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Col6a1 Gene Detail
Summary
  • Symbol
    Col6a1
  • Name
    collagen, type VI, alpha 1
  • Synonyms
    Col6a-1
  • Feature Type
    protein coding gene
  • IDs
    MGI:88459
    NCBI Gene: 12833
  • Alliance
    gene page
  • Transcription Start Sites
    16 TSS
Location &
Maps
more
  • Sequence Map
    Chr10:76544626-76561869 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 10, 39.71 cM, cytoband B5-C1
  • Mapping Data
    24 experiments
Strain
Comparison
more
  • SNPs within 2kb
    625 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    3
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_88459
 protein coding gene Chr10:76544626-76562002 (-)
129S1/SvImJ MGP_129S1SvImJ_G0017389
 protein coding gene Chr10:76968470-76987940 (-)
A/J MGP_AJ_G0017366
 protein coding gene Chr10:74305551-74323411 (-)
AKR/J MGP_AKRJ_G0017327
 protein coding gene Chr10:76306144-76323520 (-)
BALB/cJ MGP_BALBcJ_G0017326
 protein coding gene Chr10:74509939-74527321 (-)
C3H/HeJ MGP_C3HHeJ_G0017150
 protein coding gene Chr10:76389467-76406837 (-)
C57BL/6NJ MGP_C57BL6NJ_G0017784
 protein coding gene Chr10:79676420-79695020 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0015474
 protein coding gene Chr10:70750606-70767835 (-)
CAST/EiJ MGP_CASTEiJ_G0016720
 protein coding gene Chr10:76712847-76734363 (-)
CBA/J MGP_CBAJ_G0017122
 protein coding gene Chr10:82801674-82821910 (-)
DBA/2J MGP_DBA2J_G0017227
 protein coding gene Chr10:73605602-73623401 (-)
FVB/NJ MGP_FVBNJ_G0017219
 protein coding gene Chr10:72766352-72783727 (-)
LP/J MGP_LPJ_G0017300
 protein coding gene Chr10:77449773-77467146 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0017248
 protein coding gene Chr10:84847694-84866281 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0017823
 protein coding gene Chr10:76371814-76389184 (-)
PWK/PhJ MGP_PWKPhJ_G0016504
 protein coding gene Chr10:73457660-73475268 (-)
SPRET/EiJ MGP_SPRETEiJ_G0016287
 protein coding gene Chr10:75605535-75622962 (-)
WSB/EiJ MGP_WSBEiJ_G0016783
 protein coding gene Chr10:76349659-76367056 (-)



Homology
more
  • Human Ortholog
    COL6A1, collagen type VI alpha 1 chain
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    COL6A1, collagen type VI alpha 1 chain
  • Synonyms
    BTHLM1, BTHLM1A, OPLL, UCHMD1, UCHMD1A
  • Links
    NCBI Gene ID: 1291
    neXtProt AC: NX_P12109
    UniProt: P12109

  • Chr Location
    21q22.3; chr21:45981770-46005050 (+)  GRCh38
Human Diseases
more
  • Diseases
    2 with Col6a1 mouse models; 2 with human COL6A1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
 View 1 model
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    5 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    25 phenotypes from 2 alleles in 2 genetic backgrounds
    84 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for this targeted mutation display a myopathic disorder that resembles human Bethlem myopathy. Loss of contractile strength in affected muscles is associated with an unexpected latent mitochondrial dysfunction in myofibers, as well as spontaneous apoptosis.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    118
  • GO References
    38
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    1380
  • Tissues
    484
  • cDNA Data
    233
  • Literature Summary
    49
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12833 NCBI Gene Model | MGI Sequence Detail 17244 C57BL/6J ±  kb
    transcript NM_009933 RefSeq | MGI Sequence Detail 3967 C57BL/6  
    polypeptide Q04857 UniProt | EBI | MGI Sequence Detail 1025 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      5 Sequences
    • Protein Ontology
      PR:000003353 collagen alpha-1(VI) chain
      (term hierarchy)
    • InterPro Domains
      IPR008160 Collagen triple helix repeat
      IPR052229 Collagen VI and Biomineralization Protein PIF
      IPR050525 Extracellular Matrix Assembly and Organization
      IPR036465 von Willebrand factor A-like domain superfamily
      IPR002035 von Willebrand factor, type A
    • GlyGen
      Q04857 6 sites, 4 N-linked glycans (4 sites), 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 266
      Genomic 18
      cDNA 236
      Primer pair 8
      Other 4

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-2073, MGD-MRK-2076, MGI:2143667
    References
    more
    • Summaries
      All 199
      Developmental Gene Expression 49
      Diseases 5
      Gene Ontology 38
      Phenotypes 84
    • Earliest
      J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
    • Latest
      J:351211 Wu Y, et al., Cathepsin B abundance, activity and microglial localisation in Alzheimer's disease-Down syndrome and early onset Alzheimer's disease; the role of elevated cystatin B. Acta Neuropathol Commun. 2023 Aug 14;11(1):132
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/12/2024
    MGI 6.24     		The Jackson Laboratory