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Aliases for COL6A1 Gene

Aliases for COL6A1 Gene

  • Collagen Type VI Alpha 1 2 3
  • Collagen, Type VI, Alpha 1 2 3 5
  • Collagen VI, Alpha-1 Polypeptide 3
  • Alpha 1 (VI) Chain (61 AA) 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) is a Protein Coding gene. Diseases associated with COL6A1 include ullrich congenital muscular dystrophy 1 and bethlem myopathy 1. Among its related pathways are Degradation of the extracellular matrix and Signaling by GPCR. GO annotations related to this gene include platelet-derived growth factor binding. An important paralog of this gene is COL28A1.

UniProtKB/Swiss-Prot for COL6A1 Gene

  • Collagen VI acts as a cell-binding protein.

Gene Wiki entry for COL6A1 Gene

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

Genomics for COL6A1 Gene

Regulatory Elements for COL6A1 Gene

Promoters for COL6A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL6A1 on UCSC Golden Path with GeneCards custom track

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 StructureGene Density

RefSeq DNA sequence for COL6A1 Gene

Proteins for COL6A1 Gene

  • 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

Proteomics data for COL6A1 Gene at MOPED

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 Asn 212, Asn 516, Asn 537, Asn 804, and Asn 896
  • Modification sites at PhosphoSitePlus

Other Protein References for COL6A1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for COL6A1 Gene

Domains & Families for COL6A1 Gene

Gene Families for COL6A1 Gene

Graphical View of Domain Structure for InterPro Entry

P12109

UniProtKB/Swiss-Prot:

CO6A1_HUMAN :
  • Contains 3 VWFA domains.
  • Belongs to the type VI collagen family.
Domain:
  • Contains 3 VWFA domains.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A1: view

Function for COL6A1 Gene

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.
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for COL6A1 Gene COMPARTMENTS Subcellular localization image for COL6A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
lysosome 5
vacuole 5
cytosol 3
plasma membrane 3
mitochondrion 2
cytoskeleton 1
nucleus 1

Gene Ontology (GO) - Cellular Components for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0043234 protein complex IPI 18400749
GO:0070062 extracellular exosome IDA 19056867
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:0007155 cell adhesion IEA --
GO:0007411 axon guidance TAS --
GO:0022617 extracellular matrix disassembly TAS --
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

(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

Unigene Clusters for COL6A1 Gene

Collagen, type VI, alpha 1:
Representative Sequences:

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

mRNA expression in normal human tissues 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, MOPED, and MaxQB for COL6A1 Gene



SOURCE GeneReport for Unigene cluster for COL6A1 Gene Hs.474053

genes like me logo Genes that share expression patterns with COL6A1: view

Protein tissue co-expression partners for COL6A1 Gene

- Elite partner

Primer Products

In Situ Assay 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 35
  • 99.12 (n)
  • 99.12 (a)
COL6A1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL6A1 36
  • 91 (a)
OneToOne
COL6A1 35
  • 87.44 (n)
  • 91.52 (a)
dog
(Canis familiaris)
Mammalia COL6A1 35
  • 88.37 (n)
  • 91.23 (a)
COL6A1 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a1 36
  • 90 (a)
OneToOne
Col6a1 16
Col6a1 35
  • 83.15 (n)
  • 90.31 (a)
oppossum
(Monodelphis domestica)
Mammalia COL6A1 36
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL6A1 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col6a1 35
  • 83.61 (n)
  • 89.81 (a)
chicken
(Gallus gallus)
Aves COL6A1 36
  • 69 (a)
OneToOne
COL6A1 35
  • 70.63 (n)
  • 70.3 (a)
lizard
(Anolis carolinensis)
Reptilia COL6A1 36
  • 69 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia col6a1-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a1 35
  • 63.12 (n)
  • 64.94 (a)
zebrafish
(Danio rerio)
Actinopterygii col6a1 36
  • 55 (a)
OneToOne
col6a1 35
  • 59.8 (n)
  • 56.97 (a)
worm
(Caenorhabditis elegans)
Secernentea mec-5 36
  • 39 (a)
OneToMany
Species with no ortholog for COL6A1:
  • 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
VAR_013580 Bethlem myopathy 1 (BTHLM1)
VAR_013581 Bethlem myopathy 1 (BTHLM1)
VAR_013582 Bethlem myopathy 1 (BTHLM1)
rs35059000 - 45,992,791(-) GTCCC(C/T)GCGTG reference, missense
rs1053312 - 46,003,475(+) CAAGC(A/G)CTTCG reference, missense

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

Variant ID Type Subtype PubMed ID
nsv914079 CNV Loss 21882294
nsv914083 CNV Loss 21882294
nsv509804 CNV Insertion 20534489
dgv4805n71 CNV Loss 21882294
nsv470910 CNV Gain 18288195
nsv914088 CNV Loss 21882294
dgv4806n71 CNV Loss 21882294
esv2723849 CNV Deletion 23290073
esv2723851 CNV Deletion 23290073
esv1409667 CNV Insertion 17803354
esv1025241 CNV Insertion 17803354
esv2723852 CNV Deletion 23290073
esv2723853 CNV Deletion 23290073
esv1561412 CNV Insertion 17803354
dgv4807n71 CNV Loss 21882294
dgv4808n71 CNV Loss 21882294
nsv914095 CNV Loss 21882294
dgv254n21 CNV Loss 19592680
nsv513579 CNV Insertion 21212237
esv1396032 CNV Insertion 17803354

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

HapMap Linkage Disequilibrium report
COL6A1
Human Gene Mutation Database (HGMD)
COL6A1

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

Disorders for COL6A1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
bethlem myopathy 1
  • bethlem myopathy
myosclerosis, congenital
  • myosclerosis, autosomal recessive
dystonia 27
  • dyt27
collagen type vi-related disorders
- 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}. 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. 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 23 48 67
  2. Identification and characterization of novel collagen VI non-canonical splicing mutations causing Ullrich congenital muscular dystrophy. (PMID: 19309692) Martoni E. … Gualandi F. (Hum. Mutat. 2009) 3 23
  3. Exon skipping mutations in collagen VI are common and are predictive for severity and inheritance. (PMID: 18366090) Lampe A.K. … BAPnnemann C.G. (Hum. Mutat. 2008) 3 23
  4. Single nucleotide polymorphism of COL6A1 in patients with ankylosing spondylitis. (PMID: 18634150) Kim T.H. … Jun J.B. (J. Rheumatol. 2008) 3 23
  5. Faithful tissue-specific expression of the human chromosome 21-linked COL6A1 gene in BAC-transgenic mice. (PMID: 17334655) Xing L. … Tycko B. (Mamm. Genome 2007) 3 23

Products for COL6A1 Gene

Sources for COL6A1 Gene

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