CSPG5 chondroitin sulfate proteoglycan 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CSPG5provided by HGNC
Official Full Name: chondroitin sulfate proteoglycan 5provided by HGNC
Primary source: HGNC:HGNC:2467
See related: Ensembl:ENSG00000114646 MIM:606775; AllianceGenome:HGNC:2467
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NGC
Summary: 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. [provided by RefSeq, May 2011]
Expression: Restricted expression toward brain (RPKM 49.7) See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (47562238..47580240, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (47581316..47599318, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (47603728..47621730, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Chondroitin sulfate proteoglycan-5 forms perisynaptic matrix assemblies in the adult rat cortex.
Title: Chondroitin sulfate proteoglycan-5 forms perisynaptic matrix assemblies in the adult rat cortex.
results suggest that NGC may be a novel candidate gene, and neuregulin signaling pathways may play an important role in schizophrenia
Title: Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population.
NGC IV, which was first found in the present study, had the shortest cytoplasmic domain among the four variants
Title: Expression and identification of a new splice variant of neuroglycan C, a transmembrane chondroitin sulfate proteoglycan, in the human brain.
neuroglycan C is a novel component of midkine receptors involved in process elongation
Title: Neuroglycan C is a novel midkine receptor involved in process elongation of oligodendroglial precursor-like cells.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:485924

WI-18411 (e-PCR)
- UniSTS:54603

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables growth factor activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axon regeneration	IEA Inferred from Electronic Annotation more info
involved_in cell projection morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in glial cell projection elongation	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular transport	TAS Traceable Author Statement more info	PubMed
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of substrate adhesion-dependent cell spreading	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic vesicle exocytosis	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi lumen	TAS Traceable Author Statement more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in Golgi-associated vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: chondroitin sulfate proteoglycan 5

Names: acidic leucine-rich EGF-like domain-containing brain protein; chondroitin sulfate proteoglycan 5 (neuroglycan C)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029493.1 RefSeqGene

Range

6376..23003

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001206942.2 → NP_001193871.1 chondroitin sulfate proteoglycan 5 isoform 2

See identical proteins and their annotated locations for NP_001193871.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate in-frame segment compared to variant 3. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment compared to isoform 3.

Source sequence(s)

AC112512, AK294621, BU732090

Consensus CDS

CCDS56252.1

UniProtKB/TrEMBL

B7Z2E0

Conserved Domains (2) summary

pfam06566
Location:1 → 134

Chon_Sulph_att; Chondroitin sulphate attachment domain

pfam06567
Location:309 → 400

Neural_ProG_Cyt; Neural chondroitin sulphate proteoglycan cytoplasmic domain
NM_001206943.2 → NP_001193872.1 chondroitin sulfate proteoglycan 5 isoform 3 precursor

See identical proteins and their annotated locations for NP_001193872.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) encodes the longest isoform (3).

Source sequence(s)

AC112512, AF461089, BU732090

Consensus CDS

CCDS56253.1

UniProtKB/Swiss-Prot

O95196, Q71M39, Q71M40

Related

ENSP00000373244.2, ENST00000383738.6

Conserved Domains (2) summary

pfam06566
Location:33 → 272

Chon_Sulph_att; Chondroitin sulphate attachment domain

pfam06567
Location:447 → 565

Neural_ProG_Cyt; Neural chondroitin sulphate proteoglycan cytoplasmic domain
NM_001206944.2 → NP_001193873.1 chondroitin sulfate proteoglycan 5 isoform 4 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate coding exon compared to variant 3, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 3.

Source sequence(s)

AC112512, AF461087, BU732090

Consensus CDS

CCDS74930.1

UniProtKB/TrEMBL

A0A087WUT8

Related

ENSP00000478923.1, ENST00000610462.1

Conserved Domains (2) summary

pfam01683
Location:359 → 412

EB; EB module

pfam06566
Location:33 → 272

Chon_Sulph_att; Chondroitin sulphate attachment domain
NM_001206945.2 → NP_001193874.1 chondroitin sulfate proteoglycan 5 isoform 5

See identical proteins and their annotated locations for NP_001193874.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (5) is shorter at the N-terminus compared to isoform 3.

Source sequence(s)

AC112512, AK294621, BU732090

UniProtKB/TrEMBL

B7Z2E0

Conserved Domains (2) summary

pfam06566
Location:1 → 134

Chon_Sulph_att; Chondroitin sulphate attachment domain

pfam06567
Location:309 → 427

Neural_ProG_Cyt; Neural chondroitin sulphate proteoglycan cytoplasmic domain
NM_006574.4 → NP_006565.2 chondroitin sulfate proteoglycan 5 isoform 1 precursor

See identical proteins and their annotated locations for NP_006565.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks an alternate in-frame segment compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.

Source sequence(s)

AF461087, AW003890, BM674119, DB636494

Consensus CDS

CCDS2757.1

UniProtKB/Swiss-Prot

O95196

Related

ENSP00000264723.4, ENST00000264723.9

Conserved Domains (2) summary

pfam06566
Location:33 → 272

Chon_Sulph_att; Chondroitin sulphate attachment domain

pfam06567
Location:447 → 538

Neural_ProG_Cyt; Neural chondroitin sulphate proteoglycan cytoplasmic domain