Atlas of Genetics and Cytogenetics in Oncology and Haematology

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AGRN (agrin)

Identity

Alias_namesAGRIN
agrin proteoglycan
Other aliasCMS8
CMSPPD
HGNC (Hugo) AGRN
LocusID (NCBI) 375790
Atlas_Id 49849
Location 1p36.33  [Link to chromosome band 1p36]
Location_base_pair Starts at 1020123 and ends at 1056119 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)
AGRN (1p36.33) / AGRN (1p36.33)AGRN (1p36.33) / AKT1 (14q32.33)AGRN (1p36.33) / HMGB3 (Xq28)
AGRN (1p36.33) / NOC4L (12q24.33)AGRN (1p36.33) / RPL13 (16q24.3)AGRN (1p36.33) / TIMM50 (19q13.2)
AGRN (1p36.33) / TMEM8A (16p13.3)AGRN (1p36.33) / UBE2J2 (1p36.33)PUSL1 (1p36.33) / AGRN (1p36.33)
AGRN 1p36.33 / NOC4L 12q24.33PUSL1 1p36.33 / AGRN 1p36.33

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 ]
  PUSL1/AGRN (1p36)
t(1;12)(p36;q24) AGRN/NOC4L

External links

Nomenclature
HGNC (Hugo)AGRN   329
LRG (Locus Reference Genomic)LRG_198
Cards
Entrez_Gene (NCBI)AGRN  375790  agrin
AliasesAGRIN; CMS8; CMSPPD
GeneCards (Weizmann)AGRN
Ensembl hg19 (Hinxton)ENSG00000188157 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188157 [Gene_View]  ENSG00000188157 [Sequence]  chr1:1020123-1056119 [Contig_View]  AGRN [Vega]
ICGC DataPortalENSG00000188157
TCGA cBioPortalAGRN
AceView (NCBI)AGRN
Genatlas (Paris)AGRN
WikiGenes375790
SOURCE (Princeton)AGRN
Genetics Home Reference (NIH)AGRN
Genomic and cartography
GoldenPath hg38 (UCSC)AGRN  -     chr1:1020123-1056119 +  1p36.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)AGRN  -     1p36.33   [Description]    (hg19-Feb_2009)
GoldenPathAGRN - 1p36.33 [CytoView hg19]  AGRN - 1p36.33 [CytoView hg38]
ImmunoBaseENSG00000188157
Mapping of homologs : NCBIAGRN [Mapview hg19]  AGRN [Mapview hg38]
OMIM103320   615120   
Gene and transcription
Genbank (Entrez)AB191264 AF016903 AJ309206 AK021586 AK125197
RefSeq transcript (Entrez)NM_001305275 NM_001364727 NM_198576
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)AGRN
Cluster EST : UnigeneHs.602356 [ NCBI ]
CGAP (NCI)Hs.602356
Alternative Splicing GalleryENSG00000188157
Gene ExpressionAGRN [ NCBI-GEO ]   AGRN [ EBI - ARRAY_EXPRESS ]   AGRN [ SEEK ]   AGRN [ MEM ]
Gene Expression Viewer (FireBrowse)AGRN [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)375790
GTEX Portal (Tissue expression)AGRN
Human Protein AtlasENSG00000188157-AGRN [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00468   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00468  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00468
Splice isoforms : SwissVarO00468
PhosPhoSitePlusO00468
Domaine pattern : Prosite (Expaxy)EGF_1 (PS00022)    EGF_2 (PS01186)    EGF_3 (PS50026)    EGF_LAM_1 (PS01248)    EGF_LAM_2 (PS50027)    KAZAL_2 (PS51465)    LAM_G_DOMAIN (PS50025)    NTA (PS51121)    SEA (PS50024)   
Domains : Interpro (EBI)ConA-like_dom_sf    EGF-like_Ca-bd_dom    EGF-like_CS    EGF-like_dom    FacI_MAC    Fol_N    Kazal_dom    Kazal_dom_sf    Laminin_EGF    Laminin_G    NtA_dom    SEA_dom    SEA_dom_sf    TIMP-like_OB-fold   
Domain families : Pfam (Sanger)EGF (PF00008)    Kazal_1 (PF00050)    Kazal_2 (PF07648)    Laminin_EGF (PF00053)    Laminin_G_1 (PF00054)    NtA (PF03146)    SEA (PF01390)   
Domain families : Pfam (NCBI)pfam00008    pfam00050    pfam07648    pfam00053    pfam00054    pfam03146    pfam01390   
Domain families : Smart (EMBL)EGF (SM00181)  EGF_CA (SM00179)  EGF_Lam (SM00180)  FIMAC (SM00057)  FOLN (SM00274)  KAZAL (SM00280)  LamG (SM00282)  SEA (SM00200)  
Conserved Domain (NCBI)AGRN
DMDM Disease mutations375790
Blocks (Seattle)AGRN
SuperfamilyO00468
Human Protein Atlas [tissue]ENSG00000188157-AGRN [tissue]
Peptide AtlasO00468
HPRD10550
IPIIPI00374563   IPI00514026   IPI00976820   
Protein Interaction databases
DIP (DOE-UCLA)O00468
IntAct (EBI)O00468
FunCoupENSG00000188157
BioGRIDAGRN
STRING (EMBL)AGRN
ZODIACAGRN
Ontologies - Pathways
QuickGOO00468
Ontology : AmiGOretinoid metabolic process  dystroglycan binding  structural constituent of cytoskeleton  extracellular matrix structural constituent  extracellular matrix structural constituent  calcium ion binding  protein binding  extracellular region  basement membrane  basement membrane  Golgi lumen  cytosol  plasma membrane  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  cytoskeleton organization  signal transduction  G protein-coupled acetylcholine receptor signaling pathway  axon guidance  neuromuscular junction development  animal organ morphogenesis  tissue development  integral component of membrane  cell junction  extracellular matrix organization  sialic acid binding  chondroitin sulfate binding  receptor clustering  receptor clustering  receptor clustering  lysosomal lumen  laminin binding  heparan sulfate proteoglycan binding  positive regulation of GTPase activity  clustering of voltage-gated sodium channels  synapse  positive regulation of synaptic growth at neuromuscular junction  positive regulation of transcription by RNA polymerase II  synapse organization  positive regulation of filopodium assembly  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  extracellular exosome  
Ontology : EGO-EBIretinoid metabolic process  dystroglycan binding  structural constituent of cytoskeleton  extracellular matrix structural constituent  extracellular matrix structural constituent  calcium ion binding  protein binding  extracellular region  basement membrane  basement membrane  Golgi lumen  cytosol  plasma membrane  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  cytoskeleton organization  signal transduction  G protein-coupled acetylcholine receptor signaling pathway  axon guidance  neuromuscular junction development  animal organ morphogenesis  tissue development  integral component of membrane  cell junction  extracellular matrix organization  sialic acid binding  chondroitin sulfate binding  receptor clustering  receptor clustering  receptor clustering  lysosomal lumen  laminin binding  heparan sulfate proteoglycan binding  positive regulation of GTPase activity  clustering of voltage-gated sodium channels  synapse  positive regulation of synaptic growth at neuromuscular junction  positive regulation of transcription by RNA polymerase II  synapse organization  positive regulation of filopodium assembly  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  extracellular exosome  
Pathways : KEGGECM-receptor interaction   
NDEx NetworkAGRN
Atlas of Cancer Signalling NetworkAGRN
Wikipedia pathwaysAGRN
Orthology - Evolution
OrthoDB375790
GeneTree (enSembl)ENSG00000188157
Phylogenetic Trees/Animal Genes : TreeFamAGRN
HOGENOMO00468
Homologs : HomoloGeneAGRN
Homology/Alignments : Family Browser (UCSC)AGRN
Gene fusions - Rearrangements
Fusion : MitelmanAGRN/NOC4L [1p36.33/12q24.33]  
Fusion : MitelmanPUSL1/AGRN [1p36.33/1p36.33]  [t(1;1)(p36;p36)]  
Fusion PortalAGRN 1p36.33 NOC4L 12q24.33 BRCA LUSC
Fusion PortalPUSL1 1p36.33 AGRN 1p36.33 LUSC
Fusion : QuiverAGRN
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerAGRN [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)AGRN
dbVarAGRN
ClinVarAGRN
1000_GenomesAGRN 
Exome Variant ServerAGRN
ExAC (Exome Aggregation Consortium)ENSG00000188157
GNOMAD BrowserENSG00000188157
Varsome BrowserAGRN
Genetic variants : HAPMAP375790
Genomic Variants (DGV)AGRN [DGVbeta]
DECIPHERAGRN [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisAGRN 
Mutations
ICGC Data PortalAGRN 
TCGA Data PortalAGRN 
Broad Tumor PortalAGRN
OASIS PortalAGRN [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICAGRN  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DAGRN
Mutations and Diseases : HGMDAGRN
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 AGRN
DgiDB (Drug Gene Interaction Database)AGRN
DoCM (Curated mutations)AGRN (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)AGRN (select a term)
intoGenAGRN
Cancer3DAGRN(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM103320    615120   
Orphanet13931    13930   
DisGeNETAGRN
MedgenAGRN
Genetic Testing Registry AGRN
NextProtO00468 [Medical]
TSGene375790
GENETestsAGRN
Target ValidationAGRN
Huge Navigator AGRN [HugePedia]
snp3D : Map Gene to Disease375790
BioCentury BCIQAGRN
ClinGenAGRN
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD375790
Chemical/Pharm GKB GenePA24626
Clinical trialAGRN
Miscellaneous
canSAR (ICR)AGRN (select the gene name)
DataMed IndexAGRN
Probes
Litterature
PubMed69 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineAGRN
EVEXAGRN
GoPubMedAGRN
iHOPAGRN
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 Nov 13 17:31:36 CET 2019
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