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COL9A1 collagen type IX alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1297, updated on 5-Mar-2024

Summary

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Official Symbol
COL9A1provided by HGNC
Official Full Name
collagen type IX alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2217
See related
Ensembl:ENSG00000112280 MIM:120210; AllianceGenome:HGNC:2217
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; EDM6; STL4; DJ149L1.1.2
Summary
This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in prostate (RPKM 6.1), testis (RPKM 1.3) and 6 other tissues See more
Orthologs
mouse all
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Genomic context

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See COL9A1 in Genome Data Viewer
Location:
6q13
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (70215061..70303084, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71395620..71483638, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70924764..71012787, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LMBR1 domain containing 1 Neighboring gene uncharacterized LOC124901337 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70623798-70624319 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730 Neighboring gene uncharacterized LOC105377848 Neighboring gene Sharpr-MPRA regulatory region 4194 Neighboring gene uncharacterized LOC105377847 Neighboring gene long intergenic non-protein coding RNA 1610

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus. Zhao J, et al. Genet Test Mol Biomarkers, 2021 Jan. PMID 33372835
  2. Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss. Hofrichter MAH, et al. Eur J Med Genet, 2019 Oct. PMID 31315069
  3. Role of COL9A1 genetic polymorphisms in development of congenital talipes equinovarus in a Chinese population. Zhao XL, et al. Genet Mol Res, 2016 Nov 3. PMID 27819742
  4. COL9A1 gene polymorphism is associated with Kashin-Beck disease in a northwest Chinese Han population. Shi X, et al. PLoS One, 2015. PMID 25774918, Free PMC Article
  5. Association of reduced type IX collagen gene expression in human osteoarthritic chondrocytes with epigenetic silencing by DNA hypermethylation. Imagawa K, et al. Arthritis Rheumatol, 2014 Nov. PMID 25048791, Free PMC Article

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
    Title: Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
  2. Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
    Title: Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
  3. 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.
  4. The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL.
    Title: Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss.
  5. Two tagSNPs, rs28647489 in FAT1 gene and rs550675 in COL9A1 gene, were significantly associated with the risk of oral malignancy.
    Title: Variants in FAT1 and COL9A1 genes in male population with or without substance use to assess the risk factors for oral malignancy.
  6. Whole-genome sequencing reveals possible role of deleterious mutation of COL9A1 in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
    Title: Whole-genome sequencing reveals novel genes in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
  7. the COL9A1 rs35470562 variant may contribute to congenital talipes equinovarus susceptibility in the Chinese population examined.
    Title: Role of COL9A1 genetic polymorphisms in development of congenital talipes equinovarus in a Chinese population.
  8. We observed a significant association between rs6910140 of COL9A1 and KBD, suggesting a role of COL9A1 in the development of KBD.
    Title: COL9A1 gene polymorphism is associated with Kashin-Beck disease in a northwest Chinese Han population.
  9. The study demonstrated that hypermethylation is associated with down-regulation of COL9A1 expression in osteoarthritic (OA) cartilage and highlights the pivotal role of epigenetics in OA.
    Title: Association of reduced type IX collagen gene expression in human osteoarthritic chondrocytes with epigenetic silencing by DNA hypermethylation.
  10. 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

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2013-11-06)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2013-11-06)

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ40263

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding EXP
Inferred from Experiment
more info
 PubMed 
enables carbohydrate binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables carbohydrate binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
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 animal organ morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of collagen type IX trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of collagen type IX trimer IDA
Inferred from Direct Assay
more info
 PubMed 
part_of collagen type IX trimer TAS
Traceable Author Statement
more info
 PubMed 
located_in collagen-containing extracellular matrix HDA 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-1(IX) chain
Names
alpha-1(IX) collagen chain
cartilage-specific short collagen
collagen IX, alpha-1 polypeptide
collagen, type IX, alpha 1

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

  1. NG_011654.1 RefSeqGene

    Range
    5000..91958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001377289.1 → NP_001364218.1  collagen alpha-1(IX) chain isoform 3 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080275, AL160262
    Consensus CDS
    CCDS93940.1
    UniProtKB/TrEMBL
    A0A804HIB6
    Related
    ENSP00000506990.1, ENST00000683980.2
    Conserved Domains (1) summary
    pfam01391
    Location:253 → 309
    Collagen; Collagen triple helix repeat (20 copies)

  2. NM_001377290.1 → NP_001364219.1  collagen alpha-1(IX) chain isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080275, AL160262
    Related
    ENSP00000508147.1, ENST00000683758.1
    Conserved Domains (1) summary
    pfam01391
    Location:244 → 298
    Collagen; Collagen triple helix repeat (20 copies)

  3. NM_001377291.1 → NP_001364220.1  collagen alpha-1(IX) chain isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080275
    Consensus CDS
    CCDS93941.1
    Related
    ENSP00000359527.3, ENST00000370496.3
    Conserved Domains (1) summary
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains

  4. NM_001851.6 → NP_001842.3  collagen alpha-1(IX) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_001842.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1, also known as the long form).
    Source sequence(s)
    AL080275, AL160262
    Consensus CDS
    CCDS4971.1
    UniProtKB/Swiss-Prot
    P20849, Q13699, Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
    Related
    ENSP00000349790.6, ENST00000357250.11
    Conserved Domains (2) summary
    pfam01391
    Location:493 → 552
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains

  5. NM_078485.4 → NP_511040.2  collagen alpha-1(IX) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_511040.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks several exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a unique AUG and an isoform (2, also known as the short form) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AL160262, AW021120, BC063646, BF196880, CA392556, X54412
    Consensus CDS
    CCDS47447.1
    UniProtKB/Swiss-Prot
    P20849
    Related
    ENSP00000315252.7, ENST00000320755.12
    Conserved Domains (1) summary
    pfam01391
    Location:250 → 309
    Collagen; Collagen triple helix repeat (20 copies)

RNA

  1. NR_165185.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL080275, AL160262

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

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    70215061..70303084 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535429.4 → XP_011533731.1  collagen alpha-1(IX) chain isoform X1

    Conserved Domains (2) summary
    pfam01391
    Location:493 → 552
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains

  2. XM_017010246.3 → XP_016865735.1  collagen alpha-1(IX) chain isoform X2

  3. XM_047418180.1 → XP_047274136.1  collagen alpha-1(IX) chain isoform X4

  4. XM_047418179.1 → XP_047274135.1  collagen alpha-1(IX) chain isoform X3

  5. XM_017010247.3 → XP_016865736.1  collagen alpha-1(IX) chain isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    71395620..71483638 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354214.1 → XP_054210189.1  collagen alpha-1(IX) chain isoform X1

  2. XM_054354215.1 → XP_054210190.1  collagen alpha-1(IX) chain isoform X2

  3. XM_054354217.1 → XP_054210192.1  collagen alpha-1(IX) chain isoform X4

  4. XM_054354216.1 → XP_054210191.1  collagen alpha-1(IX) chain isoform X3

  5. XM_054354218.1 → XP_054210193.1  collagen alpha-1(IX) chain isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P20849.3 GenPept UniProtKB/Swiss-Prot:P20849

Gene LinkOut

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