Seroatlas · Human Serome Atlas

COL9A3

Collagen alpha-3(IX) chain

Also known as: CO9A3_HUMAN, DJ885L7.4.1, EDM3, FLJ90759, IDD, MED

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q14050
Gene
COL9A3
Ensembl
ENSG00000092758
Chromosome
20
Canonical length
684 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins, Predicted secreted proteins
Subcellular location
Nucleoplasm,Intermediate filaments
Secretome location
Secreted to extracellular matrix

OverviewNCBI Gene

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. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

Canonical amino-acid sequenceUniProt

684 residues, UniProt reviewed canonical sequence.

>Q14050|COL9A3
     1  MAGPRACAPL LLLLLLGELL AAAGAQRVGL PGPPGPPGPP GKPGQDGIDG EAGPPGLPGP
    61  PGPKGAPGKP GKPGEAGLPG LPGVDGLTGR DGPPGPKGAP GERGSLGPPG PPGLGGKGLP
   121  GPPGEAGVSG PPGGIGLRGP PGPSGLPGLP GPPGPPGPPG HPGVLPEGAT DLQCPSICPP
   181  GPPGPPGMPG FKGPTGYKGE QGEVGKDGEK GDPGPPGPAG LPGSVGLQGP RGLRGLPGPL
   241  GPPGDRGPIG FRGPPGIPGA PGKAGDRGER GPEGFRGPKG DLGRPGPKGT PGVAGPSGEP
   301  GMPGKDGQNG VPGLDGQKGE AGRNGAPGEK GPNGLPGLPG RAGSKGEKGE RGRAGELGEA
   361  GPSGEPGVPG DAGMPGERGE AGHRGSAGAL GPQGPPGAPG VRGFQGQKGS MGDPGLPGPQ
   421  GLRGDVGDRG PGGAAGPKGD QGIAGSDGLP GDKGELGPSG LVGPKGESGS RGELGPKGTQ
   481  GPNGTSGVQG VPGPPGPLGL QGVPGVPGIT GKPGVPGKEA SEQRIRELCG GMISEQIAQL
   541  AAHLRKPLAP GSIGRPGPAG PPGPPGPPGS IGHPGARGPP GYRGPTGELG DPGPRGNQGD
   601  RGDKGAAGAG LDGPEGDQGP QGPQGVPGTS KDGQDGAPGE PGPPGDPGLP GAIGAQGTPG
   661  ICDTSACQGA VLGGVGEKSG SRSS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against COL9A3 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)
0.71
Highest tissue expression
71 nTPM

Expression across tissuesHPA

Tissue

  • spinal cord: 71 nTPM
  • midbrain: 53 nTPM
  • basal ganglia: 43 nTPM
  • hippocampal formation: 40 nTPM
  • amygdala: 31 nTPM
  • hypothalamus: 28 nTPM

Single-cell type

  • late spermatids: 684 nCPM
  • early spermatids: 149 nCPM
  • epididymal clear cells: 116 nCPM
  • müller glia: 102 nCPM
  • oligodendrocyte progenitor cells: 95 nCPM
  • tuft cells: 92 nCPM

Immune cell

  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM
  • MAIT T-cell: 0 nTPM

Brain region

  • white matter: 82 nTPM
  • medulla oblongata: 79 nTPM
  • basal ganglia: 73 nTPM
  • choroid plexus: 73 nTPM
  • thalamus: 65 nTPM
  • midbrain: 63 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about COL9A3.

Disease | AllUniProt

Conditions COL9A3 is implicated in, by any mechanism.

Disease | GeneticClinVar

54 pathogenic / likely-pathogenic of 1,758 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
0.75
gnomAD pLI
0
gnomAD missense Z
-0.38
DepMap mean gene effect
-0.01
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads COL9A3 as an antibody target. Whether an autoantibody or antibody against COL9A3 could matter depends on whether native COL9A3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

COL9A3 is annotated as secreted, so native COL9A3 circulates and is directly accessible to antibodies. Secreted and cell-surface proteins are the autoantibody targets most likely to act like drugs, blocking or depleting the native protein.

Annotation status

The present source text does not explicitly label COL9A3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/COL9A3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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