CSPG5

gene
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Also known as NGC

Summary

CSPG5 (chondroitin sulfate proteoglycan 5, HGNC:2467) is a protein-coding gene on chromosome 3p21.31, encoding Chondroitin sulfate proteoglycan 5 (O95196). May function as a growth and differentiation factor involved in neuritogenesis.

The protein encoded by this gene is a proteoglycan that may function as a neural growth and differentiation factor. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10675 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 94 total
  • MANE Select transcript: NM_006574

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2467
Approved symbolCSPG5
Namechondroitin sulfate proteoglycan 5
Location3p21.31
Locus typegene with protein product
StatusApproved
AliasesNGC
Ensembl geneENSG00000114646
Ensembl biotypeprotein_coding
OMIM606775
Entrez10675

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000264723, ENST00000383738, ENST00000456150, ENST00000465441, ENST00000610462

RefSeq mRNA: 5 — MANE Select: NM_006574 NM_001206942, NM_001206943, NM_001206944, NM_001206945, NM_006574

CCDS: CCDS2757, CCDS56252, CCDS56253, CCDS74930

Canonical transcript exons

ENST00000264723 — 5 exons

ExonStartEnd
ENSE000007503654757683347577928
ENSE000012065224756915247569227
ENSE000012065244757268647572874
ENSE000038458364756223847562761
ENSE000038459344757859747578865

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 99.35.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7536 / max 106.8560, expressed in 345 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
420491.2209287
420480.276588
420500.196989
420510.059342

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011599.35gold quality
pigmented layer of retinaUBERON:000178298.11gold quality
frontal poleUBERON:000279598.10gold quality
retinaUBERON:000096698.09gold quality
Brodmann (1909) area 23UBERON:001355498.04gold quality
choroid plexus epitheliumUBERON:000391197.86gold quality
Brodmann (1909) area 10UBERON:001354197.67gold quality
CA1 field of hippocampusUBERON:000388197.50gold quality
orbitofrontal cortexUBERON:000416797.25gold quality
entorhinal cortexUBERON:000272897.21gold quality
Brodmann (1909) area 46UBERON:000648397.15gold quality
primary visual cortexUBERON:000243697.07gold quality
superior frontal gyrusUBERON:000266196.99gold quality
temporal lobeUBERON:000187196.88gold quality
amygdalaUBERON:000187696.78gold quality
postcentral gyrusUBERON:000258196.68gold quality
occipital lobeUBERON:000202196.67gold quality
parietal lobeUBERON:000187296.58gold quality
middle frontal gyrusUBERON:000270296.09gold quality
nucleus accumbensUBERON:000188296.07gold quality
prefrontal cortexUBERON:000045196.03gold quality
caudate nucleusUBERON:000187395.78gold quality
frontal cortexUBERON:000187095.70gold quality
cerebral cortexUBERON:000095695.64gold quality
dorsolateral prefrontal cortexUBERON:000983495.62gold quality
Ammon’s hornUBERON:000195495.60gold quality
telencephalonUBERON:000189395.59gold quality
neocortexUBERON:000195095.58gold quality
paraflocculusUBERON:000535195.43gold quality
cingulate cortexUBERON:000302795.41gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-84465yes23.59
E-GEOD-135922yes14.27
E-ANND-3no2.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting CSPG5, 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-3613-3P100.0076.367965
HSA-MIR-1213699.9872.815713
HSA-MIR-60799.9773.625593
HSA-MIR-568899.9673.234504
HSA-LET-7C-3P99.9573.422862
HSA-MIR-205-3P99.9269.923165
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-548E-5P99.8972.734486
HSA-LET-7A-2-3P99.8770.531921
HSA-LET-7G-3P99.8570.431929
HSA-MIR-684499.8270.692423
HSA-MIR-498-5P99.7669.641807
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-561-3P99.6470.903647
HSA-MIR-548AV-5P99.6070.842107
HSA-MIR-548K99.6070.842107
HSA-MIR-486-5P99.5170.39707
HSA-MIR-805499.4870.812084
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-520E-5P99.2768.901513
HSA-MIR-397399.2069.191990
HSA-MIR-478499.1567.411733
HSA-MIR-224-3P98.9168.421815
HSA-MIR-522-3P98.9168.561817
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-4659A-5P98.0366.42819
HSA-MIR-4659B-5P98.0366.84979
HSA-MIR-6791-3P97.4564.311123
HSA-MIR-6829-3P97.4564.311137

Literature-anchored findings (GeneRIF, showing 4)

  • NGC IV, which was first found in the present study, had the shortest cytoplasmic domain among the four variants (PMID:16299773)
  • neuroglycan C is a novel component of midkine receptors involved in process elongation (PMID:16901907)
  • results suggest that NGC may be a novel candidate gene, and neuregulin signaling pathways may play an important role in schizophrenia (PMID:19367581)
  • Chondroitin sulfate proteoglycan-5 forms perisynaptic matrix assemblies in the adult rat cortex. (PMID:32653642)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocspg5aENSDARG00000069981
danio_reriocspg5bENSDARG00000099793
mus_musculusCspg5ENSMUSG00000032482
rattus_norvegicusCspg5ENSRNOG00000020833

Protein

Protein identifiers

Chondroitin sulfate proteoglycan 5O95196 (reviewed: O95196)

Alternative names: Acidic leucine-rich EGF-like domain-containing brain protein, Neuroglycan C

All UniProt accessions (2): O95196, A0A087WUT8

UniProt curated annotations — full annotation on UniProt →

Function. May function as a growth and differentiation factor involved in neuritogenesis. May induce ERBB3 activation.

Subunit / interactions. Binds TNR and probably TNC. Interacts with ERBB3 and GOPC. Interacts with MDK; this interaction is independent of the presence of chondroitin sulfate chains and promotes elongation of oligodendroglial precursor-like cells.

Subcellular location. Cell membrane. Synaptic cell membrane. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cell surface. Secreted.

Tissue specificity. Detected in cerebrospinal fluid (at protein level). Detected in urine (at protein level). Expressed in brain (at protein level).

Post-translational modifications. N-glycosylated. O-glycosylated; contains chondroitin sulfate glycans. Part-time proteoglycan, expressed in part as a proteoglycan exhibiting chondroitin sulfate glycans and in part as a non-proteoglycan form. The relative amount of both forms depends on tissues and tissue maturation. Phosphorylated; in intracellular and extracellular parts.

Miscellaneous. Different forms of various molecular weight have been observed. Such forms are possibly due to different levels of glycosylation, phosphorylation and/or protein cleavage.

Isoforms (3)

UniProt IDNamesCanonical?
O95196-11yes
O95196-22, CSPG5-I
O95196-33, CSPG5-II

RefSeq proteins (5): NP_001193871, NP_001193872, NP_001193873, NP_001193874, NP_006565* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009505Neural_ProG_CytDomain
IPR010555CSPG5_S_attach_domDomain

Pfam: PF06566, PF06567

UniProt features (28 total): region of interest 6, modified residue 4, glycosylation site 4, disulfide bond 3, topological domain 2, splice variant 2, sequence variant 2, signal peptide 1, chain 1, compositionally biased region 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95196-F152.520.11

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 (4): 467, 475, 483, 543

Disulfide bonds (3): 374–387, 381–397, 399–412

Glycosylation sites (4): 38, 57, 117, 165

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

IDPathway
R-HSA-1971475Glycosaminoglycan-protein linkage region biosynthesis
R-HSA-2022870CS-GAG biosynthesis
R-HSA-2022923DS-GAG biosynthesis
R-HSA-2024101CS/DS degradation
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: 186 (showing top): GNF2_RTN1, BROWNE_HCMV_INFECTION_8HR_UP, GOBP_GLIAL_CELL_DEVELOPMENT, GOBP_REGULATION_OF_EXOCYTOSIS, GOCC_CELL_SURFACE, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_REGENERATION, GOBP_NEUROGENESIS, GOMF_GROWTH_FACTOR_ACTIVITY, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_RESPONSE_TO_AXON_INJURY, HASLINGER_B_CLL_WITH_11Q23_DELETION, GOBP_POSITIVE_REGULATION_OF_SUBSTRATE_ADHESION_DEPENDENT_CELL_SPREADING, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT

GO Biological Process (10): cytoskeleton organization (GO:0007010), nervous system development (GO:0007399), intracellular transport (GO:0046907), cell projection morphogenesis (GO:0048858), glial cell projection elongation (GO:0106091), positive regulation of substrate adhesion-dependent cell spreading (GO:1900026), regulation of synaptic vesicle exocytosis (GO:2000300), signal transduction (GO:0007165), cell differentiation (GO:0030154), modulation of chemical synaptic transmission (GO:0050804)

GO Molecular Function (2): growth factor activity (GO:0008083), protein binding (GO:0005515)

GO Cellular Component (16): Golgi membrane (GO:0000139), extracellular region (GO:0005576), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), Golgi lumen (GO:0005796), plasma membrane (GO:0005886), cell surface (GO:0009986), membrane (GO:0016020), Golgi-associated vesicle membrane (GO:0030660), lysosomal lumen (GO:0043202), synapse (GO:0045202), postsynaptic membrane (GO:0045211), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), endoplasmic reticulum (GO:0005783), synaptic membrane (GO:0097060)

Reactome top-level categories

Rollup of top-3 pathways:

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
synapse3
Golgi apparatus2
bounding membrane of organelle2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
organelle organization1
system development1
intracellular anatomical structure1
transport1
cellular localization1
establishment of localization in cell1
cell morphogenesis1
anatomical structure morphogenesis1
cell projection organization1
glial cell development1
cell projection morphogenesis1
positive regulation of cell-substrate adhesion1
substrate adhesion-dependent cell spreading1
regulation of substrate adhesion-dependent cell spreading1
synaptic vesicle exocytosis1
regulation of neurotransmitter secretion1
regulation of regulated secretory pathway1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cellular developmental process1
chemical synaptic transmission1
regulation of trans-synaptic signaling1
receptor ligand activity1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular organelle lumen1
membrane1
cell periphery1

Protein interactions and networks

STRING

1036 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CSPG5LACRTQ9GZZ8911
CSPG5FBLN2P98095790
CSPG5PTNP21246605
CSPG5PTPRZ1P23471594
CSPG5MDKP21741579
CSPG5PHF6Q8IWS0525
CSPG5NCANO14594519
CSPG5ERBB3P21860512
CSPG5GOPCQ9HD26512
CSPG5EGFP01133499
CSPG5RTN4RQ9BZR6461
CSPG5BCANQ96GW7449
CSPG5NID1P14543447
CSPG5MFAP3LO75121447
CSPG5PAK1IP1Q9NWT1432

IntAct

19 interactions, top by confidence:

ABTypeScore
CSPG5Gopcpsi-mi:“MI:0915”(physical association)0.580
DLK1TCAF2psi-mi:“MI:0914”(association)0.530
COLEC12CSPG5psi-mi:“MI:0914”(association)0.530
HIRACSPG5psi-mi:“MI:0914”(association)0.530
CSPG5HIRApsi-mi:“MI:0914”(association)0.530
APPCSPG5psi-mi:“MI:0407”(direct interaction)0.440
PTPN2GOLIM4psi-mi:“MI:0914”(association)0.350
CAPZBENAHpsi-mi:“MI:0914”(association)0.350
DIAPH1CSPG5psi-mi:“MI:0914”(association)0.350
SRP14EIF3Fpsi-mi:“MI:0914”(association)0.350
SCN4AC2CD4Bpsi-mi:“MI:0914”(association)0.350
NOGTCAF2psi-mi:“MI:0914”(association)0.350
CSPG5TCAF2psi-mi:“MI:0914”(association)0.350
MLXBACH1psi-mi:“MI:0914”(association)0.350
SLC7A7KLRG2psi-mi:“MI:0914”(association)0.350

BioGRID (40): CSPG5 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), CSPG5 (Reconstituted Complex), CSPG5 (Affinity Capture-Western), CSPG5 (Two-hybrid), GOPC (Two-hybrid), HS2ST1 (Affinity Capture-MS), CSPG5 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), GALNT16 (Affinity Capture-MS), LMBR1 (Affinity Capture-MS)

ESM2 similar proteins: A1KXC4, B2RQL2, B2RTN2, O35188, O55145, O60667, O95196, P06484, P07141, P16382, P24394, P25918, P78423, Q29RT9, Q3SYS8, Q58CT8, Q5BK39, Q5FVQ5, Q5M871, Q5U2P6, Q63257, Q64322, Q68CR7, Q68DV7, Q6AXU5, Q6P1B3, Q6PNM1, Q6RFH4, Q71M36, Q863Z5, Q8BHB3, Q8BHE4, Q8BHW6, Q8BSU2, Q8C708, Q8IXW0, Q8JZQ0, Q8K0B3, Q8NET5, Q8R183

Diamond homologs: O95196, P70628, Q1XI86, Q71M36, Q80XH2, Q8JIR8, Q9BZV3, Q9DF69, Q9ERQ6, Q17R60, Q8R1W8, Q9ET62, Q9GMS5, P28826, Q16820, Q61847

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance86
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1023 predictions. Top by Δscore:

VariantEffectΔscore
3:47572681:CTCA:Cdonor_gain1.0000
3:47572684:A:ACdonor_gain1.0000
3:47572685:C:CAdonor_gain1.0000
3:47572695:CGCAG:Cdonor_gain1.0000
3:47572699:G:Cdonor_gain1.0000
3:47569150:A:ACdonor_gain0.9900
3:47569151:C:CCdonor_gain0.9900
3:47569232:T:Cacceptor_gain0.9900
3:47569232:T:TCacceptor_gain0.9900
3:47572679:GACT:Gdonor_loss0.9900
3:47572680:A:ACdonor_gain0.9900
3:47572680:ACTC:Adonor_loss0.9900
3:47572681:C:CCdonor_gain0.9900
3:47572683:C:CCdonor_loss0.9900
3:47572684:ACT:Adonor_loss0.9900
3:47572685:CT:Cdonor_gain0.9900
3:47572685:CTTG:Cdonor_gain0.9900
3:47577925:CGCG:Cacceptor_gain0.9900
3:47577927:CG:Cacceptor_gain0.9900
3:47577928:GCTG:Gacceptor_loss0.9900
3:47577929:C:CCacceptor_gain0.9900
3:47577929:C:Gacceptor_loss0.9900
3:47577930:T:Cacceptor_loss0.9900
3:47577936:C:CTacceptor_gain0.9900
3:47569224:TTTG:Tacceptor_gain0.9800
3:47569228:C:CCacceptor_gain0.9800
3:47572685:CTTGG:Cdonor_gain0.9800
3:47572874:CCT:Cacceptor_loss0.9800
3:47572875:CTGCA:Cacceptor_loss0.9800
3:47577924:ACGCG:Aacceptor_gain0.9800

AlphaMissense

3499 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:47572850:C:AW406C1.000
3:47572850:C:GW406C1.000
3:47572812:A:CF419C0.999
3:47572832:G:CC412W0.999
3:47572833:C:AC412F0.999
3:47572833:C:GC412S0.999
3:47572833:C:TC412Y0.999
3:47572834:A:GC412R0.999
3:47572834:A:TC412S0.999
3:47572872:C:GC399S0.999
3:47572873:A:GC399R0.999
3:47572873:A:TC399S0.999
3:47576835:G:CC397W0.999
3:47576836:C:GC397S0.999
3:47576836:C:TC397Y0.999
3:47576837:A:GC397R0.999
3:47576837:A:TC397S0.999
3:47576865:G:CC387W0.999
3:47576866:C:GC387S0.999
3:47576867:A:GC387R0.999
3:47576867:A:TC387S0.999
3:47576883:A:CC381W0.999
3:47576884:C:GC381S0.999
3:47576884:C:TC381Y0.999
3:47576885:A:GC381R0.999
3:47576885:A:TC381S0.999
3:47576905:C:TC374Y0.999
3:47572719:A:GL450P0.998
3:47572728:A:GL447P0.998
3:47572733:C:AK445N0.998

dbSNP variants (sampled 300 via entrez): RS1000195787 (3:47564796 T>C), RS1000215023 (3:47572558 G>A,T), RS1000247418 (3:47572147 C>T), RS1000283650 (3:47578344 G>C,T), RS1000291210 (3:47563171 G>T), RS1000311574 (3:47576948 G>A,C,T), RS1000320632 (3:47576615 C>G,T), RS1000546612 (3:47571792 G>A), RS1000576965 (3:47570213 G>A), RS1000694659 (3:47578175 C>A), RS1000938529 (3:47563438 C>T), RS1000966172 (3:47570885 A>C), RS1001057040 (3:47564992 T>C), RS1001072814 (3:47578142 A>C,G), RS1001298900 (3:47576477 G>T)

Disease associations

OMIM: gene MIM:606775 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008129_92Body mass index2.000000e-08
GCST011703_57Smoking initiation3.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0005670smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
mercuric bromidedecreases expression, affects cotreatment2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tretinoindecreases expression2
Valproic Acidaffects expression, increases expression2
methylmercuric chlorideincreases expression1
bisphenol Aaffects expression1
sodium arseniteincreases expression1
ferrous chloridedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
4-phenylbutyric acidincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophenincreases expression1
Amphotericin Bdecreases expression1
Benzo(a)pyreneaffects methylation1
Coumestrolincreases expression, affects cotreatment1
Leadaffects expression1
Mercuryincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Progesteronedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Thapsigargindecreases expression1
Okadaic Acidincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_D9CKUbigene HEK293 CSPG5 KOTransformed cell lineFemale

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.