COL9A1

Protein identityUniProt · HPA

UniProt accession

P20849

Gene

COL9A1

Ensembl

ENSG00000112280

Chromosome

6

Canonical length

921 aa

Protein class

Disease related genes, Human disease related genes, Predicted secreted proteins

Secretome location

Secreted to extracellular matrix

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

921 residues, UniProt reviewed canonical sequence.

>P20849|COL9A1
     1  MKTCWKIPVF FFVCSFLEPW ASAAVKRRPR FPVNSNSNGG NELCPKIRIG QDDLPGFDLI
    61  SQFQVDKAAS RRAIQRVVGS ATLQVAYKLG NNVDFRIPTR NLYPSGLPEE YSFLTTFRMT
   121  GSTLKKNWNI WQIQDSSGKE QVGIKINGQT QSVVFSYKGL DGSLQTAAFS NLSSLFDSQW
   181  HKIMIGVERS SATLFVDCNR IESLPIKPRG PIDIDGFAVL GKLADNPQVS VPFELQWMLI
   241  HCDPLRPRRE TCHELPARIT PSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP
   301  PGPPGPAGEP GKPGAPGKPG TPGADGLTGP DGSPGSIGSK GQKGEPGVPG SRGFPGRGIP
   361  GPPGPPGTAG LPGELGRVGP VGDPGRRGPP GPPGPPGPRG TIGFHDGDPL CPNACPPGRS
   421  GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE GDQGELGEVG AQGPPGAQGL RGITGIVGDK
   481  GEKGARGLDG EPGPQGLPGA PGDQGQRGPP GEAGPKGDRG AEGARGIPGL PGPKGDTGLP
   541  GVDGRDGIPG MPGTKGEPGK PGPPGDAGLQ GLPGVPGIPG AKGVAGEKGS TGAPGKPGQM
   601  GNSGKPGQQG PPGEVGPRGP QGLPGSRGEL GPVGSPGLPG KLGSLGSPGL PGLPGPPGLP
   661  GMKGDRGVVG EPGPKGEQGA SGEEGEAGER GELGDIGLPG PKGSAGNPGE PGLRGPEGSR
   721  GLPGVEGPRG PPGPRGVQGE QGATGLPGVQ GPPGRAPTDQ HIKQVCMRVI QEHFAEMAAS
   781  LKRPDSGATG LPGRPGPPGP PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK
   841  GERGPPGRGP NGLPGAIGLP GDPGPASYGR NGRDGERGPP GVAGIPGVPG PPGPPGLPGF
   901  CEPASCTMQA GQRAFNKGPD P

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against COL9A1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Secreted

Secreted

Yes

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.62

Highest tissue expression

24 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about COL9A1.

Disease | AllUniProt

Conditions COL9A1 is implicated in, by any mechanism.

• Multiple epiphyseal dysplasia 6 (EDM6) MIM:614135
• Stickler syndrome 4 (STL4) MIM:614134

Disease | GeneticClinVar

101 pathogenic / likely-pathogenic of 1,497 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• COL9A1-related disorder
• Stickler syndrome, type 4
• See cases
• Connective tissue disorder
• Epiphyseal dysplasia, multiple, 6

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.81

gnomAD pLI

0

gnomAD missense Z

0.19

DepMap mean gene effect

0

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• animal organ morphogenesis

Molecular functions

• carbohydrate binding
• extracellular matrix structural constituent conferring tensile strength
• metal ion binding
• protein homodimerization activity

Cellular components

• collagen type IX trimer
• endoplasmic reticulum lumen
• extracellular matrix
• extracellular region

Protein domainsUniProt · Pfam · InterPro

• Collagen triple helix repeat
• Concanavalin A-like lectin/glucanase domain superfamily
• Thrombospondin-like, N-terminal domain
• Collagen superfamily
• Collagen triple helix repeat (20 copies)

KeywordsUniProt

• Collagen
• Deafness
• Disulfide bond
• Extracellular matrix
• Glycoprotein
• Hydroxylation
• Metal-binding
• Repeat
• Secreted
• Signal
• Stickler syndrome
• Zinc