BCAN

gene
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Also known as BEHABMGC13038CSPG7

Summary

BCAN (brevican, HGNC:23059) is a protein-coding gene on chromosome 1q23.1, encoding Brevican core protein (Q96GW7). May play a role in the terminally differentiating and the adult nervous system during postnatal development.

This gene encodes a member of the lectican family of chondroitin sulfate proteoglycans that is specifically expressed in the central nervous system. This protein is developmentally regulated and may function in the formation of the brain extracellular matrix. This protein is highly expressed in gliomas and may promote the growth and cell motility of brain tumor cells. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 63827 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 149 total — 1 likely-pathogenic
  • MANE Select transcript: NM_021948

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23059
Approved symbolBCAN
Namebrevican
Location1q23.1
Locus typegene with protein product
StatusApproved
AliasesBEHAB, MGC13038, CSPG7
Ensembl geneENSG00000132692
Ensembl biotypeprotein_coding
OMIM600347
Entrez63827

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000329117, ENST00000361588, ENST00000424639, ENST00000441358, ENST00000457777, ENST00000479949, ENST00000491823, ENST00000496038, ENST00000884916, ENST00000884917, ENST00000884918, ENST00000884919, ENST00000916621

RefSeq mRNA: 2 — MANE Select: NM_021948 NM_021948, NM_198427

CCDS: CCDS1149, CCDS1150

Canonical transcript exons

ENST00000329117 — 14 exons

ExonStartEnd
ENSE00001802024156642117156642275
ENSE00002327966156659027156659528
ENSE00002360284156656938156657096
ENSE00002407509156656282156656389
ENSE00002429428156657675156657757
ENSE00002692373156652248156652892
ENSE00003507644156651456156651689
ENSE00003514828156648568156648861
ENSE00003520044156647983156648110
ENSE00003541316156658127156658271
ENSE00003591119156658543156658733
ENSE00003706936156646047156646145
ENSE00003711006156646801156647175
ENSE00003787078156647508156647682

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 98.91.

FANTOM5 (CAGE): breadth broad, TPM avg 12.0368 / max 1217.2312, expressed in 283 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
57537.1272243
57542.4326165
57551.4867145
57520.9779112
57560.01242

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305398.91gold quality
amygdalaUBERON:000187697.84gold quality
anterior cingulate cortexUBERON:000983597.17gold quality
cingulate cortexUBERON:000302797.14gold quality
right frontal lobeUBERON:000281096.85gold quality
nucleus accumbensUBERON:000188296.84gold quality
caudate nucleusUBERON:000187396.77gold quality
putamenUBERON:000187496.25gold quality
ganglionic eminenceUBERON:000402396.05gold quality
prefrontal cortexUBERON:000045195.27gold quality
Brodmann (1909) area 9UBERON:001354095.24gold quality
hypothalamusUBERON:000189895.09gold quality
C1 segment of cervical spinal cordUBERON:000646994.48gold quality
dorsolateral prefrontal cortexUBERON:000983494.10gold quality
right hemisphere of cerebellumUBERON:001489093.86gold quality
neocortexUBERON:000195093.40gold quality
telencephalonUBERON:000189393.30gold quality
spinal cordUBERON:000224093.28gold quality
frontal cortexUBERON:000187093.24gold quality
Ammon’s hornUBERON:000195493.17gold quality
cerebellar hemisphereUBERON:000224592.92gold quality
cerebellar cortexUBERON:000212992.90gold quality
substantia nigraUBERON:000203892.77gold quality
cerebral cortexUBERON:000095692.51gold quality
temporal lobeUBERON:000187192.35gold quality
cerebellumUBERON:000203791.66gold quality
midbrainUBERON:000189191.55gold quality
forebrainUBERON:000189090.81gold quality
brainUBERON:000095590.75gold quality
corpus callosumUBERON:000233689.03gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-GEOD-93593yes2147.28
E-MTAB-9435yes1896.92
E-MTAB-8894yes1388.71
E-HCAD-56yes701.46
E-GEOD-84465yes27.72
E-HCAD-25yes26.40
E-MTAB-8142yes20.03
E-ENAD-20no1041.59
E-ANND-3no1.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting BCAN, 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-4455100.0065.481587
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-449299.8768.253611
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-449899.4767.422360
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-312599.1468.492269
HSA-MIR-66199.0965.942062
HSA-MIR-1295B-5P99.0367.50810
HSA-MIR-391698.9968.042155
HSA-MIR-6859-5P98.9968.072049
HSA-MIR-939-3P98.9765.072347
HSA-MIR-548Q98.7165.35563
HSA-MIR-4436B-3P98.2565.261494
HSA-MIR-6735-5P98.2465.361488
HSA-MIR-7843-5P98.1265.261421
HSA-MIR-4632-5P97.8265.381470
HSA-MIR-6879-5P97.7765.521521
HSA-MIR-7106-3P97.3365.33644
HSA-MIR-129196.2865.891224
HSA-MIR-6834-5P96.2564.88823

Literature-anchored findings (GeneRIF, showing 9)

  • gene locus at chromosome 1q21-23. (PMID:11873941)
  • Authors describe the expression of BEHAB/brevican in human brain and characterize two novel glioma-specific isoforms which are generated by differential glycosylation and are absent from normal adult brain and other neuropathologies. (PMID:16061654)
  • These results demonstrate for the first time that ADAMTS-5 is capable of degrading brevican and is overexpressed in glioblastoma cells, and suggest that ADAMTS-5 may play a role in glioma cell invasion through the cleavage of brevican. (PMID:16133547)
  • The proteoglycan brevican binds to fibronectin after proteolytic cleavage and promotes glioma cell motility (PMID:18611854)
  • High Brevican is associated with the invasive phenotype of low-grade astrocytoma. (PMID:21997179)
  • Data indicate that median methylation levels of BCAN, HOXD1, KCTD8, KLF11, NXPH1, POU4F1, SIM1, and TCF7L1 were >/=30% higher than in normal samples, representing potential biomarkers for tumor diagnosis. (PMID:22930747)
  • The CNS-specific proteoglycan, brevican, and its ADAMTS4-cleaved fragment show differential serological levels in Alzheimer’s disease, other types of dementia and non-demented controls: A cross-sectional study. (PMID:32559242)
  • The Role of BEHAB/Brevican in the Tumor Microenvironment: Mediating Glioma Cell Invasion and Motility. (PMID:32845505)
  • Serum Brevican as a Biomarker of Cerebrovascular Disease in an Elderly Cognitively Impaired Cohort. (PMID:38254675)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobcanENSDARG00000099412
mus_musculusBcanENSMUSG00000004892
rattus_norvegicusBcanENSRNOG00000018798

Paralogs (7): VCAN (ENSG00000038427), NCAN (ENSG00000130287), HAPLN2 (ENSG00000132702), HAPLN3 (ENSG00000140511), HAPLN1 (ENSG00000145681), ACAN (ENSG00000157766), HAPLN4 (ENSG00000187664)

Protein

Protein identifiers

Brevican core proteinQ96GW7 (reviewed: Q96GW7)

Alternative names: Brain-enriched hyaluronan-binding protein, Chondroitin sulfate proteoglycan 7

All UniProt accessions (6): Q96GW7, Q5T3I6, Q5T3I7, Q5T3I8, V9GXZ8, V9GY88

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the terminally differentiating and the adult nervous system during postnatal development. Could stabilize interactions between hyaluronan (HA) and brain proteoglycans.

Subunit / interactions. Interacts with TNR.

Subcellular location. Secreted Secreted. Extracellular space. Extracellular matrix Membrane.

Tissue specificity. Expressed in the retina, specifically in the inner nuclear layer, inner plexiform layer and ganglion cell layer (at protein level). Detected in cerebrospinal fluid (at protein level). Detected in urine (at protein level).

Post-translational modifications. O-glycosylated; contains chondroitin sulfate. O-glycosylated with a core 1 or possibly core 8 glycan.

Similarity. Belongs to the aggrecan/versican proteoglycan family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96GW7-11yes
Q96GW7-22

RefSeq proteins (2): NP_068767, NP_940819 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000436Sushi_SCR_CCP_domDomain
IPR000538Link_domDomain
IPR000742EGFDomain
IPR001304C-type_lectin-likeDomain
IPR003006Ig/MHC_CSConserved_site
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR018378C-type_lectin_CSConserved_site
IPR035976Sushi/SCR/CCP_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050691Hyaluronan_bind_ProteoglycanFamily

Pfam: PF00008, PF00059, PF00084, PF00193, PF07686

UniProt features (39 total): disulfide bond 13, domain 6, glycosylation site 5, region of interest 4, compositionally biased region 2, splice variant 2, sequence variant 2, signal peptide 1, chain 1, modified residue 1, sequence conflict 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96GW7-F170.060.42

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 (2): 418, 646

Disulfide bonds (13): 57–137, 179–250, 203–224, 277–352, 301–322, 650–661, 655–670, 672–681, 688–699, 716–808, 784–800, 815–858, 844–871

Glycosylation sites (5): 130, 337, 418, 905, 906

Function

Pathways and Gene Ontology

Reactome pathways

12 pathways

IDPathway
R-HSA-1474228Degradation of the extracellular matrix
R-HSA-1971475Glycosaminoglycan-protein linkage region biosynthesis
R-HSA-2022870CS-GAG biosynthesis
R-HSA-2022923DS-GAG biosynthesis
R-HSA-2024101CS/DS degradation
R-HSA-3000178ECM proteoglycans
R-HSA-3560783Defective B4GALT7 causes EDS, progeroid type
R-HSA-3560801Defective B3GAT3 causes JDSSDHD
R-HSA-3595172Defective CHST3 causes SEDCJD
R-HSA-3595174Defective CHST14 causes EDS, musculocontractural type
R-HSA-3595177Defective CHSY1 causes TPBS
R-HSA-4420332Defective B3GALT6 causes EDSP2 and SEMDJL1

MSigDB gene sets: 126 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_FOREBRAIN_DEVELOPMENT, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_HIPPOCAMPUS_DEVELOPMENT, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_PALLIUM_DEVELOPMENT, GOBP_HEAD_DEVELOPMENT, GOMF_GLYCOSAMINOGLYCAN_BINDING, GOBP_TELENCEPHALON_DEVELOPMENT, EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION, GOBP_LIMBIC_SYSTEM_DEVELOPMENT

GO Biological Process (5): skeletal system development (GO:0001501), cell adhesion (GO:0007155), central nervous system development (GO:0007417), hippocampus development (GO:0021766), synapse maturation (GO:0060074)

GO Molecular Function (3): hyaluronic acid binding (GO:0005540), carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (10): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), Golgi lumen (GO:0005796), lysosomal lumen (GO:0043202), synapse (GO:0045202), perineuronal net (GO:0072534), side of membrane (GO:0098552), glutamatergic synapse (GO:0098978), membrane (GO:0016020), extracellular matrix (GO:0031012)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Diseases associated with glycosaminoglycan metabolism6
Chondroitin sulfate/dermatan sulfate metabolism3
Extracellular matrix organization2
Glycosaminoglycan metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
system development2
nervous system development2
binding2
cellular process1
pallium development1
limbic system development1
anatomical structure development1
developmental maturation1
synapse organization1
carboxylic acid binding1
Golgi apparatus1
intracellular organelle lumen1
lysosome1
vacuolar lumen1
cell junction1
perisynaptic extracellular matrix1
membrane1
leaflet of membrane bilayer1
synapse1
external encapsulating structure1

Protein interactions and networks

STRING

1886 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BCANPTPRZ1P23471988
BCANACANP16112983
BCANVCANP13611909
BCANNCANO14594908
BCANNRCAMQ92823679
BCANADAMTS5Q9UNA0669
BCANFN1P02751669
BCANADAMTS4O75173667
BCANSPTBN4Q9H254655
BCANLUMP51884650
BCANFMODQ06828650
BCANPVALBP20472629
BCANHAPLN4Q86UW8617
BCANCD44P16070617
BCANADAMTS8Q9UP79614
BCANNFASCO94856614

IntAct

21 interactions, top by confidence:

ABTypeScore
APLP2BCANpsi-mi:“MI:0915”(physical association)0.560
CSNK1DBCANpsi-mi:“MI:0915”(physical association)0.560
BCANLYNpsi-mi:“MI:0915”(physical association)0.560
APPBCANpsi-mi:“MI:0915”(physical association)0.560
APPBCANpsi-mi:“MI:0407”(direct interaction)0.440
BCANpsi-mi:“MI:0915”(physical association)0.370
PRNPCARNS1psi-mi:“MI:0914”(association)0.350
PRNPWDR91psi-mi:“MI:0914”(association)0.350
BCANVCANpsi-mi:“MI:0914”(association)0.350
BCANHSPA5psi-mi:“MI:0914”(association)0.350
BCANLAMA5psi-mi:“MI:0914”(association)0.350
BCANPCBD1psi-mi:“MI:0915”(physical association)0.000

BioGRID (37): FBXO11 (Affinity Capture-MS), VCAN (Affinity Capture-MS), ULK3 (Affinity Capture-MS), REPIN1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), VCAN (Affinity Capture-MS), ULK3 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), FBLN2 (Reconstituted Complex), BCAN (Affinity Capture-MS), BCAN (Biochemical Activity), BCAN (Biochemical Activity), BCAN (Biochemical Activity), BCAN (Biochemical Activity), BCAN (Biochemical Activity)

ESM2 similar proteins: A1L0T3, A1L4H1, A6QNY1, D3YZF7, O95428, P28698, P30203, P55068, P55106, P59222, P98162, Q04756, Q14767, Q28019, Q28062, Q28256, Q28343, Q28670, Q3U515, Q4G0T1, Q5F378, Q5HZW5, Q61003, Q61361, Q6H9L7, Q6KF10, Q6PGE4, Q6QNF4, Q7TQH7, Q7Z4F1, Q86T13, Q86VR7, Q86VZ4, Q8BV57, Q8BZE1, Q8CB67, Q8VCP9, Q8WTU2, Q91V98, Q96DN2

Diamond homologs: A0ZT93, B0VXV2, B4XT08, B5U6Y6, B5U6Y7, C0HKZ7, O60449, P05140, P06027, P06734, P0DJL5, P10716, P13611, P14371, P20693, P34472, P55066, P55067, P81018, P81282, P81996, Q01758, Q02988, Q26627, Q28062, Q28670, Q28858, Q4PRD0, Q4TU93, Q4V885, Q61830, Q62059, Q64449, Q66S03, Q6X5S2, Q6X5S3, Q6X5S5, Q6X5S6, Q6X5S7, Q6X5S8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance132
Likely benign8
Benign3

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
149564GRCh38/hg38 1q22-23.1(chr1:156256495-156681863)x1Likely pathogenic

SpliceAI

2374 predictions. Top by Δscore:

VariantEffectΔscore
1:156646032:A:AGacceptor_gain1.0000
1:156646032:AT:Aacceptor_gain1.0000
1:156646033:T:Gacceptor_gain1.0000
1:156646033:T:TAacceptor_gain1.0000
1:156646041:T:TAacceptor_gain1.0000
1:156646045:A:AGacceptor_gain1.0000
1:156646046:G:GAacceptor_gain1.0000
1:156646046:GC:Gacceptor_gain1.0000
1:156646046:GCC:Gacceptor_gain1.0000
1:156646046:GCCT:Gacceptor_gain1.0000
1:156646142:TCAGG:Tdonor_loss1.0000
1:156646145:GGT:Gdonor_loss1.0000
1:156646146:G:GAdonor_loss1.0000
1:156646146:G:GGdonor_gain1.0000
1:156647171:CAAAG:Cdonor_loss1.0000
1:156647172:AAAGG:Adonor_loss1.0000
1:156647173:AAGGT:Adonor_loss1.0000
1:156647506:AGG:Aacceptor_gain1.0000
1:156647507:GGG:Gacceptor_gain1.0000
1:156647979:CTA:Cacceptor_loss1.0000
1:156647981:A:ACacceptor_loss1.0000
1:156647981:A:AGacceptor_gain1.0000
1:156647981:AG:Aacceptor_gain1.0000
1:156647982:G:Aacceptor_loss1.0000
1:156647982:G:GGacceptor_gain1.0000
1:156647982:GG:Gacceptor_gain1.0000
1:156647982:GGT:Gacceptor_gain1.0000
1:156647982:GGTA:Gacceptor_gain1.0000
1:156647982:GGTAT:Gacceptor_gain1.0000
1:156648080:GATGT:Gdonor_gain1.0000

AlphaMissense

5818 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:156647660:T:AW207R1.000
1:156647660:T:CW207R1.000
1:156647662:G:CW207C1.000
1:156647662:G:TW207C1.000
1:156648713:G:CW305C1.000
1:156648713:G:TW305C1.000
1:156658141:G:CW769C1.000
1:156658141:G:TW769C1.000
1:156646944:T:AW79R0.999
1:156646944:T:CW79R0.999
1:156646946:G:CW79C0.999
1:156646946:G:TW79C0.999
1:156647112:T:GY135D0.999
1:156647118:T:AC137S0.999
1:156647118:T:CC137R0.999
1:156647119:G:CC137S0.999
1:156647577:G:AC179Y0.999
1:156647648:T:AC203S0.999
1:156647649:G:AC203Y0.999
1:156647649:G:CC203S0.999
1:156648011:T:AC224S0.999
1:156648011:T:CC224R0.999
1:156648012:G:AC224Y0.999
1:156648012:G:CC224S0.999
1:156648013:T:GC224W0.999
1:156648090:G:AC250Y0.999
1:156648091:T:GC250W0.999
1:156648680:G:CW294C0.999
1:156648680:G:TW294C0.999
1:156648711:T:AW305R0.999

dbSNP variants (sampled 300 via entrez): RS1000147163 (1:156655957 T>C), RS1000166226 (1:156656727 G>C,T), RS1000277130 (1:156650834 T>A), RS1000329119 (1:156658322 G>C), RS1000429503 (1:156644536 T>A), RS1000595108 (1:156652196 G>A,T), RS1000734600 (1:156645818 G>A,T), RS1001108579 (1:156655049 G>T), RS1001365352 (1:156642626 CG>C), RS1001944369 (1:156659668 T>A,C), RS1001998526 (1:156659990 C>T), RS1002159081 (1:156653990 G>A,C,T), RS1002419375 (1:156641532 C>T), RS1002776771 (1:156641246 A>G), RS1003231751 (1:156648175 C>T)

Disease associations

OMIM: gene MIM:600347 | 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
GCST006585_46Blood protein levels6.000000e-12

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression2
Benzo(a)pyreneincreases expression, affects methylation, decreases methylation2
Valproic Acidincreases expression2
FR900359decreases phosphorylation1
aminomethylphosphonic acid (AMPA)decreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
titanium dioxideincreases expression1
arseniteincreases methylation1
perfluorooctane sulfonic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
NSC 689534affects binding, increases expression1
Resveratrolaffects cotreatment, decreases expression1
Decitabineaffects expression1
Sunitinibincreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Cisplatinaffects expression1
Copperaffects binding, increases expression1
Estradiolincreases expression1
Leadaffects expression1
Phenylmercuric Acetateaffects cotreatment, increases expression1
Plant Extractsdecreases expression, affects cotreatment1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1
Asbestos, Crocidoliteincreases expression1
Okadaic Aciddecreases expression1
Acrylamidedecreases 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.