COL9A2 collagen type IX alpha 2 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL9A2provided by HGNC
Official Full Name: collagen type IX alpha 2 chainprovided by HGNC
Primary source: HGNC:HGNC:2218
See related: Ensembl:ENSG00000049089 MIM:120260; AllianceGenome:HGNC:2218
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: MED; EDM2; STL5; DJ39G22.4
Summary: This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
Expression: Broad expression in prostate (RPKM 5.8), brain (RPKM 5.5) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (40300489..40317286, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (40169995..40187371, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (40766161..40782958, complement)

Chromosome 1 - NC_000001.11 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?

Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene.
Title: Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene.
Lack of association between COL1A1 and COL9A2 single nucleotide polymorphisms and intervertebral disc degeneration.
Title: Lack of association between COL1A1 and COL9A2 single nucleotide polymorphisms and intervertebral disc degeneration.
Homozygous type IX collagen variants, COL9A1, COL9A2, and COL9A3, causing recessive Stickler syndrome, expand the disease phenotype.
Title: Homozygous Type IX collagen variants (COL9A1, COL9A2, and COL9A3) causing recessive Stickler syndrome-Expanding the phenotype.
No significant association was found between COL9A2 polymorphism rs7533552 and the risk of lumbar disc degeneration.
Title: Association of CILP, COL9A2 and MMP3 Gene Polymorphisms with Lumbar Disc Degeneration in an Indian Population.
rs12077871, rs12722877, and rs7533552 variants in COL9A2 were not significantly associated with a predisposition to lumbar disc degeneration.
Title: Collagen IX gene polymorphisms and lumbar disc degeneration: a systematic review and meta-analysis.
Study provides evidence that the COL9A2 Gln326Arg polymorphism contributes to the development of intervertebral disc disease in the Chinese population.
Title: Association between COL9A2 Gln326Arg mutations and the development of intervertebral disc disease in a Chinese population.
Meta-analysis. Our results suggest that the COL9A2 rs12077871, rs12722877, and rs7533552 polymorphisms may not be associated with lumbar disc disease.
Title: Meta-analysis of the association between COL9A2 genetic polymorphisms and lumbar disc disease susceptibility.
Two novel mutations, c.143G>C in exon 2 and c.884G>A in exon 17 of the COL9A2 gene, may contribute to the development of pathological myopia.
Title: [Analysis of COL9A2 gene mutations in a Chinese Han population with pathological myopia].
The allelic variants in the collagen IX genes - COL9A2 and COL9A3 have been identified as genetic risk factors for intervertebral disc disease--{review}
Title: The role of polymorphisms of genes encoding collagen IX and XI in lumbar disc disease.
The NC2 domain of type IX collagen determines the chain composition but also the chain register of the triple helix.
Title: The NC2 domain of type IX collagen determines the chain register of the triple helix.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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
Epiphyseal dysplasia, multiple, 2 MedGen: C1838429 OMIM: 600204 GeneReviews: Multiple Epiphyseal Dysplasia, Dominant	Compare labs
Stickler syndrome, type 5 MedGen: C3280342 OMIM: 614284 GeneReviews: Stickler Syndrome	Compare labs

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2013-10-09) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2013-10-09) ClinGen Genome Curation Page

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

A009S44 (e-PCR)
- UniSTS:57090

RH69207 (e-PCR)
- UniSTS:44360

RH103036 (e-PCR)
- UniSTS:97370

SHGC-30746 (e-PCR)
- UniSTS:10337

G32827 (e-PCR)
- UniSTS:117406

SHGC-35672 (e-PCR)
- UniSTS:14560

GDB:593218 (e-PCR)
- UniSTS:157942

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	IC Inferred by Curator more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of collagen type IX trimer	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum 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

General protein information

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Preferred Names: collagen alpha-2(IX) chain

Names: alpha 2 type IX collagen; collagen IX, alpha-2 polypeptide; collagen, type IX, alpha 2

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_008031.1 RefSeqGene

Range

4982..21779

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001852.4 → NP_001843.1 collagen alpha-2(IX) chain precursor

See identical proteins and their annotated locations for NP_001843.1

Status: REVIEWED

Source sequence(s)

BC136326, CB305733, CD722372

Consensus CDS

CCDS450.1

UniProtKB/Swiss-Prot

B2RMP9, Q14055

Related

ENSP00000361834.3, ENST00000372748.8

Conserved Domains (1) summary

pfam01391
Location:259 → 316

Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

40300489..40317286 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017000332.2 → XP_016855821.1 collagen alpha-2(IX) chain isoform X1

Conserved Domains (1) summary

pfam01391
Location:263 → 320

Collagen; Collagen triple helix repeat (20 copies)
XM_011540715.3 → XP_011539017.1 collagen alpha-2(IX) chain isoform X2

See identical proteins and their annotated locations for XP_011539017.1

Conserved Domains (1) summary

pfam01391
Location:169 → 226

Collagen; Collagen triple helix repeat (20 copies)
XM_017000333.2 → XP_016855822.1 collagen alpha-2(IX) chain isoform X3

Conserved Domains (1) summary

pfam01391
Location:165 → 222

Collagen; Collagen triple helix repeat (20 copies)
XM_011540716.3 → XP_011539018.1 collagen alpha-2(IX) chain isoform X2

See identical proteins and their annotated locations for XP_011539018.1

Conserved Domains (1) summary

pfam01391
Location:169 → 226

Collagen; Collagen triple helix repeat (20 copies)
XM_047446392.1 → XP_047302348.1 collagen alpha-2(IX) chain isoform X4