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    COL6A6 collagen type VI alpha 6 chain [ Homo sapiens (human) ]

    Gene ID: 131873, updated on 3-Nov-2024

    Summary

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    Official Symbol
    COL6A6provided by HGNC
    Official Full Name
    collagen type VI alpha 6 chainprovided by HGNC
    Primary source
    HGNC:HGNC:27023
    See related
    Ensembl:ENSG00000206384 MIM:616613; AllianceGenome:HGNC:27023
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a large protein that contains multiple von Willebrand factor domains and forms a component of the basal lamina of epithelial cells. This protein may regulate epithelial cell-fibronectin interactions. Variation in this gene may be implicated in skin diseases. [provided by RefSeq, May 2017]
    Expression
    Biased expression in lung (RPKM 3.3), fat (RPKM 0.9) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL6A6 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (130516720..130677042)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (133260574..133420884)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (130236021..130395886)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATP5MC2 pseudogene 5 Neighboring gene collagen type VI alpha 5 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:130126750-130127949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:130161092-130161649 Neighboring gene MPRA-validated peak4833 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14733 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:130297667-130297916 Neighboring gene phosphoinositide-3-kinase regulatory subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14734 Neighboring gene uncharacterized LOC107986023 Neighboring gene RN7SK pseudogene 212

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. New COL6A6 Variant Causes Autosomal Dominant Retinitis Pigmentosa in a Four-Generation Family. Vaclavik V, et al. Invest Ophthalmol Vis Sci, 2022 Mar 2. PMID 35333290, Free PMC Article
    2. Identification of novel candidate variants including COL6A6 polymorphisms in early-onset atopic dermatitis using whole-exome sequencing. Heo WI, et al. BMC Med Genet, 2017 Jan 26. PMID 28125976, Free PMC Article
    3. Collagen VI is a basement membrane component that regulates epithelial cell-fibronectin interactions. Groulx JF, et al. Matrix Biol, 2011 Apr. PMID 21406227
    4. Defective collagen VI α6 chain expression in the skeletal muscle of patients with collagen VI-related myopathies. Tagliavini F, et al. Biochim Biophys Acta, 2014 Sep. PMID 24907562, Free PMC Article
    5. Expression of the collagen VI α5 and α6 chains in normal human skin and in skin of patients with collagen VI-related myopathies. Sabatelli P, et al. J Invest Dermatol, 2011 Jan. PMID 20882040

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. New COL6A6 Variant Causes Autosomal Dominant Retinitis Pigmentosa in a Four-Generation Family.
      Title: New COL6A6 Variant Causes Autosomal Dominant Retinitis Pigmentosa in a Four-Generation Family.
    2. Whole-genome sequencing reveals possible role of deleterious mutation of COL6A6 in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
      Title: Whole-genome sequencing reveals novel genes in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
    3. Study identified SNPs in COL6A6 associated with atopic dermatitis suggesting that COL6A6 variants may constitute candidate risk factors for early-onset atopic dermatitis.
      Title: Identification of novel candidate variants including COL6A6 polymorphisms in early-onset atopic dermatitis using whole-exome sequencing.
    4. A whole-exome sequencing approach led to identification of a deletion in RHO through detection of a new linked variant in COL6A6 in autosomal dominant retinitis pigmentosa.
      Title: New COL6A6 variant detected by whole-exome sequencing is linked to break points in intron 4 and 3'-UTR, deleting exon 5 of RHO, and causing adRP.
    5. Reduced collagen VI alpha6 chain expression in the skeletal muscle is associated with collagen VI-related myopathies.
      Title: Defective collagen VI α6 chain expression in the skeletal muscle of patients with collagen VI-related myopathies.
    6. The collagen VI alpha6 chain, but not the alpha5 chain, is up-regulated in dystrophic muscles.
      Title: Expression of collagen VI α5 and α6 chains in human muscle and in Duchenne muscular dystrophy-related muscle fibrosis.
    7. collagen VI alpha 6 is an important basal lamina component involved in the regulation of epithelial cell behavior most notably as a regulator of epithelial cell-fibronectin interactions
      Title: Collagen VI is a basement membrane component that regulates epithelial cell-fibronectin interactions.
    8. localization of alpha5, and to a lesser extent alpha6, is restricted to the papillary dermis, where the protein mainly colocalizes with collagen fibrils; both chains were found around blood vessels
      Title: Expression of the collagen VI α5 and α6 chains in normal human skin and in skin of patients with collagen VI-related myopathies.
    9. The discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix.
      Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-6(VI) chain
    Names
    collagen, type VI, alpha 6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_054914.1 RefSeqGene

      Range
      5469..165334
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001102608.3 → NP_001096078.1  collagen alpha-6(VI) chain precursor

      See identical proteins and their annotated locations for NP_001096078.1

      Status: REVIEWED

      Source sequence(s)
      AC093006, AC117398, AC128683
      Consensus CDS
      CCDS46911.1
      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Related
      ENSP00000351310.6, ENST00000358511.11
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      130516720..130677042
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017005713.3 → XP_016861202.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    2. XM_017005711.3 → XP_016861200.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    3. XM_011512426.4 → XP_011510728.1  collagen alpha-6(VI) chain isoform X2

      See identical proteins and their annotated locations for XP_011510728.1

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    4. XM_005247121.6 → XP_005247178.1  collagen alpha-6(VI) chain isoform X2

      See identical proteins and their annotated locations for XP_005247178.1

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    5. XM_011512424.3 → XP_011510726.1  collagen alpha-6(VI) chain isoform X1

      See identical proteins and their annotated locations for XP_011510726.1

      Conserved Domains (6) summary
      pfam01391
      Location:1474 → 1531
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1222 → 1361
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:451 → 609
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1980 → 2158
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:638 → 806
      VWA; von Willebrand factor type A domain
      cl00057
      Location:42 → 208
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    6. XM_011512431.3 → XP_011510733.1  collagen alpha-6(VI) chain isoform X3

      Conserved Domains (5) summary
      pfam01391
      Location:1474 → 1531
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1222 → 1361
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:451 → 609
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      pfam00092
      Location:638 → 806
      VWA; von Willebrand factor type A domain
      cl00057
      Location:42 → 208
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    7. XM_017005716.2 → XP_016861205.1  collagen alpha-6(VI) chain isoform X4

    8. XM_011512432.3 → XP_011510734.1  collagen alpha-6(VI) chain isoform X5

      Conserved Domains (5) summary
      pfam01391
      Location:1474 → 1531
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1222 → 1361
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:451 → 609
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      pfam00092
      Location:638 → 806
      VWA; von Willebrand factor type A domain
      cl00057
      Location:42 → 208
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    9. XM_017005712.3 → XP_016861201.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    10. XM_047447448.1 → XP_047303404.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0

    11. XM_047447445.1 → XP_047303401.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0

    12. XM_047447447.1 → XP_047303403.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0

    13. XM_017005714.3 → XP_016861203.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
      Conserved Domains (6) summary
      pfam01391
      Location:1458 → 1515
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1206 → 1345
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:435 → 593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1964 → 2142
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam00092
      Location:622 → 790
      VWA; von Willebrand factor type A domain
      cl00057
      Location:26 → 192
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    14. XM_047447446.1 → XP_047303402.1  collagen alpha-6(VI) chain isoform X2

      UniProtKB/Swiss-Prot
      A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0

    RNA

    1. XR_924103.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      133260574..133420884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345237.1 → XP_054201212.1  collagen alpha-6(VI) chain isoform X2

    2. XM_054345236.1 → XP_054201211.1  collagen alpha-6(VI) chain isoform X2

    3. XM_054345240.1 → XP_054201215.1  collagen alpha-6(VI) chain isoform X2

    4. XM_054345241.1 → XP_054201216.1  collagen alpha-6(VI) chain isoform X2

    5. XM_054345233.1 → XP_054201208.1  collagen alpha-6(VI) chain isoform X1

    6. XM_054345244.1 → XP_054201219.1  collagen alpha-6(VI) chain isoform X3

    7. XM_054345245.1 → XP_054201220.1  collagen alpha-6(VI) chain isoform X4

    8. XM_054345246.1 → XP_054201221.1  collagen alpha-6(VI) chain isoform X5

    9. XM_054345234.1 → XP_054201209.1  collagen alpha-6(VI) chain isoform X2

    10. XM_054345243.1 → XP_054201218.1  collagen alpha-6(VI) chain isoform X2

    11. XM_054345238.1 → XP_054201213.1  collagen alpha-6(VI) chain isoform X2

    12. XM_054345242.1 → XP_054201217.1  collagen alpha-6(VI) chain isoform X2

    13. XM_054345239.1 → XP_054201214.1  collagen alpha-6(VI) chain isoform X2

    14. XM_054345235.1 → XP_054201210.1  collagen alpha-6(VI) chain isoform X2

    RNA

    1. XR_008486657.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NMZ7.2 GenPept UniProtKB/Swiss-Prot:A6NMZ7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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