Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

COL6A3 (collagen type VI alpha 3)

Identity

Other namesBTHLM1
DYT27
UCMD1
HGNC (Hugo) COL6A3
LocusID (NCBI) 1293
Atlas_Id 50019
Location 2q37.3  [Link to chromosome band 2q37]
Location_base_pair Starts at 238232655 and ends at 238322850 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
APOL3 (22q12.3) / COL6A3 (2q37.3)ARHGEF11 (1q23.1) / COL6A3 (2q37.3)COL3A1 (2q32.2) / COL6A3 (2q37.3)
COL6A3 (2q37.3) / ARHGEF11 (1q23.1)COL6A3 (2q37.3) / BBC3 (19q13.32)COL6A3 (2q37.3) / CSF1 (1p13.3)
COL6A3 (2q37.3) / EBF1 (5q33.3)COL6A3 (2q37.3) / LGMN (14q32.12)COL6A3 (2q37.3) / PICALM (11q14.2)
COL6A3 (2q37.3) / POSTN (13q13.3)COL6A3 (2q37.3) / STK39 (2q24.3)CREB3L1 (11p11.2) / COL6A3 (2q37.3)
CSF1 (1p13.3) / COL6A3 (2q37.3)FYN (6q21) / COL6A3 (2q37.3)LYAR (4p16.3) / COL6A3 (2q37.3)
PARD3 (10p11.22) / COL6A3 (2q37.3)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 0 ]
  Soft tissue tumors: an overview

External links

Nomenclature
HGNC (Hugo)COL6A3   2213
Cards
Entrez_Gene (NCBI)COL6A3  1293  collagen type VI alpha 3
AliasesBTHLM1; DYT27; UCMD1
GeneCards (Weizmann)COL6A3
Ensembl hg19 (Hinxton)ENSG00000163359 [Gene_View]  chr2:238232655-238322850 [Contig_View]  COL6A3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000163359 [Gene_View]  chr2:238232655-238322850 [Contig_View]  COL6A3 [Vega]
ICGC DataPortalENSG00000163359
TCGA cBioPortalCOL6A3
AceView (NCBI)COL6A3
Genatlas (Paris)COL6A3
WikiGenes1293
SOURCE (Princeton)COL6A3
Genomic and cartography
GoldenPath hg19 (UCSC)COL6A3  -     chr2:238232655-238322850 -  2q37.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL6A3  -     2q37.3   [Description]    (hg38-Dec_2013)
EnsemblCOL6A3 - 2q37.3 [CytoView hg19]  COL6A3 - 2q37.3 [CytoView hg38]
Mapping of homologs : NCBICOL6A3 [Mapview hg19]  COL6A3 [Mapview hg38]
OMIM120250   158810   254090   616411   
Gene and transcription
Genbank (Entrez)AB209636 AK092021 AK303290 AK304870 AK308451
RefSeq transcript (Entrez)NM_004369 NM_057164 NM_057165 NM_057166 NM_057167
RefSeq genomic (Entrez)NC_000002 NC_018913 NG_008676 NT_005403 NW_004929306
Consensus coding sequences : CCDS (NCBI)COL6A3
Cluster EST : UnigeneHs.233240 [ NCBI ]
CGAP (NCI)Hs.233240
Alternative Splicing GalleryENSG00000163359
Gene ExpressionCOL6A3 [ NCBI-GEO ]   COL6A3 [ EBI - ARRAY_EXPRESS ]   COL6A3 [ SEEK ]   COL6A3 [ MEM ]
Gene Expression Viewer (FireBrowse)COL6A3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1293
GTEX Portal (Tissue expression)COL6A3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP12111 (Uniprot)
NextProtP12111  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP12111
Splice isoforms : SwissVarP12111 (Swissvar)
PhosPhoSitePlusP12111
Domaine pattern : Prosite (Expaxy)BPTI_KUNITZ_1 (PS00280)    BPTI_KUNITZ_2 (PS50279)    FN3 (PS50853)    VWFA (PS50234)   
Domains : Interpro (EBI)Collagen    FN3_dom    Ig-like_fold    Kunitz_BPTI    Prtase_inh_Kunz-CS    VWF_A   
Domain families : Pfam (Sanger)Collagen (PF01391)    Kunitz_BPTI (PF00014)    VWA (PF00092)   
Domain families : Pfam (NCBI)pfam01391    pfam00014    pfam00092   
Domain families : Smart (EMBL)FN3 (SM00060)  KU (SM00131)  VWA (SM00327)  
DMDM Disease mutations1293
Blocks (Seattle)COL6A3
PDB (SRS)1KNT    1KTH    1KUN    2KNT   
PDB (PDBSum)1KNT    1KTH    1KUN    2KNT   
PDB (IMB)1KNT    1KTH    1KUN    2KNT   
PDB (RSDB)1KNT    1KTH    1KUN    2KNT   
Structural Biology KnowledgeBase1KNT    1KTH    1KUN    2KNT   
SCOP (Structural Classification of Proteins)1KNT    1KTH    1KUN    2KNT   
CATH (Classification of proteins structures)1KNT    1KTH    1KUN    2KNT   
SuperfamilyP12111
Human Protein AtlasENSG00000163359
Peptide AtlasP12111
HPRD00371
IPIIPI00022200   IPI00220701   IPI00072918   IPI00941465   IPI00072917   IPI00853061   IPI00946286   
Protein Interaction databases
DIP (DOE-UCLA)P12111
IntAct (EBI)P12111
FunCoupENSG00000163359
BioGRIDCOL6A3
STRING (EMBL)COL6A3
ZODIACCOL6A3
Ontologies - Pathways
QuickGOP12111
Ontology : AmiGOserine-type endopeptidase inhibitor activity  extracellular region  proteinaceous extracellular matrix  collagen type VI trimer  extracellular space  endoplasmic reticulum lumen  cell adhesion  muscle organ development  negative regulation of endopeptidase activity  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  sarcolemma  extracellular exosome  extracellular vesicle  
Ontology : EGO-EBIserine-type endopeptidase inhibitor activity  extracellular region  proteinaceous extracellular matrix  collagen type VI trimer  extracellular space  endoplasmic reticulum lumen  cell adhesion  muscle organ development  negative regulation of endopeptidase activity  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  sarcolemma  extracellular exosome  extracellular vesicle  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption   
NDEx Network
Atlas of Cancer Signalling NetworkCOL6A3
Wikipedia pathwaysCOL6A3
Orthology - Evolution
OrthoDB1293
GeneTree (enSembl)ENSG00000163359
Phylogenetic Trees/Animal Genes : TreeFamCOL6A3
Homologs : HomoloGeneCOL6A3
Homology/Alignments : Family Browser (UCSC)COL6A3
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL6A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL6A3
dbVarCOL6A3
ClinVarCOL6A3
1000_GenomesCOL6A3 
Exome Variant ServerCOL6A3
ExAC (Exome Aggregation Consortium)COL6A3 (select the gene name)
Genetic variants : HAPMAP1293
Genomic Variants (DGV)COL6A3 [DGVbeta]
Mutations
ICGC Data PortalCOL6A3 
TCGA Data PortalCOL6A3 
Broad Tumor PortalCOL6A3
OASIS PortalCOL6A3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL6A3 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch COL6A3
DgiDB (Drug Gene Interaction Database)COL6A3
DoCM (Curated mutations)COL6A3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL6A3 (select a term)
intoGenCOL6A3
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)2:238232655-238322850  ENSG00000163359
CONAN: Copy Number AnalysisCOL6A3 
Mutations and Diseases : HGMDCOL6A3
OMIM120250    158810    254090    616411   
MedgenCOL6A3
Genetic Testing Registry COL6A3
NextProtP12111 [Medical]
TSGene1293
GENETestsCOL6A3
Huge Navigator COL6A3 [HugePedia]
snp3D : Map Gene to Disease1293
BioCentury BCIQCOL6A3
ClinGenCOL6A3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1293
Chemical/Pharm GKB GenePA26729
Clinical trialCOL6A3
Miscellaneous
canSAR (ICR)COL6A3 (select the gene name)
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL6A3
EVEXCOL6A3
GoPubMedCOL6A3
iHOPCOL6A3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Aug 9 19:01:01 CEST 2016

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.