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COL4A6 (collagen type IV alpha 6)

Identity

Other namesCXDELq22.3
DELXq22.3
DFNX6
HGNC (Hugo) COL4A6
LocusID (NCBI) 1288
Atlas_Id 40127
Location Xq22.3  [Link to chromosome band Xq22]
Location_base_pair Starts at 107398837 and ends at 107681660 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
COL4A5 (Xq22.3) / COL4A6 (Xq22.3)COL4A6 (Xq22.3) / ZNF589 (3p21.31)GBX1 (7q36.1) / COL4A6 (Xq22.3)

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

External links

Nomenclature
HGNC (Hugo)COL4A6   2208
Cards
Entrez_Gene (NCBI)COL4A6  1288  collagen type IV alpha 6
AliasesCXDELq22.3; DELXq22.3; DFNX6
GeneCards (Weizmann)COL4A6
Ensembl hg19 (Hinxton)ENSG00000197565 [Gene_View]  chrX:107398837-107681660 [Contig_View]  COL4A6 [Vega]
Ensembl hg38 (Hinxton)ENSG00000197565 [Gene_View]  chrX:107398837-107681660 [Contig_View]  COL4A6 [Vega]
ICGC DataPortalENSG00000197565
TCGA cBioPortalCOL4A6
AceView (NCBI)COL4A6
Genatlas (Paris)COL4A6
WikiGenes1288
SOURCE (Princeton)COL4A6
Genomic and cartography
GoldenPath hg19 (UCSC)COL4A6  -     chrX:107398837-107681660 -  Xq22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL4A6  -     Xq22.3   [Description]    (hg38-Dec_2013)
EnsemblCOL4A6 - Xq22.3 [CytoView hg19]  COL4A6 - Xq22.3 [CytoView hg38]
Mapping of homologs : NCBICOL4A6 [Mapview hg19]  COL4A6 [Mapview hg38]
OMIM300914   303631   
Gene and transcription
Genbank (Entrez)AK300502 AK302734 AW082083 BC000874 BC005305
RefSeq transcript (Entrez)NM_001287758 NM_001287759 NM_001287760 NM_001847 NM_033641
RefSeq genomic (Entrez)NC_000023 NC_018934 NG_012059 NT_011651 NW_004929444
Consensus coding sequences : CCDS (NCBI)COL4A6
Cluster EST : UnigeneHs.145586 [ NCBI ]
CGAP (NCI)Hs.145586
Alternative Splicing GalleryENSG00000197565
Gene ExpressionCOL4A6 [ NCBI-GEO ]   COL4A6 [ EBI - ARRAY_EXPRESS ]   COL4A6 [ SEEK ]   COL4A6 [ MEM ]
Gene Expression Viewer (FireBrowse)COL4A6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1288
GTEX Portal (Tissue expression)COL4A6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14031 (Uniprot)
NextProtQ14031  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14031
Splice isoforms : SwissVarQ14031 (Swissvar)
PhosPhoSitePlusQ14031
Domaine pattern : Prosite (Expaxy)NC1_IV (PS51403)   
Domains : Interpro (EBI)C-type_lectin_fold    Collagen    Collagen_VI_NC   
Domain families : Pfam (Sanger)C4 (PF01413)    Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01413    pfam01391   
Domain families : Smart (EMBL)C4 (SM00111)  
DMDM Disease mutations1288
Blocks (Seattle)COL4A6
SuperfamilyQ14031
Human Protein AtlasENSG00000197565
Peptide AtlasQ14031
HPRD02364
IPIIPI00514030   IPI00472200   IPI00871740   IPI00910835   IPI01014952   IPI01013871   IPI00922220   IPI00478108   
Protein Interaction databases
DIP (DOE-UCLA)Q14031
IntAct (EBI)Q14031
FunCoupENSG00000197565
BioGRIDCOL4A6
STRING (EMBL)COL4A6
ZODIACCOL4A6
Ontologies - Pathways
QuickGOQ14031
Ontology : AmiGOextracellular matrix structural constituent  extracellular region  collagen type IV trimer  endoplasmic reticulum lumen  cell adhesion  extracellular matrix organization  collagen catabolic process  
Ontology : EGO-EBIextracellular matrix structural constituent  extracellular region  collagen type IV trimer  endoplasmic reticulum lumen  cell adhesion  extracellular matrix organization  collagen catabolic process  
Pathways : BIOCARTAAcute Myocardial Infarction [Genes]    Platelet Amyloid Precursor Protein Pathway [Genes]    Intrinsic Prothrombin Activation Pathway [Genes]    Regulators of Bone Mineralization [Genes]    Angiotensin-converting enzyme 2 regulates heart function [Genes]    Vitamin C in the Brain [Genes]   
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption    Amoebiasis    Pathways in cancer    Small cell lung cancer   
NDEx Network
Atlas of Cancer Signalling NetworkCOL4A6
Wikipedia pathwaysCOL4A6
Orthology - Evolution
OrthoDB1288
GeneTree (enSembl)ENSG00000197565
Phylogenetic Trees/Animal Genes : TreeFamCOL4A6
Homologs : HomoloGeneCOL4A6
Homology/Alignments : Family Browser (UCSC)COL4A6
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL4A6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL4A6
dbVarCOL4A6
ClinVarCOL4A6
1000_GenomesCOL4A6 
Exome Variant ServerCOL4A6
ExAC (Exome Aggregation Consortium)COL4A6 (select the gene name)
Genetic variants : HAPMAP1288
Genomic Variants (DGV)COL4A6 [DGVbeta]
Mutations
ICGC Data PortalCOL4A6 
TCGA Data PortalCOL4A6 
Broad Tumor PortalCOL4A6
OASIS PortalCOL4A6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL4A6 
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)Collagen, type IV, alpha
BioMutasearch COL4A6
DgiDB (Drug Gene Interaction Database)COL4A6
DoCM (Curated mutations)COL4A6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL4A6 (select a term)
intoGenCOL4A6
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)X:107398837-107681660  ENSG00000197565
CONAN: Copy Number AnalysisCOL4A6 
Mutations and Diseases : HGMDCOL4A6
OMIM300914    303631   
MedgenCOL4A6
Genetic Testing Registry COL4A6
NextProtQ14031 [Medical]
TSGene1288
GENETestsCOL4A6
Huge Navigator COL4A6 [HugePedia]
snp3D : Map Gene to Disease1288
BioCentury BCIQCOL4A6
ClinGenCOL4A6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1288
Chemical/Pharm GKB GenePA26723
Clinical trialCOL4A6
Miscellaneous
canSAR (ICR)COL4A6 (select the gene name)
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL4A6
EVEXCOL4A6
GoPubMedCOL4A6
iHOPCOL4A6
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 : Tue Aug 9 19:01:00 CEST 2016

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