Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumors   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

COL4A3 (collagen type IV alpha 3 chain)

Identity

Alias_namescollagen
Other alias-
HGNC (Hugo) COL4A3
LocusID (NCBI) 1285
Atlas_Id 40126
Location 2q36.3  [Link to chromosome band 2q36]
Location_base_pair Starts at 227164565 and ends at 227314792 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)
COL4A3 (2q36.3) / FBXO36 (2q36.3)EPHA4 (2q36.1) / COL4A3 (2q36.3)MFF (2q36.3) / COL4A3 (2q36.3)
EPHA4 2q36.1 / COL4A3 2q36.3MFF 2q36.3 / COL4A3 2q36.3

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) [ 2 ]
  t(2;2)(q36;q36) EPHA4/COL4A3
t(2;2)(q36;q36) MFF/COL4A3

Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Alport syndrome and diffuse leiomyomatosis

External links

Nomenclature
HGNC (Hugo)COL4A3   2204
LRG (Locus Reference Genomic)LRG_230
Cards
Entrez_Gene (NCBI)COL4A3  1285  collagen type IV alpha 3 chain
Aliases
GeneCards (Weizmann)COL4A3
Ensembl hg19 (Hinxton)ENSG00000169031 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000169031 [Gene_View]  chr2:227164565-227314792 [Contig_View]  COL4A3 [Vega]
ICGC DataPortalENSG00000169031
TCGA cBioPortalCOL4A3
AceView (NCBI)COL4A3
Genatlas (Paris)COL4A3
WikiGenes1285
SOURCE (Princeton)COL4A3
Genetics Home Reference (NIH)COL4A3
Genomic and cartography
GoldenPath hg38 (UCSC)COL4A3  -     chr2:227164565-227314792 +  2q36.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL4A3  -     2q36.3   [Description]    (hg19-Feb_2009)
EnsemblCOL4A3 - 2q36.3 [CytoView hg19]  COL4A3 - 2q36.3 [CytoView hg38]
Mapping of homologs : NCBICOL4A3 [Mapview hg19]  COL4A3 [Mapview hg38]
OMIM104200   120070   141200   203780   
Gene and transcription
Genbank (Entrez)AF258351 AU099354 BM670570 BM712932 CD675393
RefSeq transcript (Entrez)NM_000091 NM_031362 NM_031363 NM_031364 NM_031365 NM_031366
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL4A3
Cluster EST : UnigeneHs.570065 [ NCBI ]
CGAP (NCI)Hs.570065
Alternative Splicing GalleryENSG00000169031
Gene ExpressionCOL4A3 [ NCBI-GEO ]   COL4A3 [ EBI - ARRAY_EXPRESS ]   COL4A3 [ SEEK ]   COL4A3 [ MEM ]
Gene Expression Viewer (FireBrowse)COL4A3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1285
GTEX Portal (Tissue expression)COL4A3
Human Protein AtlasENSG00000169031-COL4A3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ01955   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ01955  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ01955
Splice isoforms : SwissVarQ01955
PhosPhoSitePlusQ01955
Domaine pattern : Prosite (Expaxy)NC1_IV (PS51403)   
Domains : Interpro (EBI)Collagen    Collagen_VI_NC    CTDL_fold   
Domain families : Pfam (Sanger)C4 (PF01413)    Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01413    pfam01391   
Domain families : Smart (EMBL)C4 (SM00111)  
Conserved Domain (NCBI)COL4A3
DMDM Disease mutations1285
Blocks (Seattle)COL4A3
SuperfamilyQ01955
Human Protein Atlas [tissue]ENSG00000169031-COL4A3 [tissue]
Peptide AtlasQ01955
HPRD00354
IPIIPI00010360   IPI00332623   IPI00413923   IPI00829991   IPI00396322   IPI00977256   IPI01018645   IPI01018950   
Protein Interaction databases
DIP (DOE-UCLA)Q01955
IntAct (EBI)Q01955
FunCoupENSG00000169031
BioGRIDCOL4A3
STRING (EMBL)COL4A3
ZODIACCOL4A3
Ontologies - Pathways
QuickGOQ01955
Ontology : AmiGOintegrin binding  integrin binding  structural molecule activity  extracellular matrix structural constituent  protein binding  extracellular region  collagen type IV trimer  basement membrane  endoplasmic reticulum  endoplasmic reticulum lumen  activation of cysteine-type endopeptidase activity involved in apoptotic process  cell adhesion  cell surface receptor signaling pathway  sensory perception of sound  blood circulation  metalloendopeptidase inhibitor activity  cell proliferation  negative regulation of cell proliferation  negative regulation of endopeptidase activity  negative regulation of angiogenesis  extracellular matrix organization  collagen catabolic process  glomerular basement membrane development  collagen-activated tyrosine kinase receptor signaling pathway  intracellular membrane-bounded organelle  endothelial cell apoptotic process  
Ontology : EGO-EBIintegrin binding  integrin binding  structural molecule activity  extracellular matrix structural constituent  protein binding  extracellular region  collagen type IV trimer  basement membrane  endoplasmic reticulum  endoplasmic reticulum lumen  activation of cysteine-type endopeptidase activity involved in apoptotic process  cell adhesion  cell surface receptor signaling pathway  sensory perception of sound  blood circulation  metalloendopeptidase inhibitor activity  cell proliferation  negative regulation of cell proliferation  negative regulation of endopeptidase activity  negative regulation of angiogenesis  extracellular matrix organization  collagen catabolic process  glomerular basement membrane development  collagen-activated tyrosine kinase receptor signaling pathway  intracellular membrane-bounded organelle  endothelial cell apoptotic process  
Pathways : BIOCARTARegulators of Bone Mineralization [Genes]    Platelet Amyloid Precursor Protein Pathway [Genes]    Intrinsic Prothrombin Activation Pathway [Genes]    Angiotensin-converting enzyme 2 regulates heart function [Genes]    Vitamin C in the Brain [Genes]    Acute Myocardial Infarction [Genes]   
NDEx NetworkCOL4A3
Atlas of Cancer Signalling NetworkCOL4A3
Wikipedia pathwaysCOL4A3
Orthology - Evolution
OrthoDB1285
GeneTree (enSembl)ENSG00000169031
Phylogenetic Trees/Animal Genes : TreeFamCOL4A3
HOVERGENQ01955
HOGENOMQ01955
Homologs : HomoloGeneCOL4A3
Homology/Alignments : Family Browser (UCSC)COL4A3
Gene fusions - Rearrangements
Fusion : MitelmanEPHA4/COL4A3 [2q36.1/2q36.3]  [t(2;2)(q36;q36)]  
Fusion : MitelmanMFF/COL4A3 [2q36.3/2q36.3]  [t(2;2)(q36;q36)]  
Fusion: TCGA_MDACCEPHA4 2q36.1 COL4A3 2q36.3 LUSC
Fusion: TCGA_MDACCMFF 2q36.3 COL4A3 2q36.3 HNSC
Fusion PortalEPHA4 2q36.1 COL4A3 2q36.3 LUSC
Fusion PortalMFF 2q36.3 COL4A3 2q36.3 HNSC
Fusion : QuiverCOL4A3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL4A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL4A3
dbVarCOL4A3
ClinVarCOL4A3
1000_GenomesCOL4A3 
Exome Variant ServerCOL4A3
ExAC (Exome Aggregation Consortium)ENSG00000169031
GNOMAD BrowserENSG00000169031
Genetic variants : HAPMAP1285
Genomic Variants (DGV)COL4A3 [DGVbeta]
DECIPHERCOL4A3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL4A3 
Mutations
ICGC Data PortalCOL4A3 
TCGA Data PortalCOL4A3 
Broad Tumor PortalCOL4A3
OASIS PortalCOL4A3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL4A3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL4A3
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)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch COL4A3
DgiDB (Drug Gene Interaction Database)COL4A3
DoCM (Curated mutations)COL4A3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL4A3 (select a term)
intoGenCOL4A3
Cancer3DCOL4A3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM104200    120070    141200    203780   
Orphanet11850    11851    12191   
DisGeNETCOL4A3
MedgenCOL4A3
Genetic Testing Registry COL4A3
NextProtQ01955 [Medical]
TSGene1285
GENETestsCOL4A3
Target ValidationCOL4A3
Huge Navigator COL4A3 [HugePedia]
snp3D : Map Gene to Disease1285
BioCentury BCIQCOL4A3
ClinGenCOL4A3 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1285
Chemical/Pharm GKB GenePA26719
Clinical trialCOL4A3
Miscellaneous
canSAR (ICR)COL4A3 (select the gene name)
Probes
Litterature
PubMed132 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL4A3
EVEXCOL4A3
GoPubMedCOL4A3
iHOPCOL4A3
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 May 14 11:38:37 CEST 2018
Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.