Atlas of Genetics and Cytogenetics in Oncology and Haematology

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COL3A1 (collagen type III alpha 1 chain)

Identity

Alias_namesEDS4A
Ehlers-Danlos syndrome type IV, autosomal dominant
collagen, type III, alpha 1
Other alias
HGNC (Hugo) COL3A1
LocusID (NCBI) 1281
Atlas_Id 50204
Location 2q32.2  [Link to chromosome band 2q32]
Location_base_pair Starts at 188974373 and ends at 189012746 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)		AD_1 () / COL3A1 (2q32.2)BRI3 (7q21.3) / COL3A1 (2q32.2)CIZ1 (9q34.11) / COL3A1 (2q32.2)
COL3A1 (2q32.2) / AMOT (Xq23)COL3A1 (2q32.2) / ARHGAP18 (6q22.33)COL3A1 (2q32.2) / ARHGEF26 (3q25.2)
COL3A1 (2q32.2) / CHST12 (7p22.3)COL3A1 (2q32.2) / CLU (8p21.1)COL3A1 (2q32.2) / COL16A1 (1p35.2)
COL3A1 (2q32.2) / COL3A1 (2q32.2)COL3A1 (2q32.2) / COL6A3 (2q37.3)COL3A1 (2q32.2) / DYNC1H1 (14q32.31)
COL3A1 (2q32.2) / HSH2D (19p13.12)COL3A1 (2q32.2) / PLAG1 (8q12.1)COL3A1 (2q32.2) / SMC4 (3q25.33)
COL3A1 (2q32.2) / THBS2 (6q27)COL3A1 (2q32.2) / YWHAB (20q13.12)COL3A1 (2q32.2) / ZNF43 (19p12)
DCLK1 (13q13.3) / COL3A1 (2q32.2)EPS8 (12p12.3) / COL3A1 (2q32.2)GNL3 (3p21.1) / COL3A1 (2q32.2)
GRSF1 (4q13.3) / COL3A1 (2q32.2)PHB2 (12p13.31) / COL3A1 (2q32.2)POLD3 (11q13.4) / COL3A1 (2q32.2)
PRRC2C (1q24.3) / COL3A1 (2q32.2)RPAIN (17p13.2) / COL3A1 (2q32.2)SPATS2L (2q33.1) / COL3A1 (2q32.2)

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 ]
  Soft Tissues: Lipoblastoma with t(2;8)(q31;q12.1) COL3A1/PLAG1

External links

Nomenclature
HGNC (Hugo)COL3A1   2201
LRG (Locus Reference Genomic)LRG_3
Cards
Entrez_Gene (NCBI)COL3A1  1281  collagen type III alpha 1 chain
AliasesEDS4A
GeneCards (Weizmann)COL3A1
Ensembl hg19 (Hinxton)ENSG00000168542 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000168542 [Gene_View]  chr2:188974373-189012746 [Contig_View]  COL3A1 [Vega]
ICGC DataPortalENSG00000168542
TCGA cBioPortalCOL3A1
AceView (NCBI)COL3A1
Genatlas (Paris)COL3A1
WikiGenes1281
SOURCE (Princeton)COL3A1
Genetics Home Reference (NIH)COL3A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL3A1  -     chr2:188974373-189012746 +  2q32.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL3A1  -     2q32.2   [Description]    (hg19-Feb_2009)
EnsemblCOL3A1 - 2q32.2 [CytoView hg19]  COL3A1 - 2q32.2 [CytoView hg38]
Mapping of homologs : NCBICOL3A1 [Mapview hg19]  COL3A1 [Mapview hg38]
OMIM120180   130020   130050   
Gene and transcription
Genbank (Entrez)AI755052 AK091853 AK308010 BC028178 BP374999
RefSeq transcript (Entrez)NM_000090
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL3A1
Cluster EST : UnigeneHs.443625 [ NCBI ]
CGAP (NCI)Hs.443625
Alternative Splicing GalleryENSG00000168542
Gene ExpressionCOL3A1 [ NCBI-GEO ]   COL3A1 [ EBI - ARRAY_EXPRESS ]   COL3A1 [ SEEK ]   COL3A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL3A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1281
GTEX Portal (Tissue expression)COL3A1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP02461   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP02461  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP02461
Splice isoforms : SwissVarP02461
PhosPhoSitePlusP02461
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)COL3A1
DMDM Disease mutations1281
Blocks (Seattle)COL3A1
PDB (SRS)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
PDB (PDBSum)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
PDB (IMB)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
PDB (RSDB)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
Structural Biology KnowledgeBase2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
SCOP (Structural Classification of Proteins)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
CATH (Classification of proteins structures)2V53    3DMW    4AE2    4AEJ    4AK3    4GYX   
SuperfamilyP02461
Human Protein AtlasENSG00000168542
Peptide AtlasP02461
HPRD00365
IPIIPI00021033   IPI00167087   IPI00981037   IPI00925581   
Protein Interaction databases
DIP (DOE-UCLA)P02461
IntAct (EBI)P02461
FunCoupENSG00000168542
BioGRIDCOL3A1
STRING (EMBL)COL3A1
ZODIACCOL3A1
Ontologies - Pathways
QuickGOP02461
Ontology : AmiGOskeletal system development  protease binding  integrin binding  integrin binding  extracellular matrix structural constituent  protein binding  extracellular region  collagen type III trimer  collagen type III trimer  collagen type III trimer  extracellular space  extracellular space  endoplasmic reticulum lumen  cell-matrix adhesion  transforming growth factor beta receptor signaling pathway  integrin-mediated signaling pathway  heart development  aging  response to radiation  response to mechanical stimulus  peptide cross-linking  cerebral cortex development  platelet activation  extracellular matrix organization  collagen fibril organization  collagen fibril organization  collagen catabolic process  extracellular matrix  extracellular matrix  response to cytokine  positive regulation of Rho protein signal transduction  wound healing  wound healing  skin development  SMAD binding  metal ion binding  platelet-derived growth factor binding  digestive tract development  regulation of immune response  negative regulation of immune response  aorta smooth muscle tissue morphogenesis  cellular response to amino acid stimulus  supramolecular fiber organization  negative regulation of neuron migration  
Ontology : EGO-EBIskeletal system development  protease binding  integrin binding  integrin binding  extracellular matrix structural constituent  protein binding  extracellular region  collagen type III trimer  collagen type III trimer  collagen type III trimer  extracellular space  extracellular space  endoplasmic reticulum lumen  cell-matrix adhesion  transforming growth factor beta receptor signaling pathway  integrin-mediated signaling pathway  heart development  aging  response to radiation  response to mechanical stimulus  peptide cross-linking  cerebral cortex development  platelet activation  extracellular matrix organization  collagen fibril organization  collagen fibril organization  collagen catabolic process  extracellular matrix  extracellular matrix  response to cytokine  positive regulation of Rho protein signal transduction  wound healing  wound healing  skin development  SMAD binding  metal ion binding  platelet-derived growth factor binding  digestive tract development  regulation of immune response  negative regulation of immune response  aorta smooth muscle tissue morphogenesis  cellular response to amino acid stimulus  supramolecular fiber organization  negative regulation of neuron migration  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption    Amoebiasis   
NDEx NetworkCOL3A1
Atlas of Cancer Signalling NetworkCOL3A1
Wikipedia pathwaysCOL3A1
Orthology - Evolution
OrthoDB1281
GeneTree (enSembl)ENSG00000168542
Phylogenetic Trees/Animal Genes : TreeFamCOL3A1
HOVERGENP02461
HOGENOMP02461
Homologs : HomoloGeneCOL3A1
Homology/Alignments : Family Browser (UCSC)COL3A1
Gene fusions - Rearrangements
Fusion : MitelmanCOL3A1/COL16A1 [2q32.2/1p35.2]  
Fusion : MitelmanCOL3A1/PLAG1 [2q32.2/8q12.1]  [t(2;8)(q32;q12)]  
Fusion : MitelmanCOL3A1/ZNF43 [2q32.2/19p12]  [t(2;19)(q32;p12)]  
Fusion : MitelmanDCLK1/COL3A1 [13q13.3/2q32.2]  [t(2;13)(q32;q13)]  
Fusion : MitelmanPOLD3/COL3A1 [11q13.4/2q32.2]  [t(2;11)(q32;q13)]  
Fusion : MitelmanPRRC2C/COL3A1 [1q24.3/2q32.2]  [t(1;2)(q24;q32)]  
Fusion : MitelmanSPATS2L/COL3A1 [2q33.1/2q32.2]  [t(2;2)(q32;q33)]  
Fusion Cancer (Beijing)AD_1 [COL3A1]  -  2q32.2 [FUSC004446]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL3A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL3A1
dbVarCOL3A1
ClinVarCOL3A1
1000_GenomesCOL3A1 
Exome Variant ServerCOL3A1
ExAC (Exome Aggregation Consortium)COL3A1 (select the gene name)
Genetic variants : HAPMAP1281
Genomic Variants (DGV)COL3A1 [DGVbeta]
DECIPHERCOL3A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL3A1 
Mutations
ICGC Data PortalCOL3A1 
TCGA Data PortalCOL3A1 
Broad Tumor PortalCOL3A1
OASIS PortalCOL3A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL3A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL3A1
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)Ehlers Danlos Syndrome Variant Database
BioMutasearch COL3A1
DgiDB (Drug Gene Interaction Database)COL3A1
DoCM (Curated mutations)COL3A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL3A1 (select a term)
intoGenCOL3A1
Cancer3DCOL3A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120180    130020    130050   
Orphanet1010    2312    19166    4042   
MedgenCOL3A1
Genetic Testing Registry COL3A1
NextProtP02461 [Medical]
TSGene1281
GENETestsCOL3A1
Target ValidationCOL3A1
Huge Navigator COL3A1 [HugePedia]
snp3D : Map Gene to Disease1281
BioCentury BCIQCOL3A1
ClinGenCOL3A1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1281
Chemical/Pharm GKB GenePA26716
Clinical trialCOL3A1
Miscellaneous
canSAR (ICR)COL3A1 (select the gene name)
Probes
Litterature
PubMed215 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL3A1
EVEXCOL3A1
GoPubMedCOL3A1
iHOPCOL3A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:29:08 CEST 2017
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