GeneBe

CSPG4

chondroitin sulfate proteoglycan 4, the group of Proteoglycans

Basic information

Region (hg38): 15:75674322-75712848

Links

ENSG00000173546 ∙ NCBI:1464 ∙ OMIM:601172 ∙ HGNC:2466 ∙ Uniprot:Q6UVK1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSPG4 gene.

  • not_specified (352 variants)
  • not_provided (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSPG4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001897.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
10
clinvar
2
clinvar
 12
missense
331
clinvar
28
clinvar
2
clinvar
 361
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 331 38 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CSPG4protein_codingprotein_codingENST00000308508 1038527
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00002621.001256540901257440.000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.4112441.39e+30.8940.000090314643
Missense in Polyphen289369.890.781314294
Synonymous0.6516146350.9670.00004235264
Loss of Function5.132165.90.3180.00000364646

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001100.00109
Ashkenazi Jewish0.0001010.0000992
East Asian0.0004910.000435
Finnish0.0002390.000231
European (Non-Finnish)0.0003690.000360
Middle Eastern0.0004910.000435
South Asian0.0002940.000294
Other0.0003300.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Proteoglycan playing a role in cell proliferation and migration which stimulates endothelial cells motility during microvascular morphogenesis. May also inhibit neurite outgrowth and growth cone collapse during axon regeneration. Cell surface receptor for collagen alpha 2(VI) which may confer cells ability to migrate on that substrate. Binds through its extracellular N- terminus growth factors, extracellular matrix proteases modulating their activity. May regulate MPP16-dependent degradation and invasion of type I collagen participating in melanoma cells invasion properties. May modulate the plasminogen system by enhancing plasminogen activation and inhibiting angiostatin. Functions also as a signal transducing protein by binding through its cytoplasmic C-terminus scaffolding and signaling proteins. May promote retraction fiber formation and cell polarization through Rho GTPase activation. May stimulate alpha-4, beta-1 integrin- mediated adhesion and spreading by recruiting and activating a signaling cascade through CDC42, ACK1 and BCAR1. May activate FAK and ERK1/ERK2 signaling cascades. {ECO:0000269|PubMed:10587647, ECO:0000269|PubMed:11278606, ECO:0000269|PubMed:15210734}.;
Pathway
Spinal Cord Injury;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate biosynthesis;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

pRec
0.142

Intolerance Scores

loftool
0.654
rvis_EVS
0.35
rvis_percentile_EVS
73.79

Haploinsufficiency Scores

pHI
0.143
hipred
Y
hipred_score
0.595
ghis
0.497

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.619

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cspg4
Phenotype
hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; normal phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
activation of MAPK activity;angiogenesis;transmembrane receptor protein tyrosine kinase signaling pathway;cell population proliferation;glial cell migration;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process;intracellular signal transduction;tissue remodeling;positive regulation of peptidyl-tyrosine phosphorylation
Cellular component
extracellular region;Golgi lumen;integral component of plasma membrane;focal adhesion;cell surface;apical plasma membrane;lamellipodium membrane;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome
Molecular function
protein kinase binding