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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
  • DYT27 3
  • UCMD1 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 ERK Signaling and Collagen chain trimerization. Gene Ontology (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

Additional gene information for COL6A3 Gene

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

Genomics for COL6A3 Gene

GeneHancer (GH) Regulatory Elements for COL6A3 Gene

Promoters and enhancers for COL6A3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J237406 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 657.5 +3.2 3246 8.3 CTCF ZNF654 FOXA2 TAF1 ZNF398 ZNF384 RAD21 FOXA1 ZNF335 ZFHX2 COL6A3 MLPH RAMP1 COPS8 GC02P237385
GH02J237429 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 650.4 -18.8 -18756 7.4 HDAC1 TEAD4 MAX EBF1 TCF12 ZFHX2 POLR2A EGR1 VEZF1 EED ENSG00000222032 COL6A3 MLPH ENSG00000222022
GH02J238283 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.5 -873.3 -873282 8 HDGF PKNOX1 CLOCK FOXA2 MLX ARNT ARID4B NEUROD1 SIN3A FEZF1 ENSG00000283635 PER2 RBM44 LOC151174 COL6A3 LOC643387 TRAF3IP1 ERFE SCLY PIR48935
GH02J237312 Enhancer 1.8 VISTA FANTOM5 Ensembl ENCODE dbSUPER 14.9 +97.9 97910 7.3 SOX13 USF1 FOXA2 ZFP64 MAX CEBPG KMT2B RAD21 TEAD3 POLR2A GC02P237317 COL6A3 LOC105373953 ENSG00000222022 MLPH UBE2F IQCA1 LOC105373954
GH02J237485 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 9.9 -75.2 -75224 7.7 PKNOX1 NEUROD1 SIN3A YY1 FOS RCOR1 RXRA USF2 ELF1 REST MLPH ENSG00000222022 COL6A3 LOC105373957 MIR6811
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL6A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL6A3 gene promoter:
  • LHX3b
  • Lhx3a
  • RelA
  • NF-kappaB1
  • NF-kappaB
  • AML1a
  • Pax-4a
  • RSRFC4
  • POU2F1
  • POU2F1a

Genomic Locations for COL6A3 Gene

Genomic Locations for COL6A3 Gene
90,373 bases
Minus strand
90,373 bases
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:
    Recommended name:
    Collagen alpha-3(VI) chain
    Protein Accession:
    Secondary Accessions:
    • A8MT30
    • B4E3U5
    • B7ZMJ7
    • E9PFQ6
    • E9PGQ9
    • Q16501
    • Q53QF4
    • Q53QF6

    Protein attributes for COL6A3 Gene

    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


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 Asn3037, Asn2861, posLast=26772677, posLast=25582558, Lys2337, posLast=23312331, posLast=23222322, posLast=22122212, Lys2209, posLast=21032103, posLast=20792079, Asn251, Asn202, Asn116, and posLast=108108
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A3 Gene

Domains & Families for COL6A3 Gene

Gene Families for COL6A3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the type VI collagen 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

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

Phenotypes From GWAS Catalog for COL6A3 Gene

Gene Ontology (GO) - Molecular Function for COL6A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004867 serine-type endopeptidase inhibitor activity IEA --
GO:0005515 protein binding IEA --
GO:0030414 peptidase 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

miRNA for COL6A3 Gene

miRTarBase miRNAs that target COL6A3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL6A3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 4
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for COL6A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA,TAS --
GO:0005581 collagen trimer IEA --
GO:0005589 collagen type VI trimer TAS 8782832
GO:0005615 extracellular space IDA,HDA 20551380
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL6A3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL6A3 Gene

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:0010466 negative regulation of peptidase activity IEA --
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0030198 extracellular matrix organization 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

mRNA/cDNA for COL6A3 Gene

Unigene Clusters for COL6A3 Gene

Collagen, type VI, alpha 3:
Representative Sequences:

Clone 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 ^
SP4: - -
SP8: - - - - - -
SP9: -
SP11: - - -
SP15: -
SP16: -

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 ·
SP5: - - - - - - - - - - - -

ExUns: 41b ^ 42 ^ 43 ^ 44a · 44b ^ 45a · 45b ^ 46
SP6: -
SP14: - - -

Relevant External Links for COL6A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL6A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, 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:


SOURCE GeneReport for Unigene cluster for COL6A3 Gene:


Evidence on tissue expression from TISSUES for COL6A3 Gene

  • Liver(4.5)
  • Bone(4.1)
  • Bone marrow(4.1)
  • Muscle(3.8)
  • Pancreas(3.5)
  • Lung(3.2)
  • Intestine(3)
  • Gall bladder(2.9)
  • Heart(2.8)
  • Adrenal gland(2.7)
  • Kidney(2.6)
  • Skin(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • epiglottis
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • skull
  • tooth
  • vocal cord
  • bronchus
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
  • kidney
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with COL6A3: view

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
(Pan troglodytes)
Mammalia COL6A3 34 33
  • 99.32 (n)
(Canis familiaris)
Mammalia COL6A3 34 33
  • 86.81 (n)
(Bos Taurus)
Mammalia COL6A3 34 33
  • 85.8 (n)
(Mus musculus)
Mammalia Col6a3 16 34 33
  • 83.46 (n)
(Rattus norvegicus)
Mammalia Col6a3 33
  • 82.9 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 73 (a)
-- 34
  • 66 (a)
(Monodelphis domestica)
Mammalia COL6A3 34
  • 72 (a)
(Gallus gallus)
Aves COL6A3 34 33
  • 68.94 (n)
(Anolis carolinensis)
Reptilia COL6A3 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a3 33
  • 55.98 (n)
(Danio rerio)
Actinopterygii col6a3 34 33
  • 52.06 (n)
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

Gene Tree for COL6A3 (if available)
Gene Tree for COL6A3 (if available)
Evolutionary constrained regions (ECRs) for COL6A3: view image

Paralogs for COL6A3 Gene

Paralogs for COL6A3 Gene

(17) SIMAP similar genes for COL6A3 Gene using alignment to 7 proteins:

  • B7ZW00_HUMAN
  • I3L392_HUMAN
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 Variation AA Info Type
rs10084221 benign, not specified, Collagen VI-related myopathy, Bethlem myopathy 1, Ullrich congenital muscular dystrophy 1 237,344,689(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs10201909 benign, not specified, Collagen VI-related myopathy, Bethlem myopathy 1 237,334,726(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs1041006651 uncertain-significance, Collagen VI-related myopathy 237,342,139(-) T/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1050785 benign, Collagen VI-related myopathy 237,324,109(-) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1057518127 uncertain-significance, not specified, Bethlem myopathy 1 237,372,208(-) C/T coding_sequence_variant, missense_variant

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)

Additional Variant Information for COL6A3 Gene

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

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: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
dystonia 27
  • dyt27
bethlem myopathy 1
  • bthlm1
ullrich congenital muscular dystrophy 1
  • ucmd1
  • muscular diseases
collagen vi-related myopathy
  • collagen type vi-related disorders
- elite association - COSMIC cancer census association via MalaCards


  • 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.
  • 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.
  • 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.

Additional Disease Information for COL6A3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (American journal of human genetics 2002) 2 3 4 58
  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 TC … Speer MC (Human molecular genetics 1998) 3 4 22 58
  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 (The Journal of biological chemistry 1992) 2 3 4 58
  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 ML … Deutzmann R (The EMBO journal 1990) 3 4 22 58
  5. Recessive mutations in the α3 (VI) collagen gene COL6A3 cause early-onset isolated dystonia. (PMID: 26004199) Zech M … Winkelmann J (American journal of human genetics 2015) 3 4 58

Products for COL6A3 Gene

Sources for COL6A3 Gene

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