This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcri... See more...

Aliases for COL6A5 Gene

Aliases for COL6A5 Gene

  • Collagen Type VI Alpha 5 Chain 2 3 5
  • VWA4 2 3 4
  • Von Willebrand Factor A Domain-Containing Protein 4 3 4
  • Collagen, Type XXIX, Alpha 1 2 3
  • Collagen, Type VI, Alpha 5 2 3
  • Collagen Alpha-5(VI) Chain 3 4
  • COL29A1 3 4
  • Von Willebrand Factor A Domain Containing 4 2
  • Collagen Alpha-1(XXIX) Chain 4
  • Collagen Type VI Alpha 5 2
  • FLJ35880 2
  • COL6A5 5

External Ids for COL6A5 Gene

Previous HGNC Symbols for COL6A5 Gene

  • COL29A1

Previous GeneCards Identifiers for COL6A5 Gene

  • GC03P130065
  • GC03P127449

Summaries for COL6A5 Gene

Entrez Gene Summary for COL6A5 Gene

  • This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

GeneCards Summary for COL6A5 Gene

COL6A5 (Collagen Type VI Alpha 5 Chain) is a Protein Coding gene. Diseases associated with COL6A5 include Chronic Dacryoadenitis and Dermatitis. Among its related pathways are Collagen chain trimerization and Signaling by GPCR. An important paralog of this gene is COL6A6.

UniProtKB/Swiss-Prot Summary for COL6A5 Gene

Additional gene information for COL6A5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL6A5 Gene

Genomics for COL6A5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COL6A5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J130342 Promoter 0.9 Ensembl 600.7 +0.4 384 0.6 ZIC2 EZH2 SCRT2 HMBOX1 CTBP1 ZBTB26 MYC SCRT1 NCOR1 NFIC COL6A5 COL6A4P2 piR-39006 COL6A6
GH03J130354 Enhancer 0.8 FANTOM5 Ensembl 5.5 +9.1 9085 1.6 ZNF512 PKNOX1 YBX3 ZNF184 ZBTB2 EP400 ZC3H8 TBP SPI1 SMAD5 COL6A5 COL6A4P2 ATP2C1 piR-39006 COL6A6
GH03J130414 Enhancer 0.3 Ensembl 12.3 +69.4 69385 1 SPI1 MAX COL6A5 piR-39006 piR-51354-003 COL6A6
GH03J130395 Enhancer 0.7 Ensembl ENCODE 4.8 +50.4 50434 1.7 TEAD4 RFX1 OSR2 ESRRA FOSL2 JUN FOS JUND SMARCE1 COL6A5 piR-39006 COL6A6
GH03J130427 Enhancer 0.5 Ensembl 4.4 +84.2 84185 1 TEAD4 ZNF184 ZNF189 CBX8 GATA2 COL6A5 piR-51354-003 piR-39006 COL6A6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL6A5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL6A5

Genomic Locations for COL6A5 Gene

Genomic Locations for COL6A5 Gene
chr3:130,345,516-130,484,846
(GRCh38/hg38)
Size:
139,331 bases
Orientation:
Plus strand
chr3:130,064,359-130,203,688
(GRCh37/hg19)
Size:
139,330 bases
Orientation:
Plus strand

Genomic View for COL6A5 Gene

Genes around COL6A5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A5 Gene

Proteins for COL6A5 Gene

  • Protein details for COL6A5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A8TX70-CO6A5_HUMAN
    Recommended name:
    Collagen alpha-5(VI) chain
    Protein Accession:
    A8TX70
    Secondary Accessions:
    • A9J6L2
    • A9J6L4
    • A9J6L6
    • A9J6L7
    • A9J6M0
    • A9J6M1
    • A9J6M2
    • B5MEA7
    • Q6ZW26
    • Q8NA36

    Protein attributes for COL6A5 Gene

    Size:
    2615 amino acids
    Molecular mass:
    289926 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).
    SequenceCaution:
    • Sequence=BAC04092.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC04092.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAC85681.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for COL6A5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL6A5 Gene

Post-translational modifications for COL6A5 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 Asn201, Asn260, Asn835, and Asn2509
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A5 Gene

Domains & Families for COL6A5 Gene

Gene Families for COL6A5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for COL6A5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for COL6A5 Gene

GenScript: Design optimal peptide antigens:
  • von Willebrand factor A domain-containing protein 4 (CO6A5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A8TX70

UniProtKB/Swiss-Prot:

CO6A5_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 COL6A5: view

Function for COL6A5 Gene

Molecular function for COL6A5 Gene

UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein.

Phenotypes From GWAS Catalog for COL6A5 Gene

Gene Ontology (GO) - Molecular Function for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19478074
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 28675934
genes like me logo Genes that share ontologies with COL6A5: view
genes like me logo Genes that share phenotypes with COL6A5: view

Animal Model Products

CRISPR Products

miRNA for COL6A5 Gene

miRTarBase miRNAs that target COL6A5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL6A5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COL6A5 Gene

Localization for COL6A5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A5 Gene

Secreted, extracellular space, extracellular matrix. Note=Deposed in the extracellular matrix of skeletal muscle. {ECO:0000250}.

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 COL6A5 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA,TAS --
GO:0005581 collagen trimer IEA --
GO:0062023 collagen-containing extracellular matrix ISS,HDA 28344315
genes like me logo Genes that share ontologies with COL6A5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL6A5 Gene

Pathways & Interactions for COL6A5 Gene

genes like me logo Genes that share pathways with COL6A5: view

Gene Ontology (GO) - Biological Process for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with COL6A5: view

No data available for SIGNOR curated interactions for COL6A5 Gene

Drugs & Compounds for COL6A5 Gene

No Compound Related Data Available

Transcripts for COL6A5 Gene

mRNA/cDNA for COL6A5 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL6A5

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A5 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1:
SP2: - -

Relevant External Links for COL6A5 Gene

GeneLoc Exon Structure for
COL6A5

Expression for COL6A5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COL6A5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL6A5 Gene

This gene is overexpressed in Lung (x24.1), Testis (x10.1), and Skin - Not Sun Exposed (Suprapubic) (x6.6).

Protein differential expression in normal tissues from HIPED for COL6A5 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (57.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for COL6A5 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL6A5

SOURCE GeneReport for Unigene cluster for COL6A5 Gene:

Hs.205403

mRNA Expression by UniProt/SwissProt for COL6A5 Gene:

A8TX70-CO6A5_HUMAN
Tissue specificity: Expressed in skin, followed by lung, small intestine, colon and testis. In skin, it is expressed in the epidermis with strongest staining in suprabasal viable layers. In ATOD patients, it is absent in the most differentiated upper spinous and granular layers (at protein level).

Evidence on tissue expression from TISSUES for COL6A5 Gene

  • Lung(4.5)
  • Skin(4.4)
genes like me logo Genes that share expression patterns with COL6A5: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A5 Gene

Orthologs for COL6A5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL6A5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia COL6A5 30 31
  • 99.12 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia COL6A5 30 31
  • 83.55 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Col6a5 30 17 31
  • 78.89 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Col6a5 30
  • 77.67 (n)
Cow
(Bos Taurus)
Mammalia COL6A5 31
  • 74 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 54 (a)
OneToMany
-- 31
  • 51 (a)
OneToMany
-- 31
  • 48 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia COL6A5 31
  • 30 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 33 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 21 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia col6a6 30
  • 54.36 (n)
Zebrafish
(Danio rerio)
Actinopterygii col6a6 31
  • 30 (a)
ManyToMany
Species where no ortholog for COL6A5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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 COL6A5 Gene

ENSEMBL:
Gene Tree for COL6A5 (if available)
TreeFam:
Gene Tree for COL6A5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COL6A5: view image

Paralogs for COL6A5 Gene

Paralogs for COL6A5 Gene

(8) SIMAP similar genes for COL6A5 Gene using alignment to 6 proteins:

  • CO6A5_HUMAN
  • E9PAL5_HUMAN
  • F8W8G8_HUMAN
  • H0Y393_HUMAN
  • H0Y935_HUMAN
  • H0Y9T2_HUMAN
genes like me logo Genes that share paralogs with COL6A5: view

Variants for COL6A5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL6A5 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
771353 Benign: not provided 130,376,649(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
781840 Benign: not provided 130,388,639(+) A/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
781841 Benign: not provided 130,469,277(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
912021 Benign: COL6A5 POLYMORPHISM 130,468,818(+) G/T NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
rs1553749041 Uncertain Significance: not provided 130,389,072(+) AG/A FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for COL6A5 Gene

Structural Variations from Database of Genomic Variants (DGV) for COL6A5 Gene

Variant ID Type Subtype PubMed ID
dgv301e215 CNV deletion 23714750
dgv8588n54 CNV loss 21841781
dgv8589n54 CNV loss 21841781
dgv8590n54 CNV loss 21841781
esv23758 CNV loss 19812545
esv2662769 CNV deletion 23128226
esv2665713 CNV deletion 23128226
esv3305478 CNV mobile element insertion 20981092
esv3376350 CNV insertion 20981092
esv34166 CNV loss 18971310
esv3597762 CNV loss 21293372
esv3597766 CNV loss 21293372
esv3597767 CNV loss 21293372
esv3597769 CNV loss 21293372
esv3597770 CNV loss 21293372
nsv1005410 CNV loss 25217958
nsv437854 CNV loss 16327808
nsv437881 CNV loss 16468122
nsv460854 CNV loss 19166990
nsv515803 CNV loss 19592680
nsv526814 CNV gain 19592680
nsv591719 CNV loss 21841781
nsv591722 CNV loss 21841781
nsv591723 CNV loss 21841781

Variation tolerance for COL6A5 Gene

Gene Damage Index Score: 24.99; 99.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL6A5 Gene

Human Gene Mutation Database (HGMD)
COL6A5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A5 Gene

Disorders for COL6A5 Gene

MalaCards: The human disease database

(6) MalaCards diseases for COL6A5 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO6A5_HUMAN
  • Note=Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.

Additional Disease Information for COL6A5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with COL6A5: view

No data available for Genatlas for COL6A5 Gene

Publications for COL6A5 Gene

  1. Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis. (PMID: 17850181) Söderhäll C … Lee YA (PLoS biology 2007) 2 3 4
  2. The expanded collagen VI family: new chains and new questions. (PMID: 23869615) Fitzgerald J … Hansen U (Connective tissue research 2013) 2 3
  3. Three novel collagen VI chains with high homology to the alpha3 chain. (PMID: 18276594) Gara SK … Wagener R (The Journal of biological chemistry 2008) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Atopic Eczema: Genetic Analysis of COL6A5, COL8A1, and COL10A1 in Mediterranean Populations. (PMID: 31275967) Strafella C … Giardina E (BioMed research international 2019) 3

Products for COL6A5 Gene

Sources for COL6A5 Gene