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COL6A1 Gene(Protein Coding)

Collagen Type VI Alpha 1 Chain

GCID:
GC21P045981
GIFtS:
61
Genes Participants
UDN Logo

Aliases for COL6A1 Gene

Aliases for COL6A1 Gene

  • Collagen Type VI Alpha 1 Chain 2 3 5
  • Collagen, Type VI, Alpha 1 2 3
  • Collagen VI, Alpha-1 Polypeptide 3
  • Alpha 1 (VI) Chain (61 AA) 3
  • Collagen Alpha-1(VI) Chain 3
  • BTHLM1 3
  • UCHMD1 3
  • OPLL 3

External Ids for COL6A1 Gene

Previous GeneCards Identifiers for COL6A1 Gene

  • GC21P043908
  • GC21P046259
  • GC21P046260
  • GC21P046261
  • GC21P046226
  • GC21P047401
  • GC21P032782

Summaries for COL6A1 Gene

Entrez Gene Summary for COL6A1 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]

GeneCards Summary for COL6A1 Gene

COL6A1 (Collagen Type VI Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL6A1 include Bethlem Myopathy 1 and Ullrich Congenital Muscular Dystrophy 1. Among its related pathways are Collagen chain trimerization and Phospholipase-C Pathway. GO annotations related to this gene include platelet-derived growth factor binding. An important paralog of this gene is COL6A2.

UniProtKB/Swiss-Prot for COL6A1 Gene

  • Collagen VI acts as a cell-binding protein.

Gene Wiki entry for COL6A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A1 Gene

Genomics for COL6A1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for COL6A1 Gene

Enhancers for COL6A1 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
GH21G045970 1.6 FANTOM5 ENCODE dbSUPER 24.3 -8.8 -8787 5.6 PKNOX1 ARID4B ZNF2 ZNF48 GLIS2 ZNF143 KLF7 FOS SP3 REST COL6A1 PCBP3 COL6A2 LSS SPATC1L LOC101928796 ENSG00000280604
GH21G045976 1.5 Ensembl ENCODE dbSUPER 17.1 +0.4 442 11.2 HDGF PKNOX1 ATF1 ARNT SIN3A YBX1 GLI4 ZNF2 ZNF48 ZBTB7B COL6A1 ENSG00000228137 ENSG00000227438 MCM3AP S100B DSTNP1 LOC105372842 PCBP3 LSS
GH21G046048 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13.6 +76.8 76793 19.8 CBX3 ZNF473 AGO1 ZSCAN4 INSM2 KLF17 RAD21 ETS1 CBX5 ZNF350 ENSG00000228137 MCM3AP MCM3AP-AS1 DSTNP1 ENSG00000215447 LINC00205 COL6A1 ENSG00000227438 LOC100129027 COL6A2
GH21G045952 1 Ensembl ENCODE dbSUPER 18.4 -27.9 -27870 1.9 CTCF PKNOX1 ZNF512 COL6A1 PCBP3 LSS LOC101928796 ENSG00000280604
GH21G045949 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10 -31.1 -31129 2.6 ZNF263 CTCF MAZ SP3 KLF1 SP2 KLF17 ZIC2 ZFHX2 ZNF341 PCBP3 COL6A1 MCM3AP-AS1 LOC101928796 ENSG00000280604
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL6A1 on UCSC Golden Path with GeneCards custom track

Promoters for COL6A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000143315 763 2601 HDGF SIN3A GLI4 ZNF2 ZNF48 ZBTB7B GLIS2 FOS KLF7 SP3

Transcription factor binding sites by QIAGEN in the COL6A1 gene promoter:

Genomic Location for COL6A1 Gene

Chromosome:
21
Start:
45,981,737 bp from pter
End:
46,005,050 bp from pter
Size:
23,314 bases
Orientation:
Plus strand

Genomic View for COL6A1 Gene

Genes around COL6A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for COL6A1 Gene

Proteins for COL6A1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for COL6A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P12109-CO6A1_HUMAN
    Recommended name:
    Collagen alpha-1(VI) chain
    Protein Accession:
    P12109
    Secondary Accessions:
    • O00117
    • O00118
    • Q14040
    • Q14041
    • Q16258
    • Q7Z645
    • Q9BSA8

    Protein attributes for COL6A1 Gene

    Size:
    1028 amino acids
    Molecular mass:
    108529 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).

neXtProt entry for COL6A1 Gene

Protein Expression for COL6A1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for COL6A1 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
  • Glycosylation at Asn212, Asn516, posLast=537537, Asn804, and posLast=896896
  • Modification sites at PhosphoSitePlus

Other Protein References for COL6A1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COL6A1 Gene

Domains & Families for COL6A1 Gene

Gene Families for COL6A1 Gene

HGNC:

Protein Domains for COL6A1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for COL6A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P12109

UniProtKB/Swiss-Prot:

CO6A1_HUMAN :
  • Belongs to the type VI collagen family.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A1: view

Function for COL6A1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for COL6A1 Gene

GENATLAS Biochemistry:
collagen type VI,alpha 1 (150kDa),microfibrillar
UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein.

Gene Ontology (GO) - Molecular Function for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0048407 platelet-derived growth factor binding IDA 8900172
genes like me logo Genes that share ontologies with COL6A1: view
genes like me logo Genes that share phenotypes with COL6A1: view

Human Phenotype Ontology for COL6A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL6A1 Gene

MGI Knock Outs for COL6A1:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COL6A1 Gene

Localization for COL6A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
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 COL6A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
lysosome 5
cytosol 3
plasma membrane 2
mitochondrion 2
nucleus 1

Gene Ontology (GO) - Cellular Components for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005589 collagen type VI trimer NAS 2551668
GO:0005615 extracellular space IEA --
genes like me logo Genes that share ontologies with COL6A1: view

Pathways & Interactions for COL6A1 Gene

genes like me logo Genes that share pathways with COL6A1: view

Gene Ontology (GO) - Biological Process for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001649 osteoblast differentiation IDA 16210410
GO:0007155 cell adhesion IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
GO:0035987 endodermal cell differentiation IEP 23154389
genes like me logo Genes that share ontologies with COL6A1: view

No data available for SIGNOR curated interactions for COL6A1 Gene

Drugs & Compounds for COL6A1 Gene

Products:

  1. Drug

(1) Drugs for COL6A1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with COL6A1: view

Transcripts for COL6A1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for COL6A1 Gene

(1) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(700) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL6A1 Gene

Collagen, type VI, alpha 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A1 Gene

No ASD Table

Relevant External Links for COL6A1 Gene

GeneLoc Exon Structure for
COL6A1
ECgene alternative splicing isoforms for
COL6A1

Expression for COL6A1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL6A1 Gene

mRNA expression in normal human tissues for COL6A1 Gene
mRNA expression by BioGPS for COL6A1 GenemRNA expression by GTEx for COL6A1 Gene

Protein differential expression in normal tissues from HIPED for COL6A1 Gene

This gene is overexpressed in Adipocyte (16.2), Urinary Bladder (11.7), Bone marrow mesenchymal stem cell (8.0), and Colon muscle (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL6A1 Gene



Protein tissue co-expression partners for COL6A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COL6A1 Gene:

COL6A1

SOURCE GeneReport for Unigene cluster for COL6A1 Gene:

Hs.474053

Evidence on tissue expression from TISSUES for COL6A1 Gene

  • Kidney(4.4)
  • Liver(4.4)
  • Lung(4.1)
  • Bone(3.9)
  • Skin(3.7)
  • Nervous system(3.7)
  • Heart(3.4)
  • Intestine(2.9)
  • Muscle(2.9)
  • Eye(2.8)
  • Gall bladder(2.6)
  • Pancreas(2.4)
  • Adrenal gland(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • skull
Thorax:
  • bronchus
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
Limb:
  • 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
General:
  • 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 COL6A1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for COL6A1 Gene

Orthologs for COL6A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL6A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia COL6A1 34 35
  • 99.12 (n)
dog
(Canis familiaris)
 Mammalia COL6A1 34 35
  • 88.37 (n)
cow
(Bos Taurus)
 Mammalia COL6A1 34 35
  • 87.44 (n)
rat
(Rattus norvegicus)
 Mammalia Col6a1 34
  • 83.61 (n)
mouse
(Mus musculus)
 Mammalia Col6a1 34 16 35
  • 83.15 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia COL6A1 35
  • 74 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia COL6A1 35
  • 69 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves COL6A1 34 35
  • 70.63 (n)
lizard
(Anolis carolinensis)
 Reptilia COL6A1 35
  • 69 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia col6a1 34
  • 63.12 (n)
African clawed frog
(Xenopus laevis)
 Amphibia col6a1-prov 34
zebrafish
(Danio rerio)
 Actinopterygii col6a1 34 35
  • 59.8 (n)
worm
(Caenorhabditis elegans)
 Secernentea mec-5 35
  • 39 (a)
 OneToMany
Species where no ortholog for COL6A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)

Evolution for COL6A1 Gene

ENSEMBL:
Gene Tree for COL6A1 (if available)
TreeFam:
Gene Tree for COL6A1 (if available)

Paralogs for COL6A1 Gene

Paralogs for COL6A1 Gene

(7) SIMAP similar genes for COL6A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL6A1: view

Variants for COL6A1 Gene

Sequence variations from dbSNP and Humsavar for COL6A1 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs11553519 other, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 45,984,388(+) AAGCA(A/C/G)CGTGG reference, missense
rs121912935 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 45,990,792(+) CCCAG(A/G/T)CCTGC reference, missense
rs121912936 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 45,984,403(+) GGTCA(A/G)GTACT reference, missense
rs121912938 Pathogenic, Ullrich congenital muscular dystrophy 1 (UCMD1) [MIM:254090] 45,989,129(+) AAGCC(A/G)GAGAT reference, missense
rs121912939 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810], Ullrich congenital muscular dystrophy 1 (UCMD1) [MIM:254090] 45,989,617(+) GACCC(A/C/G)GGGAC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL6A1 Gene

Variant ID Type Subtype PubMed ID
dgv2416n106 CNV deletion 24896259
dgv254n21 CNV loss 19592680
dgv7919n54 CNV loss 21841781
dgv7920n54 CNV loss 21841781
esv1025241 CNV insertion 17803354
esv1396032 CNV insertion 17803354
esv1409667 CNV insertion 17803354
esv1561412 CNV insertion 17803354
esv2723849 CNV deletion 23290073
esv2723851 CNV deletion 23290073
esv2723852 CNV deletion 23290073
esv2723853 CNV deletion 23290073
esv3557859 CNV deletion 23714750
nsv1109448 CNV deletion 24896259
nsv1126010 CNV deletion 24896259
nsv1129227 CNV insertion 24896259
nsv470910 CNV gain 18288195
nsv509804 CNV insertion 20534489
nsv513579 CNV insertion 21212237
nsv587930 CNV loss 21841781
nsv587933 CNV loss 21841781
nsv587934 CNV loss 21841781
nsv587935 CNV gain 21841781
nsv953657 CNV deletion 24416366

Variation tolerance for COL6A1 Gene

Residual Variation Intolerance Score: 94.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.20; 95.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL6A1 Gene

Human Gene Mutation Database (HGMD)
COL6A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A1 Gene

Disorders for COL6A1 Gene

MalaCards: The human disease database

(23) MalaCards diseases for COL6A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bethlem myopathy 1
  • bethlem myopathy
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
collagen type vi-related disorders
diffuse idiopathic skeletal hyperostosis
  • ankylosing vertebral hyperostosis
myopathy
  • muscular diseases
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO6A1_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:11865138, ECO:0000269 PubMed:15689448, ECO:0000269 PubMed:15955946, ECO:0000269 PubMed:8782832}. 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, ECO:0000269 PubMed:16130093, ECO:0000269 PubMed:17785674}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL6A1

Genetic Association Database (GAD)
COL6A1
Human Genome Epidemiology (HuGE) Navigator
COL6A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL6A1
genes like me logo Genes that share disorders with COL6A1: view

No data available for Genatlas for COL6A1 Gene

Publications for COL6A1 Gene

  1. Single nucleotide polymorphism of COL6A1 in patients with ankylosing spondylitis. (PMID: 18634150) Kim T.H. … Jun J.B. (J. Rheumatol. 2008) 3 22 46 64
  2. COL6A1 polymorphisms associated with ossification of the ligamentum flavum and ossification of the posterior longitudinal ligament. (PMID: 18246005) Kong Q. … Chen Z. (Spine 2007) 3 22 46 64
  3. Dominant and recessive COL6A1 mutations in Ullrich scleroatonic muscular dystrophy. (PMID: 16130093) Giusti B. … Pepe G. (Ann. Neurol. 2005) 3 4 22 64
  4. COL6A1, the candidate gene for ossification of the posterior longitudinal ligament, is associated with diffuse idiopathic skeletal hyperostosis in Japanese. (PMID: 16227896) Tsukahara S. … Inoue I. (Spine 2005) 3 22 46 64
  5. New molecular mechanism for Ullrich congenital muscular dystrophy: a heterozygous in-frame deletion in the COL6A1 gene causes a severe phenotype. (PMID: 12840783) Pan T.C. … Chu M.L. (Am. J. Hum. Genet. 2003) 3 22 46 64

Products for COL6A1 Gene

  • Cloud-Clone Corp. Antibodies for COL6A1
  • Cloud-Clone Corp. Proteins for COL6A1
  • Cloud-Clone Corp Assay Kits for COL6A1

Sources for COL6A1 Gene

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