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Aliases for COL6A2 Gene

Aliases for COL6A2 Gene

  • Collagen Type VI Alpha 2 Chain 2 3 5
  • Human MRNA For Collagen VI Alpha-2 C-Terminal Globular Domain 3
  • Collagen VI, Alpha-2 Polypeptide 3
  • Collagen Alpha-2(VI) Chain 3
  • Collagen, Type VI, Alpha 2 3
  • Collagen Type VI Alpha 2 2
  • BTHLM1 3
  • PP3610 3
  • UCMD1 3

External Ids for COL6A2 Gene

Previous GeneCards Identifiers for COL6A2 Gene

  • GC21P044024
  • GC21P046374
  • GC21P046342
  • GC21P047518
  • GC21P032899

Summaries for COL6A2 Gene

Entrez Gene Summary for COL6A2 Gene

  • This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. 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 this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL6A2 Gene

COL6A2 (Collagen Type VI Alpha 2 Chain) is a Protein Coding gene. Diseases associated with COL6A2 include Ullrich Congenital Muscular Dystrophy 1 and Myosclerosis, Congenital. Among its related pathways are Collagen chain trimerization and Phospholipase-C Pathway. An important paralog of this gene is COL6A1.

UniProtKB/Swiss-Prot for COL6A2 Gene

  • Collagen VI acts as a cell-binding protein.

Gene Wiki entry for COL6A2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A2 Gene

Genomics for COL6A2 Gene

Regulatory Elements for COL6A2 Gene

Enhancers for COL6A2 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 7.9 -124.7 -124656 5.6 PKNOX1 ARID4B ZNF2 ZNF48 GLIS2 ZNF143 KLF7 FOS SP3 REST COL6A1 PCBP3 COL6A2 LSS SPATC1L LOC101928796 ENSG00000280604
GH21G046048 1.8 FANTOM5 Ensembl ENCODE dbSUPER 6.9 -39.1 -39077 19.8 CBX3 ZNF473 AGO1 ZSCAN4 INSM2 KLF17 RAD21 ETS1 CBX5 ZNF350 ENSG00000228137 MCM3AP MCM3AP-AS1 DSTNP1 ENSG00000215447 LINC00205 COL6A1 ENSG00000227438 LOC100129027 COL6A2
GH21G046091 1.6 FANTOM5 Ensembl ENCODE dbSUPER 6.8 -4.8 -4832 3.4 CTCF ZNF473 ZNF175 YBX1 ZKSCAN1 ZNF791 POLR2A FOS MAFK HES1 ENSG00000227438 ENSG00000228137 MCM3AP DSTNP1 MCM3AP-AS1 COL6A2 FTCD COL6A1 PIR33401
GH21G046096 1.1 ENCODE dbSUPER 7.1 +1.4 1392 4.8 ZSCAN4 RAD21 ZNF121 SCRT2 ZNF207 FOS SP3 ZNF398 AEBP2 IKZF1 COL6A2 FTCD ENSG00000227438 GC21P046125
GH21G046115 1 ENCODE dbSUPER 7.8 +20.1 20129 4.5 CTCF KLF1 ZSCAN4 KLF17 ZIC2 ZFHX2 CTBP1 ZNF207 RCOR1 KLF8 FTCD FTCD-AS1 COL6A2 SPATC1L GC21P046125
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL6A2 on UCSC Golden Path with GeneCards custom track

Promoters for COL6A2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000143349 1194 2401 CTCF MAZ PHF8 SP3 ZNF398 ZBTB7A RAD21 ZFHX2 POLR2A GLIS1

Genomic Location for COL6A2 Gene

Chromosome:
21
Start:
46,097,606 bp from pter
End:
46,132,849 bp from pter
Size:
35,244 bases
Orientation:
Plus strand

Genomic View for COL6A2 Gene

Genes around COL6A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A2 Gene

Proteins for COL6A2 Gene

  • Protein details for COL6A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P12110-CO6A2_HUMAN
    Recommended name:
    Collagen alpha-2(VI) chain
    Protein Accession:
    P12110
    Secondary Accessions:
    • Q13909
    • Q13910
    • Q13911
    • Q14048
    • Q14049
    • Q16259
    • Q16597
    • Q6P0Q1
    • Q9UML3
    • Q9Y4S8

    Protein attributes for COL6A2 Gene

    Size:
    1019 amino acids
    Molecular mass:
    108579 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). Interacts with CSPG4.

    Alternative splice isoforms for COL6A2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL6A2 Gene

Post-translational modifications for COL6A2 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 Asn140, Asn327, posLast=630630, posLast=785785, Asn897, and Asn954
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A2 Gene

Domains & Families for COL6A2 Gene

Gene Families for COL6A2 Gene

Suggested Antigen Peptide Sequences for COL6A2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P12110

UniProtKB/Swiss-Prot:

CO6A2_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 COL6A2: view

Function for COL6A2 Gene

Molecular function for COL6A2 Gene

GENATLAS Biochemistry:
collagen type VI,alpha 2 (140kDa),microfibrillar
UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein.

Gene Ontology (GO) - Molecular Function for COL6A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12812986
genes like me logo Genes that share ontologies with COL6A2: view
genes like me logo Genes that share phenotypes with COL6A2: view

Human Phenotype Ontology for COL6A2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL6A2 Gene

MGI Knock Outs for COL6A2:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COL6A2 Gene

Localization for COL6A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A2 Gene

Secreted, extracellular space, extracellular matrix. Membrane; Peripheral membrane protein. Note=Recruited on membranes by CSPG4.

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 COL6A2 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 3
cytosol 2
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for COL6A2 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:0005615 extracellular space IDA 20551380
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL6A2: view

Pathways & Interactions for COL6A2 Gene

genes like me logo Genes that share pathways with COL6A2: view

Gene Ontology (GO) - Biological Process for COL6A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0009749 response to glucose IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
GO:0070208 protein heterotrimerization IPI 18400749
genes like me logo Genes that share ontologies with COL6A2: view

No data available for SIGNOR curated interactions for COL6A2 Gene

Drugs & Compounds for COL6A2 Gene

(1) Drugs for COL6A2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with COL6A2: view

Transcripts for COL6A2 Gene

Unigene Clusters for COL6A2 Gene

Collagen, type VI, alpha 2:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^
SP1:
SP2:
SP3:
SP4:
SP5: - -
SP6:
SP7:
SP8: -

ExUns: 26a · 26b ^ 27
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for COL6A2 Gene

GeneLoc Exon Structure for
COL6A2
ECgene alternative splicing isoforms for
COL6A2

Expression for COL6A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL6A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL6A2 Gene

This gene is overexpressed in Adipocyte (15.2), Urinary Bladder (9.7), Bone marrow mesenchymal stem cell (8.6), Colon muscle (8.5), and Gallbladder (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL6A2 Gene



Protein tissue co-expression partners for COL6A2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COL6A2 Gene:

COL6A2

SOURCE GeneReport for Unigene cluster for COL6A2 Gene:

Hs.420269

Evidence on tissue expression from TISSUES for COL6A2 Gene

  • Lung(4.7)
  • Liver(4.3)
  • Bone(4.2)
  • Skin(3.9)
  • Nervous system(3.8)
  • Eye(3.4)
  • Heart(3.1)
  • Intestine(3.1)
  • Muscle(3.1)
  • Pancreas(2.9)
  • Gall bladder(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A2 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 COL6A2: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for COL6A2 Gene

Orthologs for COL6A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL6A2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL6A2 34 35
  • 98.95 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 91 (a)
OneToMany
-- 35
  • 83 (a)
OneToMany
cow
(Bos Taurus)
Mammalia COL6A2 35
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col6a2 34
  • 85.51 (n)
mouse
(Mus musculus)
Mammalia Col6a2 34 16 35
  • 85.38 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COL6A2 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL6A2 34 35
  • 69.9 (n)
lizard
(Anolis carolinensis)
Reptilia COL6A2 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100145523 34
  • 63.25 (n)
Str.15727 34
zebrafish
(Danio rerio)
Actinopterygii col6a2 34 35
  • 62.08 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2562 34
worm
(Caenorhabditis elegans)
Secernentea mec-5 35
  • 40 (a)
OneToMany
Species where no ortholog for COL6A2 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 COL6A2 Gene

ENSEMBL:
Gene Tree for COL6A2 (if available)
TreeFam:
Gene Tree for COL6A2 (if available)

Paralogs for COL6A2 Gene

Paralogs for COL6A2 Gene

(14) SIMAP similar genes for COL6A2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with COL6A2: view

Variants for COL6A2 Gene

Sequence variations from dbSNP and Humsavar for COL6A2 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs117725825 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 46,132,287(+) CAGCC(C/T)GCGTG nc-transcript-variant, reference, missense
rs121912940 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 46,115,881(+) CCAAG(A/G)GCAAC nc-transcript-variant, reference, missense
rs267606747 Pathogenic, Bethlem myopathy 1 (BTHLM1) [MIM:158810] 46,126,144(+) TCGCC(C/T)GCGAC nc-transcript-variant, reference, missense
rs267606748 Pathogenic, Ullrich congenital muscular dystrophy 1 (UCMD1) [MIM:254090] 46,115,917(+) AGAAG(A/G)GAAGA nc-transcript-variant, reference, missense
rs267606749 Pathogenic, Ullrich congenital muscular dystrophy 1 (UCMD1) [MIM:254090] 46,121,590(+) ACCCC(A/G)TGGAG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL6A2 Gene

Variant ID Type Subtype PubMed ID
dgv255n21 CNV gain 19592680
dgv7921n54 CNV loss 21841781
esv1002133 CNV deletion 20482838
esv1003876 CNV insertion 20482838
esv1007380 CNV gain 20482838
esv1216777 CNV insertion 17803354
esv1546631 CNV insertion 17803354
esv2723889 CNV deletion 23290073
esv2723890 CNV deletion 23290073
esv2723891 CNV deletion 23290073
esv3647161 CNV gain 21293372
esv3647162 CNV gain 21293372
esv995411 CNV insertion 20482838
nsv1060978 CNV gain 25217958
nsv1061087 CNV loss 25217958
nsv1126616 CNV deletion 24896259
nsv187077 CNV insertion 16902084
nsv187142 CNV deletion 16902084
nsv459311 CNV loss 19166990
nsv470910 CNV gain 18288195
nsv470911 CNV loss 18288195
nsv509804 CNV insertion 20534489
nsv525728 CNV loss 19592680
nsv587943 CNV loss 21841781
nsv587944 CNV loss 21841781
nsv587946 CNV loss 21841781
nsv587947 CNV loss 21841781
nsv587948 CNV loss 21841781
nsv587950 CNV loss 21841781
nsv587951 CNV loss 21841781
nsv587952 CNV loss 21841781
nsv587953 CNV loss 21841781
nsv953658 CNV deletion 24416366

Variation tolerance for COL6A2 Gene

Residual Variation Intolerance Score: 89% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.65; 97.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL6A2 Gene

Human Gene Mutation Database (HGMD)
COL6A2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A2 Gene

Disorders for COL6A2 Gene

MalaCards: The human disease database

(11) MalaCards diseases for COL6A2 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
myosclerosis, congenital
  • myosclerosis, autosomal recessive
bethlem myopathy 1
  • bethlem myopathy
collagen type vi-related disorders
autosomal recessive myosclerosis myopathy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO6A2_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:17886299, ECO:0000269 PubMed:8782832}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Myosclerosis autosomal recessive (MYOSAR) [MIM:255600]: A condition characterized by chronic inflammation of skeletal muscle with hyperplasia of the interstitial connective tissue. The clinical picture includes slender muscles with firm woody consistency and restriction of movement of many joints because of muscle contractures. 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:15563506, ECO:0000269 PubMed:15689448}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL6A2

Genetic Association Database (GAD)
COL6A2
Human Genome Epidemiology (HuGE) Navigator
COL6A2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL6A2
genes like me logo Genes that share disorders with COL6A2: view

No data available for Genatlas for COL6A2 Gene

Publications for COL6A2 Gene

  1. Dominant collagen VI mutations are a common cause of Ullrich congenital muscular dystrophy. (PMID: 15563506) Baker N.L. … Lamande S.R. (Hum. Mol. Genet. 2005) 3 4 22 64
  2. The expanded collagen VI family: new chains and new questions. (PMID: 23869615) Fitzgerald J. … Hansen U. (Connect. Tissue Res. 2013) 2 3 64
  3. Identification of a deep intronic mutation in the COL6A2 gene by a novel custom oligonucleotide CGH array designed to explore allelic and genetic heterogeneity in collagen VI-related myopathies. (PMID: 20302629) Bovolenta M. … Gualandi F. (BMC Med. Genet. 2010) 3 22 64
  4. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PMID: 19204726) Chapuis J. … Lambert J.C. (Mol. Psychiatry 2009) 3 46 64
  5. 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 22 64

Products for COL6A2 Gene

Sources for COL6A2 Gene

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