Atlas of Genetics and Cytogenetics in Oncology and Haematology

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COL2A1 (collagen type II alpha 1 chain)

Identity

Alias_namesSEDC
AOM
collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)
arthroophthalmopathy, progressive (Stickler syndrome)
collagen, type II, alpha 1
collagen type II alpha 1
Alias_symbol (synonym)STL1
Other aliasANFH
COL11A3
HGNC (Hugo) COL2A1
LocusID (NCBI) 1280
Atlas_Id 46165
Location 12q13.11  [Link to chromosome band 12q13]
Location_base_pair Starts at 47972965 and ends at 48004502 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
COL2A1 (12q13.11) / CLIC4 (1p36.11)COL2A1 (12q13.11) / COL2A1 (12q13.11)COL2A1 (12q13.11) / ZNF609 (15q22.31)
SPARC (5q33.1) / COL2A1 (12q13.11)COL2A1 12q13.11 / ZNF609 15q22.31

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) [ 1 ]
  t(12;15)(q13;q22) COL2A1/ZNF609

External links

Nomenclature
HGNC (Hugo)COL2A1   2200
Cards
Entrez_Gene (NCBI)COL2A1  1280  collagen type II alpha 1 chain
AliasesANFH; AOM; COL11A3; SEDC; 
STL1
GeneCards (Weizmann)COL2A1
Ensembl hg19 (Hinxton)ENSG00000139219 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000139219 [Gene_View]  chr12:47972965-48004502 [Contig_View]  COL2A1 [Vega]
ICGC DataPortalENSG00000139219
TCGA cBioPortalCOL2A1
AceView (NCBI)COL2A1
Genatlas (Paris)COL2A1
WikiGenes1280
SOURCE (Princeton)COL2A1
Genetics Home Reference (NIH)COL2A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL2A1  -     chr12:47972965-48004502 -  12q13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL2A1  -     12q13.11   [Description]    (hg19-Feb_2009)
EnsemblCOL2A1 - 12q13.11 [CytoView hg19]  COL2A1 - 12q13.11 [CytoView hg38]
Mapping of homologs : NCBICOL2A1 [Mapview hg19]  COL2A1 [Mapview hg38]
OMIM108300   120140   132450   150600   151210   156550   183900   184250   200610   215150   271700   604864   608805   609162   609508   616583   
Gene and transcription
Genbank (Entrez)AL834148 BC007252 BC116449 BT007205 M63281
RefSeq transcript (Entrez)NM_001844 NM_033150
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL2A1
Cluster EST : UnigeneHs.408182 [ NCBI ]
CGAP (NCI)Hs.408182
Alternative Splicing GalleryENSG00000139219
Gene ExpressionCOL2A1 [ NCBI-GEO ]   COL2A1 [ EBI - ARRAY_EXPRESS ]   COL2A1 [ SEEK ]   COL2A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL2A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1280
GTEX Portal (Tissue expression)COL2A1
Human Protein AtlasENSG00000139219-COL2A1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP02458   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP02458  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP02458
Splice isoforms : SwissVarP02458
PhosPhoSitePlusP02458
Domaine pattern : Prosite (Expaxy)NC1_FIB (PS51461)    VWFC_1 (PS01208)    VWFC_2 (PS50184)   
Domains : Interpro (EBI)Collagen    Fib_collagen_C    VWF_dom   
Domain families : Pfam (Sanger)COLFI (PF01410)    Collagen (PF01391)    VWC (PF00093)   
Domain families : Pfam (NCBI)pfam01410    pfam01391    pfam00093   
Domain families : Smart (EMBL)COLFI (SM00038)  VWC (SM00214)  
Domain structure : Prodom (Prabi Lyon)Fib_collagen_C (PD002078)   
Conserved Domain (NCBI)COL2A1
DMDM Disease mutations1280
Blocks (Seattle)COL2A1
PDB (SRS)1U5M    2FSE    2SEB   
PDB (PDBSum)1U5M    2FSE    2SEB   
PDB (IMB)1U5M    2FSE    2SEB   
PDB (RSDB)1U5M    2FSE    2SEB   
Structural Biology KnowledgeBase1U5M    2FSE    2SEB   
SCOP (Structural Classification of Proteins)1U5M    2FSE    2SEB   
CATH (Classification of proteins structures)1U5M    2FSE    2SEB   
SuperfamilyP02458
Human Protein Atlas [tissue]ENSG00000139219-COL2A1 [tissue]
Peptide AtlasP02458
HPRD00361
IPIIPI00186460   IPI00936892   IPI00816526   IPI00816482   IPI00552474   IPI00748487   
Protein Interaction databases
DIP (DOE-UCLA)P02458
IntAct (EBI)P02458
FunCoupENSG00000139219
BioGRIDCOL2A1
STRING (EMBL)COL2A1
ZODIACCOL2A1
Ontologies - Pathways
QuickGOP02458
Ontology : AmiGOskeletal system development  cartilage condensation  tissue homeostasis  endochondral ossification  chondrocyte differentiation  heart morphogenesis  extracellular region  extracellular region  collagen type II trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  proteoglycan metabolic process  central nervous system development  visual perception  sensory perception of sound  regulation of gene expression  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  collagen fibril organization  collagen catabolic process  notochord development  extracellular matrix  extracellular matrix  MHC class II protein binding  inner ear morphogenesis  identical protein binding  metal ion binding  platelet-derived growth factor binding  regulation of immune response  cartilage development  palate development  limb bud formation  embryonic skeletal joint morphogenesis  cartilage development involved in endochondral bone morphogenesis  otic vesicle development  cellular response to BMP stimulus  negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  
Ontology : EGO-EBIskeletal system development  cartilage condensation  tissue homeostasis  endochondral ossification  chondrocyte differentiation  heart morphogenesis  extracellular region  extracellular region  collagen type II trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  proteoglycan metabolic process  central nervous system development  visual perception  sensory perception of sound  regulation of gene expression  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  collagen fibril organization  collagen catabolic process  notochord development  extracellular matrix  extracellular matrix  MHC class II protein binding  inner ear morphogenesis  identical protein binding  metal ion binding  platelet-derived growth factor binding  regulation of immune response  cartilage development  palate development  limb bud formation  embryonic skeletal joint morphogenesis  cartilage development involved in endochondral bone morphogenesis  otic vesicle development  cellular response to BMP stimulus  negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  
Pathways : KEGGFocal adhesion    ECM-receptor interaction    Cell Communication   
NDEx NetworkCOL2A1
Atlas of Cancer Signalling NetworkCOL2A1
Wikipedia pathwaysCOL2A1
Orthology - Evolution
OrthoDB1280
GeneTree (enSembl)ENSG00000139219
Phylogenetic Trees/Animal Genes : TreeFamCOL2A1
HOVERGENP02458
HOGENOMP02458
Homologs : HomoloGeneCOL2A1
Homology/Alignments : Family Browser (UCSC)COL2A1
Gene fusions - Rearrangements
Fusion : MitelmanCOL2A1/ZNF609 [12q13.11/15q22.31]  
Fusion: TCGA_MDACCCOL2A1 12q13.11 ZNF609 15q22.31 PRAD
Fusion PortalCOL2A1 12q13.11 ZNF609 15q22.31 PRAD
Fusion : QuiverCOL2A1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL2A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL2A1
dbVarCOL2A1
ClinVarCOL2A1
1000_GenomesCOL2A1 
Exome Variant ServerCOL2A1
ExAC (Exome Aggregation Consortium)ENSG00000139219
GNOMAD BrowserENSG00000139219
Genetic variants : HAPMAP1280
Genomic Variants (DGV)COL2A1 [DGVbeta]
DECIPHERCOL2A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL2A1 
Mutations
ICGC Data PortalCOL2A1 
TCGA Data PortalCOL2A1 
Broad Tumor PortalCOL2A1
OASIS PortalCOL2A1 [ Somatic mutations - Copy number]
Cancer Gene: CensusCOL2A1 
Somatic Mutations in Cancer : COSMICCOL2A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL2A1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Mendelian genes
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch COL2A1
DgiDB (Drug Gene Interaction Database)COL2A1
DoCM (Curated mutations)COL2A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL2A1 (select a term)
intoGenCOL2A1
Cancer3DCOL2A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM108300    120140    132450    150600    151210    156550    183900    184250    200610    215150    271700    604864    608805    609162    609508    616583   
Orphanet17598    841    16705    2198    3034    2852    18662    23769    12220    12280    12233    12234    12252    12253    12061    11656    11740    11633    12548   
DisGeNETCOL2A1
MedgenCOL2A1
Genetic Testing Registry COL2A1
NextProtP02458 [Medical]
TSGene1280
GENETestsCOL2A1
Target ValidationCOL2A1
Huge Navigator COL2A1 [HugePedia]
snp3D : Map Gene to Disease1280
BioCentury BCIQCOL2A1
ClinGenCOL2A1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1280
Chemical/Pharm GKB GenePA26715
Clinical trialCOL2A1
Miscellaneous
canSAR (ICR)COL2A1 (select the gene name)
Probes
Litterature
PubMed312 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL2A1
EVEXCOL2A1
GoPubMedCOL2A1
iHOPCOL2A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Feb 28 13:07:16 CET 2018
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