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

COL6A1 (collagen type VI alpha 1)

Identity

Other namesBTHLM1
OPLL
UCHMD1
HGNC (Hugo) COL6A1
LocusID (NCBI) 1291
Atlas_Id 40128
Location 21q22.3  [Link to chromosome band 21q22]
Location_base_pair Starts at 47401663 and ends at 47424963 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
COL6A1 (21q22.3) / AZIN1 (8q22.3)COL6A1 (21q22.3) / COL6A1 (21q22.3)COL6A1 (21q22.3) / DOT1L (19p13.3)
COL6A1 (21q22.3) / NPIPB7 (16q23.1)COL6A1 (21q22.3) / SFPQ (16q24.1)CYR61 (1p22.3) / COL6A1 (21q22.3)
DOT1L (19p13.3) / COL6A1 (21q22.3)PABPC4 (1p34.3) / COL6A1 (21q22.3)PVT1 (8q24.21) / COL6A1 (21q22.3)
S100A6 (1q21.3) / COL6A1 (21q22.3)SCN4B (11q23.3) / COL6A1 (21q22.3)S100A6 1q21.3 / COL6A1 21q22.3

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

 


External links

Nomenclature
HGNC (Hugo)COL6A1   2211
Cards
Entrez_Gene (NCBI)COL6A1  1291  collagen type VI alpha 1
AliasesBTHLM1; OPLL; UCHMD1
GeneCards (Weizmann)COL6A1
Ensembl hg19 (Hinxton)ENSG00000142156 [Gene_View]  chr21:47401663-47424963 [Contig_View]  COL6A1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000142156 [Gene_View]  chr21:47401663-47424963 [Contig_View]  COL6A1 [Vega]
ICGC DataPortalENSG00000142156
TCGA cBioPortalCOL6A1
AceView (NCBI)COL6A1
Genatlas (Paris)COL6A1
WikiGenes1291
SOURCE (Princeton)COL6A1
Genomic and cartography
GoldenPath hg19 (UCSC)COL6A1  -     chr21:47401663-47424963 +  21q22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL6A1  -     21q22.3   [Description]    (hg38-Dec_2013)
EnsemblCOL6A1 - 21q22.3 [CytoView hg19]  COL6A1 - 21q22.3 [CytoView hg38]
Mapping of homologs : NCBICOL6A1 [Mapview hg19]  COL6A1 [Mapview hg38]
OMIM120220   158810   254090   
Gene and transcription
Genbank (Entrez)AK298968 AK299396 AK307989 AU100220 BC005159
RefSeq transcript (Entrez)NM_001848
RefSeq genomic (Entrez)NC_000021 NC_018932 NG_008674 NT_011512 NW_004929427
Consensus coding sequences : CCDS (NCBI)COL6A1
Cluster EST : UnigeneHs.474053 [ NCBI ]
CGAP (NCI)Hs.474053
Alternative Splicing GalleryENSG00000142156
Gene ExpressionCOL6A1 [ NCBI-GEO ]   COL6A1 [ EBI - ARRAY_EXPRESS ]   COL6A1 [ SEEK ]   COL6A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL6A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1291
GTEX Portal (Tissue expression)COL6A1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP12109 (Uniprot)
NextProtP12109  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP12109
Splice isoforms : SwissVarP12109 (Swissvar)
PhosPhoSitePlusP12109
Domaine pattern : Prosite (Expaxy)VWFA (PS50234)   
Domains : Interpro (EBI)Collagen    VWF_A   
Domain families : Pfam (Sanger)Collagen (PF01391)    VWA (PF00092)   
Domain families : Pfam (NCBI)pfam01391    pfam00092   
Domain families : Smart (EMBL)VWA (SM00327)  
DMDM Disease mutations1291
Blocks (Seattle)COL6A1
SuperfamilyP12109
Human Protein AtlasENSG00000142156
Peptide AtlasP12109
HPRD00370
IPIIPI00291136   IPI01010585   IPI01009421   IPI00977566   
Protein Interaction databases
DIP (DOE-UCLA)P12109
IntAct (EBI)P12109
FunCoupENSG00000142156
BioGRIDCOL6A1
STRING (EMBL)COL6A1
ZODIACCOL6A1
Ontologies - Pathways
QuickGOP12109
Ontology : AmiGOosteoblast differentiation  extracellular region  extracellular region  collagen type VI trimer  lysosomal membrane  endoplasmic reticulum lumen  cell adhesion  membrane  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  endodermal cell differentiation  sarcolemma  protein complex  platelet-derived growth factor binding  extracellular exosome  protein heterotrimerization  cellular response to amino acid stimulus  
Ontology : EGO-EBIosteoblast differentiation  extracellular region  extracellular region  collagen type VI trimer  lysosomal membrane  endoplasmic reticulum lumen  cell adhesion  membrane  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  endodermal cell differentiation  sarcolemma  protein complex  platelet-derived growth factor binding  extracellular exosome  protein heterotrimerization  cellular response to amino acid stimulus  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption   
NDEx NetworkCOL6A1
Atlas of Cancer Signalling NetworkCOL6A1
Wikipedia pathwaysCOL6A1
Orthology - Evolution
OrthoDB1291
GeneTree (enSembl)ENSG00000142156
Phylogenetic Trees/Animal Genes : TreeFamCOL6A1
Homologs : HomoloGeneCOL6A1
Homology/Alignments : Family Browser (UCSC)COL6A1
Gene fusions - Rearrangements
Fusion: TCGAS100A6 1q21.3 COL6A1 21q22.3 LUAD
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL6A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL6A1
dbVarCOL6A1
ClinVarCOL6A1
1000_GenomesCOL6A1 
Exome Variant ServerCOL6A1
ExAC (Exome Aggregation Consortium)COL6A1 (select the gene name)
Genetic variants : HAPMAP1291
Genomic Variants (DGV)COL6A1 [DGVbeta]
Mutations
ICGC Data PortalCOL6A1 
TCGA Data PortalCOL6A1 
Broad Tumor PortalCOL6A1
OASIS PortalCOL6A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL6A1 
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
BioMutasearch COL6A1
DgiDB (Drug Gene Interaction Database)COL6A1
DoCM (Curated mutations)COL6A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL6A1 (select a term)
intoGenCOL6A1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)21:47401663-47424963  ENSG00000142156
CONAN: Copy Number AnalysisCOL6A1 
Mutations and Diseases : HGMDCOL6A1
OMIM120220    158810    254090   
MedgenCOL6A1
Genetic Testing Registry COL6A1
NextProtP12109 [Medical]
TSGene1291
GENETestsCOL6A1
Huge Navigator COL6A1 [HugePedia]
snp3D : Map Gene to Disease1291
BioCentury BCIQCOL6A1
ClinGenCOL6A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1291
Chemical/Pharm GKB GenePA26727
Clinical trialCOL6A1
Miscellaneous
canSAR (ICR)COL6A1 (select the gene name)
Probes
Litterature
PubMed86 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL6A1
EVEXCOL6A1
GoPubMedCOL6A1
iHOPCOL6A1
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 : Mon Sep 19 18:43:27 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.