ACAN aggrecan [Homo sapiens (human)] - Gene

Summary

Official Symbol: ACANprovided by HGNC
Official Full Name: aggrecanprovided by HGNC
Primary source: HGNC:HGNC:319
See related: Ensembl:ENSG00000157766 MIM:155760; AllianceGenome:HGNC:319
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: AGC1; SEDK; AGCAN; CSPG1; MSK16; CSPGCP; SSOAOD
Summary: This gene is a member of the aggrecan/versican proteoglycan family. The encoded protein is an integral part of the extracellular matrix in cartilagenous tissue and it withstands compression in cartilage. Mutations in this gene may be involved in skeletal dysplasia and spinal degeneration. Multiple alternatively spliced transcript variants that encode different protein isoforms have been observed in this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in testis (RPKM 1.8), urinary bladder (RPKM 1.4) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q26.1

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (88803436..88875353)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (86558075..86629996)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (89346667..89418584)

Chromosome 15 - NC_000015.10 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?

Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
Title: Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
The relationship between the aggrecan VNTR polymorphism and its content in lumbar intervertebral discs.
Title: The relationship between the aggrecan VNTR polymorphism and its content in lumbar intervertebral discs.
[Analysis of a Chinese pedigree affected with familial short stature due to 15q25.3q26.1 deletion involving the ACAN gene].
Title: [Analysis of a Chinese pedigree affected with familial short stature due to 15q25.3q26.1 deletion involving the ACAN gene].
Downregulation of ACAN is Associated with the Growth hormone pathway and Induces short stature.
Title: Downregulation of ACAN is Associated with the Growth hormone pathway and Induces short stature.
Identification of variants in ACAN and PAPSS2 leading to spondyloepi(meta)physeal dysplasias in four Chinese families.
Title: Identification of variants in ACAN and PAPSS2 leading to spondyloepi(meta)physeal dysplasias in four Chinese families.
Novel missense ACAN gene variants linked to familial osteochondritis dissecans cluster in the C-terminal globular domain of aggrecan.
Title: Novel missense ACAN gene variants linked to familial osteochondritis dissecans cluster in the C-terminal globular domain of aggrecan.
Identification of novel ACAN mutations in two Chinese families and genotype-phenotype correlation in patients with 74 pathogenic ACAN variations.
Title: Identification of novel ACAN mutations in two Chinese families and genotype-phenotype correlation in patients with 74 pathogenic ACAN variations.
Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
Title: Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
Blood and urine biomarkers in osteoarthritis - an update on cartilage associated type II collagen and aggrecan markers.
Title: Blood and urine biomarkers in osteoarthritis - an update on cartilage associated type II collagen and aggrecan markers.
Aggrecan: a new biomarker for acute type A aortic dissection.
Title: Aggrecan: a new biomarker for acute type A aortic dissection.

Submit: New GeneRIF Correction See all GeneRIFs (124)

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

Associated conditions

Description	Tests
Short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans MedGen: C3665488 OMIM: 165800 GeneReviews: Not available	Compare labs
Spondyloepimetaphyseal dysplasia, aggrecan type MedGen: C2748544 OMIM: 612813 GeneReviews: Not available	Compare labs
Spondyloepiphyseal dysplasia, Kimberley type MedGen: C1842149 OMIM: 608361 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 20 loci that influence adult height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-Tat peptide interferes with polyamine uptake via competition for proteoglycan binding sites rather than a putative downstream transporter in human carcinoma cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S876 (e-PCR), detects polymorphism
- UniSTS:54792

SGC30467 (e-PCR)
- UniSTS:40739

D15S1004 (e-PCR)
- UniSTS:52522

RH17913 (e-PCR)
- UniSTS:38235

Agc1 (e-PCR), detects polymorphism
- UniSTS:259691

SHGC-145650 (e-PCR)
- UniSTS:174706

UniSTS:497303 (e-PCR)
- UniSTS:497303

Acan (e-PCR), detects polymorphism
- UniSTS:497303

RH119180 (e-PCR)
- UniSTS:138689

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	TAS Traceable Author Statement more info	PubMed
enables extracellular matrix structural constituent conferring compression resistance	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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 proteolysis	NAS Non-traceable Author Statement more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
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: aggrecan core protein

Names: cartilage-specific proteoglycan core protein; chondroitin sulfate proteoglycan core protein 1; large aggregating 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.

Genomic

NG_012794.1 RefSeqGene

Range

4994..76911

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135.4 → NP_001126.3 aggrecan core protein isoform 1 precursor

See identical proteins and their annotated locations for NP_001126.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks three alternate in-frame exons in the 3' CDS, compared to variant 3. It encodes isoform 1, which lacks two internal segments, and is shorter, compared to isoform 3.

Source sequence(s)

AC103982

Consensus CDS

CCDS53971.1

UniProtKB/TrEMBL

E7ENV9

Related

ENSP00000341615.7, ENST00000352105.11

Conserved Domains (7) summary

cd03588
Location:2282 → 2405

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

PRK15387
Location:1433 → 1614

PRK15387; type III secretion system effector E3 ubiquitin transferase SspH2

TIGR00864
Location:2115 → 2403

PCC; polycystin cation channel protein

smart00409
Location:36 → 150

IG; Immunoglobulin

PHA03307
Location:716 → 975

PHA03307; transcriptional regulator ICP4; Provisional

cd03517
Location:153 → 247

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: versican, neurocan, and brevican. ...

cd03520
Location:254 → 349

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 link domain is a hyaluronan ...
NM_001369268.1 → NP_001356197.1 aggrecan core protein isoform 3 precursor

Status: REVIEWED

Description

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

Source sequence(s)

AC103982

Consensus CDS

CCDS92054.1

UniProtKB/TrEMBL

H0YMF1

Related

ENSP00000453581.2, ENST00000560601.4

Conserved Domains (8) summary

cd05900
Location:43 → 154

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

cd00033
Location:2485 → 2541

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

cd03588
Location:2358 → 2481

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

PRK15387
Location:1433 → 1614

PRK15387; E3 ubiquitin-protein ligase SspH2; Provisional

PHA03307
Location:716 → 975

PHA03307; transcriptional regulator ICP4; Provisional

cd00054
Location:2316 → 2352

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:153 → 247

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: versican, neurocan, and brevican. ...

cd03520
Location:254 → 349

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 link domain is a hyaluronan ...
NM_001411096.1 → NP_001398025.1 aggrecan core protein isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AC103982

Consensus CDS

CCDS92056.1

Related

ENSP00000453499.1, ENST00000559004.5
NM_001411097.1 → NP_001398026.1 aggrecan core protein isoform 5 precursor

Status: REVIEWED

Source sequence(s)

AC103982

Consensus CDS

CCDS92055.1

UniProtKB/TrEMBL

A0A5K1VW97

Related

ENSP00000453342.3, ENST00000561243.7
NM_013227.4 → NP_037359.3 aggrecan core protein isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' CDS, compared to variant 3. It encodes isoform 2, which lacks an internal segment, and is shorter, compared to isoform 3.

Source sequence(s)

AC103982

Consensus CDS

CCDS53970.1

UniProtKB/Swiss-Prot

B9EK55, E7ENV9, E7EX88, H0YM81, P16112, Q13650, Q9UCD3, Q9UCP4, Q9UCP5, Q9UDE0

Related

ENSP00000387356.2, ENST00000439576.7

Conserved Domains (8) summary

cd05900
Location:43 → 154

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

cd00033
Location:2447 → 2503

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

cd03588
Location:2320 → 2443

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

cd00054
Location:2283 → 2313

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:153 → 247

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:254 → 349

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 ...

cl26018
Location:1433 → 1614

NEL; C-terminal novel E3 ligase, LRR-interacting

cl28033
Location:716 → 975

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region