Basic information

Full name
collagen type VI alpha 3 chain
Ensembl
ENSG00000163359.16
Summary
This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]
Annotation
Ligand

Protein product

Phosphosites on the primary protein product
Loading...

Tumor and normal comparison

Loading, please wait
Signed p-values
Data type
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
RNA1.8e-37-3.7e-5--5.7e-171.9e-104.9e-20-0.56-
protein-3.2e-22-1e-13-3.5e-29-1-3.8e-17-9.9e-27-1.4e-61e-8-5.8e-8

* P-values are from Wilcoxon rank sum test and can be clicked to show the box plots. Positive values mean higher abundance in tumor. BRCA and GBM do not have normal samples.

mRNA expression at gene level
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC6789101112131415161718log2(RSEM+1)tumornormal
Protein expression
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC2425262728293031323334log2(MS1 intensity)tumornormal

* Mild outlier: filled circle; Extreme outlier: empty circle.

Phenotype and mutation association

Manhattan plot summarizing associations of phenotypes and mutations across all cohorts and omics data types

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC05101520253035400-5-10-15-20-25-30-35-40Pan-cancer0204060801001201401601802002202402600-20-40-60-80-100-120-140-160-180-200-220-240-260proteinRNASCNVclinicalpathwaycell typegenomicmutation-log10 of P-value

* Data points of significant associations above and below the dotted lines can be hovered to show the phenotype.

Associations of the protein abundance of COL6A3 with phenotypes and mutations

Loading, please wait
Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION6.7e-882.2e-162.5e-76.6e-62.2e-161.4e-72.2e-161e-88.7e-55.4e-82.2e-16
ESTIMATE: StromalScore6.8e-842.2e-169.3e-75.8e-62.2e-161.4e-72.2e-167.4e-74.6e-47.5e-82.2e-16
PROGENy: TGFb1.3e-742.2e-161e-72.6e-53.3e-111.7e-82.2e-161.3e-72.5e-53.9e-46.1e-11
HALLMARK_MYOGENESIS2.7e-662.2e-166.3e-84.6e-67.1e-83.1e-91.2e-52.8e-31.1e-76.5e-52.2e-16
HALLMARK_UV_RESPONSE_DN1.8e-652.2e-164.4e-104.0e-41.5e-82.6e-62.2e-165.9e-62.9e-50.0052.4e-9
HALLMARK_APICAL_JUNCTION3.9e-622.2e-162.5e-40.0431.1e-91.7e-82.2e-160.021.2e-51.1e-42.2e-16
HALLMARK_ANGIOGENESIS2.2e-582.2e-165.4e-82.1e-52.2e-161.8e-46.7e-171.5e-54.5e-30.731.7e-7
xcell: stroma score2.2e-572.2e-164.3e-103e-87.9e-72.3e-41.8e-86.5e-51.7e-62.9e-37.3e-6
HALLMARK_KRAS_SIGNALING_UP3.7e-527e-92.7e-65.1e-52.2e-161.6e-32.2e-160.0020.0111.6e-32.4e-7
ESTIMATE: ESTIMATEScore4.1e-478.3e-60.0291.2e-42.2e-168.4e-42.2e-167.3e-40.0116.7e-78.6e-6
Showing 1 to 10 of 256 rows

* P-values could be from test for Spearman correlation, Wilcoxon rank sum test, Jonckheere-Terpstra trend test or Cox regression depending on the data type. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Cis-association

Associations between omics data of COL6A3

BRCA0.73-0.14-0.18proteinmRNASCNVmethylationCCRCC0.47-0.010.09proteinmRNASCNVmethylationCOAD0.240.05-0.08proteinmRNASCNVmethylationGBM0.83-0.07-0.08proteinmRNASCNVmethylationHNSCC0.510.090.04proteinmRNASCNVmethylationLSCC0.700.370.36proteinmRNASCNVmethylationLUAD0.560.060.04proteinmRNASCNVmethylationOV0.53-0.05-0.25proteinmRNASCNVmethylationPDAC0.460.040.15proteinmRNASCNVmethylationUCEC0.680.000.09proteinmRNASCNVmethylation

* The numbers are Spearman correlation coefficients and can be clicked to show the scatter plots. The color and size of the circles correlate with the coefficients.

Trans-association

Associations of the protein abundance of COL6A3 and the protein abundance of other genes

Loading, please wait
Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values are from test for Spearman correlation. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with to WebGestalt.