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Col6a3 Gene Detail
Summary
  • Symbol
    Col6a3
  • Name
    collagen, type VI, alpha 3
  • Synonyms
    Col6a-3
  • Feature Type
    protein coding gene
  • IDs
    MGI:88461
    NCBI Gene: 12835
  • Alliance
    genome feature page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:90694582-90771710 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 45.53 cM
  • Mapping Data
    8 experiments
Strain
Comparison
more
  • SNPs within 2kb
    2648 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_88461
 protein coding gene Chr1:90693645-90771710 (-)
129S1/SvImJ ENSMUSG00200037867
 protein coding gene Chr1:87930175-88008552 (-)
A/J ENSMUSG00195028669
 protein coding gene Chr1:87484572-87562637 (-)
AKR/J ENSMUSG00220042443
 protein coding gene Chr1:87639460-87717875 (-)
BALB/cJ ENSMUSG00180016264
 protein coding gene Chr1:87790938-87868977 (-)
C3H/HeJ ENSMUSG00175001006
 protein coding gene Chr1:87670724-87748749 (-)
C57BL/6NJ ENSMUSG00215024126
 protein coding gene Chr1:87593932-87671991 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0014410
 protein coding gene Chr1:83240152-83317810 (-)
CAST/EiJ ENSTCUG00005007172
 protein coding gene Chr1:87236667-87315619 (-)
CBA/J ENSMUSG00210011472
 protein coding gene Chr1:87516052-87594048 (-)
DBA/2J ENSMUSG00185013632
 protein coding gene Chr1:91977371-92055416 (-)
FVB/NJ ENSMUSG00205038517
 protein coding gene Chr1:86922318-87000707 (-)
JF1/MsJ ENSUMUG00000010706
 protein coding gene Chr1:90728927-90806164 (-)
LP/J ENSMUSG00230015877
 protein coding gene Chr1:91266377-91344762 (-)
NOD/ShiLtJ ENSMUSG00190020639
 protein coding gene Chr1:87558628-87636667 (-)
NZO/HlLtJ ENSMUSG00225003018
 protein coding gene Chr1:95162532-95240910 (-)
PWK/PhJ ENSLUMG00010038387
 protein coding gene Chr1:87120404-87199067 (-)
SPRET/EiJ ENSMSPG00010039502
 protein coding gene Chr1:89145624-89223630 (-)
WSB/EiJ ENSIUOG00005033440
 protein coding gene Chr1:87225252-87303683 (-)



Homology
more
  • Human Ortholog
    COL6A3, collagen type VI alpha 3 chain
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    COL6A3, collagen type VI alpha 3 chain
  • Synonyms
    BTHLM1, BTHLM1C, DYT27, UCMD1, UCMD1C
  • Links
    NCBI Gene ID: 1293
    UniProt: P12111

  • Chr Location
    2q37.3; chr2:237324003-237414405 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with Col6a3 mouse models; 10 with human COL6A3 associations

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

  • Mutations/Alleles
    2 with disease annotations
  • References
    2 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    27 phenotypes from 4 alleles in 4 genetic backgrounds
    3 images
    20 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 a hypomorphic allele exhibit mild myopathy, decreased skeletal muscle weight, increased collagen deposition in muscles, skeletal muscle interstitial fibrosis and abnormal tendon collagen fibril morphology.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    18
  • GO References
    12
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
    835
  • Tissues
    184
  • cDNA Data
    137
  • Literature Summary
    25
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12835 NCBI Gene Model | MGI Sequence Detail 77129 C57BL/6J ±  kb
    transcript NM_001243008 RefSeq | MGI Sequence Detail 10845 ZRU/MplStud  
    polypeptide NP_001229937 RefSeq | MGI Sequence Detail 3284 ZRU/MplStud  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      12 Sequences
    • Protein Ontology
      PR:000003341 collagen alpha-3(VI) chain
      (term hierarchy)
    • PDB
      4IGI, 4IHK
    • InterPro Domains
      IPR041900 Collagen alpha-3(VI) chain, vWA domain
      IPR008160 Collagen triple helix repeat
      IPR050525 Extracellular Matrix Assembly and Organization
      IPR003961 Fibronectin type III
      IPR036116 Fibronectin type III superfamily
      IPR013783 Immunoglobulin-like fold
      IPR002223 Pancreatic trypsin inhibitor Kunitz domain
      IPR036880 Pancreatic trypsin inhibitor Kunitz domain superfamily
      IPR020901 Proteinase inhibitor I2, Kunitz, conserved site
      IPR050098 Tissue factor pathway inhibitor/Kunitz-type serine protease inhibitor-like
      IPR036465 von Willebrand factor A-like domain superfamily
      IPR002035 von Willebrand factor, type A
    • GlyGen
      A0A087WS16 7 sites, 6 N-linked glycans (5 sites), 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 144
      cDNA 140
      Primer pair 4
      Antibodies 5

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-2075, MGD-MRK-2078, MGI:2138284
    References
    more
    • Summaries
      All 87
      Developmental Gene Expression 25
      Diseases 2
      Gene Ontology 12
      Phenotypes 20
    • Earliest
      J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
    • Latest
      J:387578 Jo W, et al., Endotrophin- and CD44-Mediated Heterotypic Signaling Mediates Tumor-Stroma Cross-talk and Facilitates Malignant Progression in Hepatocellular Carcinoma. Cancer Res. 2026 May 15;86(10):2447-2463
    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)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory