NCAN neurocan [Homo sapiens (human)] - Gene

Summary

Official Symbol: NCANprovided by HGNC
Official Full Name: neurocanprovided by HGNC
Primary source: HGNC:HGNC:2465
See related: Ensembl:ENSG00000130287 MIM:600826; AllianceGenome:HGNC:2465
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CSPG3
Summary: Neurocan is a chondroitin sulfate proteoglycan thought to be involved in the modulation of cell adhesion and migration.[supplied by OMIM, Jul 2002]
Expression: Restricted expression toward brain (RPKM 74.5) See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (19211958..19252233)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (19349378..19389681)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (19322767..19363042)

Chromosome 19 - NC_000019.10 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?

Neurocan genome-wide psychiatric risk variant affects explicit memory performance and hippocampal function in healthy humans.
Title: Neurocan genome-wide psychiatric risk variant affects explicit memory performance and hippocampal function in healthy humans.
NCAN rs2228603 is not a risk factor for the incidence of NAFLD in Chinese population. The dual and opposite role of T variant in protecting liver with a higher level of HDL was found.
Title: Role of NCAN rs2228603 polymorphism in the incidence of nonalcoholic fatty liver disease: a case-control study.
This study aims to analyze the influences of single-nucleotide polymorphism in the NCAN-CILP2 region on non-alcoholic fatty liver disease and plasma lipid levels in the Asian and Pacific ethnic groups.
Title: Replication analysis of genetic association of the NCAN-CILP2 region with plasma lipid levels and non-alcoholic fatty liver disease in Asian and Pacific ethnic groups.
NCAN genotype is associated with limbic gray matter alterations in healthy and subjects with major depression in brain areas implicated in emotion perception and regulation
Title: NCAN Cross-Disorder Risk Variant Is Associated With Limbic Gray Matter Deficits in Healthy Subjects and Major Depression.
current data demonstrate that common genetic variation in NCAN influences both neural processing and cognitive performance in healthy subjects.
Title: A genome-wide supported psychiatric risk variant in NCAN influences brain function and cognitive performance in healthy subjects.
The frequency of the NCAN rs2228603 T allele was significantly increased in patients with HCC due to ALD (15.1%) compared to alcoholic cirrhosis without HCC (9.3%), alcoholic controls (7.2%), healthy controls (7.9%), and HCV associated HCC (9.1%).
Title: A common polymorphism in the NCAN gene is associated with hepatocellular carcinoma in alcoholic liver disease.
NCAN risk variant is associated with cortical folding and thickness in bipolar disorder and schizophrenia.
Title: Common variation in NCAN, a risk factor for bipolar disorder and schizophrenia, influences local cortical folding in schizophrenia.
Conditional analysis shows that a neighbouring gene, TM6SF2, not NCAN, is responsible for the Chr 19 GWAS locus previously associated with fibrosing non-alcoholic fatty liver disease (NAFLD).
Title: TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.
NCAN rs2228603[T] is a risk factor for liver inflammation and fibrosis, suggesting that this locus is responsible for progression from steatosis to steatohepatitis.
Title: Genetic variation at NCAN locus is associated with inflammation and fibrosis in non-alcoholic fatty liver disease in morbid obesity.
no genetic association between risk allele A for NCAN locus rs1064395 and schizophrenia.
Title: Assessment of relatedness between neurocan gene as bipolar disorder susceptibility locus and schizophrenia.

Submit: New GeneRIF Correction See all GeneRIFs (18)

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

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 13 new risk loci for schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies genetic variation in neurocan as a susceptibility factor for bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study reveals two new risk loci for bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D19S603 (e-PCR)
- UniSTS:150111

SHGC-105663 (e-PCR)
- UniSTS:169385

D19S652E (e-PCR)
- UniSTS:29361

RH35856 (e-PCR)
- UniSTS:45290

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in glial cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of neuroblast proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
is_active_in perineuronal net	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: neurocan core protein

Names: chondroitin sulfate proteoglycan 3 (neurocan); neurocan proteoglycan

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.

mRNA and Protein(s)

NM_004386.3 → NP_004377.2 neurocan core protein precursor

See identical proteins and their annotated locations for NP_004377.2

Status: VALIDATED

Source sequence(s)

AB210004, AC003110, AC138430, CN282070

Consensus CDS

CCDS12397.1

UniProtKB/Swiss-Prot

O14594, Q9UPK6

UniProtKB/TrEMBL

Q4LE67

Related

ENSP00000252575.4, ENST00000252575.11

Conserved Domains (7) summary

cd05902
Location:51 → 161

Ig_Neurocan; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan

cd00033
Location:1215 → 1271

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd00054
Location:1046 → 1082

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:160 → 254

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:261 → 356

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...

pfam00008
Location:1012 → 1042

EGF; EGF-like domain

cl02432
Location:1088 → 1211

CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain