Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL6A3 Gene

Aliases for COL6A3 Gene

  • Collagen Type VI Alpha 3 Chain 2 3 5
  • Collagen, Type VI, Alpha 3 2 3
  • Collagen VI, Alpha-3 Polypeptide 3
  • Collagen Alpha-3(VI) Chain 3
  • BTHLM1 3
  • UCMD1 3
  • DYT27 3

External Ids for COL6A3 Gene

Previous GeneCards Identifiers for COL6A3 Gene

  • GC02M236270
  • GC02M236914
  • GC02M238248
  • GC02M238519
  • GC02M238014
  • GC02M237897
  • GC02M230024
  • GC02M238233

Summaries for COL6A3 Gene

Entrez Gene Summary for COL6A3 Gene

  • This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]

GeneCards Summary for COL6A3 Gene

COL6A3 (Collagen Type VI Alpha 3 Chain) is a Protein Coding gene. Diseases associated with COL6A3 include Dystonia 27 and Bethlem Myopathy 1. Among its related pathways are Interleukin-3, 5 and GM-CSF signaling and NCAM1 interactions. GO annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is COL6A5.

UniProtKB/Swiss-Prot for COL6A3 Gene

  • Collagen VI acts as a cell-binding protein.

Gene Wiki entry for COL6A3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A3 Gene

Genomics for COL6A3 Gene

Regulatory Elements for COL6A3 Gene

Enhancers for COL6A3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around COL6A3 on UCSC Golden Path with GeneCards custom track

Promoters for COL6A3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL6A3 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL6A3 Gene

Chromosome:
2
Start:
237,324,003 bp from pter
End:
237,414,375 bp from pter
Size:
90,373 bases
Orientation:
Minus strand

Genomic View for COL6A3 Gene

Genes around COL6A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A3 Gene

Proteins for COL6A3 Gene

  • Protein details for COL6A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P12111-CO6A3_HUMAN
    Recommended name:
    Collagen alpha-3(VI) chain
    Protein Accession:
    P12111
    Secondary Accessions:
    • A8MT30
    • B4E3U5
    • B7ZMJ7
    • E9PFQ6
    • E9PGQ9
    • Q16501
    • Q53QF4
    • Q53QF6

    Protein attributes for COL6A3 Gene

    Size:
    3177 amino acids
    Molecular mass:
    343669 Da
    Quaternary structure:
    • Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI).

    Three dimensional structures from OCA and Proteopedia for COL6A3 Gene

    Alternative splice isoforms for COL6A3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL6A3 Gene

Post-translational modifications for COL6A3 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
  • The N-terminus is blocked.
  • Glycosylation at Asn 108, Asn 116, Asn 202, Asn 251, Asn 2079, Lys 2103, Lys 2209, Lys 2212, Lys 2322, Asn 2331, Lys 2337, Asn 2558, Asn 2677, Asn 2861, and Asn 3037
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A3 Gene

Domains & Families for COL6A3 Gene

Gene Families for COL6A3 Gene

Graphical View of Domain Structure for InterPro Entry

P12111

UniProtKB/Swiss-Prot:

CO6A3_HUMAN :
  • Contains 1 BPTI/Kunitz inhibitor domain.
  • Belongs to the type VI collagen family.
Domain:
  • Contains 1 BPTI/Kunitz inhibitor domain.
  • Contains 5 collagen-like domains.
  • Contains 1 fibronectin type-III domain.
  • Contains 12 VWFA domains.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A3: view

Function for COL6A3 Gene

Molecular function for COL6A3 Gene

GENATLAS Biochemistry:
collagen type VI,alpha 3 (300kDa),microfibrillar,putative down-regulated c-Myc target gene,
UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein.

Gene Ontology (GO) - Molecular Function for COL6A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004867 serine-type endopeptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with COL6A3: view
genes like me logo Genes that share phenotypes with COL6A3: view

Human Phenotype Ontology for COL6A3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for COL6A3 Gene

Localization for COL6A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A3 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL6A3 Gene COMPARTMENTS Subcellular localization image for COL6A3 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
plasma membrane 4
cytosol 1
golgi apparatus 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for COL6A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IDA 18400749
GO:0005581 collagen trimer IEA --
GO:0005589 collagen type VI trimer TAS 8782832
GO:0005615 extracellular space IDA 20551380
genes like me logo Genes that share ontologies with COL6A3: view

Pathways & Interactions for COL6A3 Gene

genes like me logo Genes that share pathways with COL6A3: view

Gene Ontology (GO) - Biological Process for COL6A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007517 muscle organ development TAS 8782832
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
genes like me logo Genes that share ontologies with COL6A3: view

No data available for SIGNOR curated interactions for COL6A3 Gene

Drugs & Compounds for COL6A3 Gene

No Compound Related Data Available

Transcripts for COL6A3 Gene

Unigene Clusters for COL6A3 Gene

Collagen, type VI, alpha 3:
Representative Sequences:

CRISPR Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b ^ 15 ^
SP1:
SP2:
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8: - - - - - -
SP9: -
SP10:
SP11: - - -
SP12:
SP13:
SP14:
SP15: -
SP16: -
SP17:
SP18:

ExUns: 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41a ·
SP1:
SP2:
SP3:
SP4:
SP5: - - - - - - - - - - - -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:

ExUns: 41b ^ 42 ^ 43 ^ 44a · 44b ^ 45a · 45b ^ 46
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14: - - -
SP15:
SP16:
SP17:
SP18:

Relevant External Links for COL6A3 Gene

GeneLoc Exon Structure for
COL6A3
ECgene alternative splicing isoforms for
COL6A3

Expression for COL6A3 Gene

mRNA expression in normal human tissues for COL6A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL6A3 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (17.2), Adipocyte (16.4), Colon muscle (8.7), and Urinary Bladder (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL6A3 Gene



Protein tissue co-expression partners for COL6A3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COL6A3 Gene:

COL6A3

SOURCE GeneReport for Unigene cluster for COL6A3 Gene:

Hs.233240
genes like me logo Genes that share expression patterns with COL6A3: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for COL6A3 Gene

Orthologs for COL6A3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL6A3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL6A3 34
  • 85.8 (n)
  • 86.85 (a)
COL6A3 35
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL6A3 34
  • 86.81 (n)
  • 87.93 (a)
COL6A3 35
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a3 34
  • 83.46 (n)
  • 84.61 (a)
Col6a3 16
Col6a3 35
  • 81 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL6A3 34
  • 99.32 (n)
  • 99.53 (a)
COL6A3 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col6a3 34
  • 82.9 (n)
  • 83.94 (a)
oppossum
(Monodelphis domestica)
Mammalia COL6A3 35
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 73 (a)
OneToMany
-- 35
  • 66 (a)
OneToMany
chicken
(Gallus gallus)
Aves COL6A3 34
  • 68.94 (n)
  • 65.79 (a)
COL6A3 35
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL6A3 35
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a3 34
  • 55.98 (n)
  • 50.45 (a)
zebrafish
(Danio rerio)
Actinopterygii col6a3 34
  • 52.06 (n)
  • 44.68 (a)
col6a3 35
  • 35 (a)
OneToOne
Species where no ortholog for COL6A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL6A3 Gene

ENSEMBL:
Gene Tree for COL6A3 (if available)
TreeFam:
Gene Tree for COL6A3 (if available)

Paralogs for COL6A3 Gene

genes like me logo Genes that share paralogs with COL6A3: view

Variants for COL6A3 Gene

Sequence variations from dbSNP and Humsavar for COL6A3 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs121434553 Bethlem myopathy 1 (BTHLM1) 237,367,151(-) AGTGG(A/G)GCTTG reference, missense
rs36104025 - 237,339,091(+) GATAT(C/G)TGGGG reference, missense
rs34741387 - 237,381,199(+) AACTC(A/G)TGAAT intron-variant, reference, missense
rs36092870 - 237,379,157(+) AGTCG(C/T)GCACA intron-variant, reference, missense
rs9630964 - 237,377,185(+) ACTCC(A/T)CCTTG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL6A3 Gene

Variant ID Type Subtype PubMed ID
esv2665065 CNV deletion 23128226
esv3561230 CNV deletion 23714750
esv3594742 CNV loss 21293372
nsv1000252 CNV loss 25217958
nsv3226 CNV insertion 18451855
nsv520263 CNV loss 19592680
nsv584727 CNV loss 21841781
nsv584728 CNV loss 21841781

Variation tolerance for COL6A3 Gene

Residual Variation Intolerance Score: 97.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.49; 96.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL6A3 Gene

Human Gene Mutation Database (HGMD)
COL6A3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A3 Gene

Disorders for COL6A3 Gene

MalaCards: The human disease database

(12) MalaCards diseases for COL6A3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
dystonia 27
  • dyt27
bethlem myopathy 1
  • bethlem myopathy
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
collagen type vi-related disorders
myopathy
  • muscular diseases
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO6A3_HUMAN
  • Bethlem myopathy 1 (BTHLM1) [MIM:158810]: A benign proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. {ECO:0000269 PubMed:10399756, ECO:0000269 PubMed:15689448, ECO:0000269 PubMed:17886299, ECO:0000269 PubMed:9536084}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Dystonia 27 (DYT27) [MIM:616411]: A form of dystonia, a disorder defined by the presence of sustained involuntary muscle contraction, often leading to abnormal postures. DYT27 is an autosomal recessive form characterized by segmental isolated dystonia involving the face, neck, bulbar muscles, and upper limbs. {ECO:0000269 PubMed:26004199}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Ullrich congenital muscular dystrophy 1 (UCMD1) [MIM:254090]: A congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy. {ECO:0000269 PubMed:15689448}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL6A3

Genetic Association Database (GAD)
COL6A3
Human Genome Epidemiology (HuGE) Navigator
COL6A3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL6A3
genes like me logo Genes that share disorders with COL6A3: view

No data available for Genatlas for COL6A3 Gene

Publications for COL6A3 Gene

  1. Mutations in COL6A3 cause severe and mild phenotypes of Ullrich congenital muscular dystrophy. (PMID: 11992252) Demir E. … Guicheney P. (Am. J. Hum. Genet. 2002) 2 3 4 65
  2. Missense mutation in a von Willebrand factor type A domain of the alpha 3(VI) collagen gene (COL6A3) in a family with Bethlem myopathy. (PMID: 9536084) Pan T.-C. … Speer M.C. (Hum. Mol. Genet. 1998) 3 4 22 65
  3. The human type VI collagen gene. mRNA and protein variants of the alpha 3 chain generated by alternative splicing of an additional 5-end exon. (PMID: 1339440) Zanussi S. … Colombatti A. (J. Biol. Chem. 1992) 2 3 4 65
  4. Mosaic structure of globular domains in the human type VI collagen alpha 3 chain: similarity to von Willebrand factor, fibronectin, actin, salivary proteins and aprotinin type protease inhibitors. (PMID: 1689238) Chu M.-L. … Timpl R. (EMBO J. 1990) 3 4 22 65
  5. Recessive mutations in the alpha3 (VI) collagen gene COL6A3 cause early-onset isolated dystonia. (PMID: 26004199) Zech M. … Winkelmann J. (Am. J. Hum. Genet. 2015) 3 4 65

Products for COL6A3 Gene

Sources for COL6A3 Gene

Content