Seroatlas · Human Serome Atlas

COL6A1

Collagen alpha-1(VI) chain

Also known as: CO6A1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: P12109
Gene: COL6A1
Ensembl: ENSG00000142156
Chromosome: 21
Canonical length: 1028 aa
Protein class: Cancer-related genes, Disease related genes, Human disease related genes, Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins
Subcellular location: Cytosol
Secretome location: Secreted to extracellular matrix

OverviewNCBI Gene

The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1028 residues, UniProt reviewed canonical sequence.

>P12109|COL6A1
     1  MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD
    61  KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV
   121  KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG GLEDAVNEAK
   181  HLGVKVFSVA ITPDHLEPRL SIIATDHTYR RNFTAADWGQ SRDAEEAISQ TIDTIVDMIK
   241  NNVEQVCCSF ECQPARGPPG LRGDPGFEGE RGKPGLPGEK GEAGDPGRPG DLGPVGYQGM
   301  KGEKGSRGEK GSRGPKGYKG EKGKRGIDGV DGVKGEMGYP GLPGCKGSPG FDGIQGPPGP
   361  KGDPGAFGLK GEKGEPGADG EAGRPGSSGP SGDEGQPGEP GPPGEKGEAG DEGNPGPDGA
   421  PGERGGPGER GPRGTPGTRG PRGDPGEAGP QGDQGREGPV GVPGDPGEAG PIGPKGYRGD
   481  EGPPGSEGAR GAPGPAGPPG DPGLMGERGE DGPAGNGTEG FPGFPGYPGN RGAPGINGTK
   541  GYPGLKGDEG EAGDPGDDNN DIAPRGVKGA KGYRGPEGPQ GPPGHQGPPG PDECEILDII
   601  MKMCSCCECK CGPIDLLFVL DSSESIGLQN FEIAKDFVVK VIDRLSRDEL VKFEPGQSYA
   661  GVVQYSHSQM QEHVSLRSPS IRNVQELKEA IKSLQWMAGG TFTGEALQYT RDQLLPPSPN
   721  NRIALVITDG RSDTQRDTTP LNVLCSPGIQ VVSVGIKDVF DFIPGSDQLN VISCQGLAPS
   781  QGRPGLSLVK ENYAELLEDA FLKNVTAQIC IDKKCPDYTC PITFSSPADI TILLDGSASV
   841  GSHNFDTTKR FAKRLAERFL TAGRTDPAHD VRVAVVQYSG TGQQRPERAS LQFLQNYTAL
   901  ASAVDAMDFI NDATDVNDAL GYVTRFYREA SSGAAKKRLL LFSDGNSQGA TPAAIEKAVQ
   961  EAQRAGIEIF VVVVGRQVNE PHIRVLVTGK TAEYDVAYGE SHLFRVPSYQ ALLRGVFHQT
  1021  VSRKVALG

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against COL6A1 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): 0.42
Highest tissue expression: 766 nTPM

Expression across tissuesHPA

Tissue

colon: 766 nTPM
endometrium: 572 nTPM
cervix: 548 nTPM
urinary bladder: 502 nTPM
ovary: 470 nTPM
fallopian tube: 413 nTPM

Single-cell type

hepatic stellate cells: 1,065 nCPM
fibroblasts: 743 nCPM
decidual stromal cells: 600 nCPM
endometrial stromal cells: 532 nCPM
pericytes: 439 nCPM
leydig cells: 403 nCPM

Immune cell

gdT-cell: 0.1 nTPM
MAIT T-cell: 0.1 nTPM
memory CD8 T-cell: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM

Brain region

cerebellum: 85 nTPM
choroid plexus: 82 nTPM
pons: 64 nTPM
medulla oblongata: 61 nTPM
cerebral cortex: 57 nTPM
midbrain: 56 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about COL6A1.

Disease | AllUniProt

Conditions COL6A1 is implicated in, by any mechanism.

Bethlem myopathy 1A (BTHLM1A) MIM:158810
Ullrich congenital muscular dystrophy 1A (UCMD1A) MIM:254090

Disease | GeneticClinVar

196 pathogenic / likely-pathogenic of 2,117 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Bethlem myopathy 1A
Ullrich congenital muscular dystrophy 1A
COL6A1-related disorder
Collagen 6-related myopathy
Inborn genetic diseases

Disease | ImmuneIEDB

Conditions an epitope on COL6A1 was assayed in.

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): 0.23
gnomAD pLI: 1
gnomAD missense Z: 0.5
DepMap mean gene effect: 0.09
DepMap dependency class: none

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

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads COL6A1 as an antibody target. Whether an autoantibody or antibody against COL6A1 could matter depends on whether native COL6A1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

COL6A1 is annotated as secreted, so native COL6A1 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 COL6A1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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