102155593:C:A	donor_loss	0.9100
X:102155594:T:A	donor_loss	0.9100

AlphaMissense

746 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:102153945:A:C	F107L	0.997
X:102153945:A:T	F107L	0.997
X:102153947:A:G	F107L	0.997
X:102154029:C:A	R79S	0.993
X:102154029:C:G	R79S	0.993
X:102153996:A:C	S90R	0.988
X:102153996:A:T	S90R	0.988
X:102153998:T:G	S90R	0.988
X:102154030:C:A	R79M	0.988
X:102154030:C:G	R79T	0.988
X:102154053:G:C	F71L	0.987
X:102154053:G:T	F71L	0.987
X:102154055:A:G	F71L	0.987
X:102153988:A:G	I93T	0.985
X:102154023:T:A	K81N	0.985
X:102154023:T:G	K81N	0.985
X:102154024:T:A	K81I	0.984
X:102153946:A:C	F107C	0.983
X:102154033:A:G	L78P	0.983
X:102154054:A:G	F71S	0.983
X:102153946:A:G	F107S	0.981
X:102154021:A:G	I82T	0.981
X:102153937:A:G	M110T	0.980
X:102153934:G:T	P111H	0.979
X:102154017:C:A	R83S	0.979
X:102154017:C:G	R83S	0.979
X:102154021:A:C	I82S	0.978
X:102154012:A:G	L85P	0.976
X:102154042:A:G	M75T	0.975
X:102154041:C:A	M75I	0.974

dbSNP variants (sampled 300 via entrez): RS1000140685 (X:102155949 C>G,T), RS1004767818 (X:102155252 A>G), RS1009695047 (X:102153404 G>T), RS1012669917 (X:102157594 C>T), RS1014314160 (X:102155850 G>C), RS1014758635 (X:102155443 C>T), RS1015794966 (X:102156684 C>T), RS1017259723 (X:102153724 G>T), RS1020251862 (X:102155513 G>A), RS1020713162 (X:102153491 A>C,T), RS1020807555 (X:102155855 C>T), RS1024357167 (X:102157626 C>T), RS1027388429 (X:102157199 C>T), RS1029689599 (X:102156977 A>G), RS1030439621 (X:102154786 C>A,T)

Disease associations

OMIM: gene MIM:300693 | 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

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	9
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	increases expression, affects cotreatment	2
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Lead	affects expression	1
Smoke	increases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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