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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
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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 (20) 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

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