Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SMG1 (SMG1, nonsense mediated mRNA decay associated PI3K related kinase)

Identity

Alias_namessmg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)
SMG1 phosphatidylinositol 3-kinase-related kinase
Alias_symbol (synonym)LIP
KIAA0421
ATX
Other alias61E3.4
HGNC (Hugo) SMG1
LocusID (NCBI) 23049
Atlas_Id 43495
Location 16p12.3  [Link to chromosome band 16p12]
Location_base_pair Starts at 18804853 and ends at 18926404 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)
ACAA2 (18q21.1) / SMG1 (16p12.3)BPTF (17q24.2) / SMG1 (16p12.3)KCNC3 (19q13.33) / SMG1 (16p12.3)
SMG1 (16p12.3) / ANO3 (11p14.2)SMG1 (16p12.3) / ARL6IP1 (16p12.3)SMG1 (16p12.3) / COMMD1 (2p15)
SMG1 (16p12.3) / CYP2C9 (10q23.33)SMG1 (16p12.3) / DOCK3 (3p21.2)SMG1 (16p12.3) / KPNA3 (13q14.2)
SMG1 (16p12.3) / SLC25A3 (12q23.1)SMG1 16p12.3 / ANO3 11p14.2

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 ]
  t(11;16)(p14;p12) SMG1/ANO3

External links

Nomenclature
HGNC (Hugo)SMG1   30045
Cards
Entrez_Gene (NCBI)SMG1  23049  SMG1, nonsense mediated mRNA decay associated PI3K related kinase
Aliases61E3.4; ATX; LIP
GeneCards (Weizmann)SMG1
Ensembl hg19 (Hinxton)ENSG00000157106 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000157106 [Gene_View]  chr16:18804853-18926404 [Contig_View]  SMG1 [Vega]
ICGC DataPortalENSG00000157106
TCGA cBioPortalSMG1
AceView (NCBI)SMG1
Genatlas (Paris)SMG1
WikiGenes23049
SOURCE (Princeton)SMG1
Genetics Home Reference (NIH)SMG1
Genomic and cartography
GoldenPath hg38 (UCSC)SMG1  -     chr16:18804853-18926404 -  16p12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMG1  -     16p12.3   [Description]    (hg19-Feb_2009)
EnsemblSMG1 - 16p12.3 [CytoView hg19]  SMG1 - 16p12.3 [CytoView hg38]
Mapping of homologs : NCBISMG1 [Mapview hg19]  SMG1 [Mapview hg38]
OMIM607032   
Gene and transcription
Genbank (Entrez)AB007881 AB061371 AF186377 AF395444 AK025794
RefSeq transcript (Entrez)NM_015092
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMG1
Cluster EST : UnigeneHs.460179 [ NCBI ]
CGAP (NCI)Hs.460179
Alternative Splicing GalleryENSG00000157106
Gene ExpressionSMG1 [ NCBI-GEO ]   SMG1 [ EBI - ARRAY_EXPRESS ]   SMG1 [ SEEK ]   SMG1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMG1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23049
GTEX Portal (Tissue expression)SMG1
Human Protein AtlasENSG00000157106-SMG1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96Q15   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96Q15  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96Q15
Splice isoforms : SwissVarQ96Q15
Catalytic activity : Enzyme2.7.11.1 [ Enzyme-Expasy ]   2.7.11.12.7.11.1 [ IntEnz-EBI ]   2.7.11.1 [ BRENDA ]   2.7.11.1 [ KEGG ]   
PhosPhoSitePlusQ96Q15
Domaine pattern : Prosite (Expaxy)FAT (PS51189)    FATC (PS51190)    PI3_4_KINASE_2 (PS00916)    PI3_4_KINASE_3 (PS50290)   
Domains : Interpro (EBI)ARM-type_fold    FATC_dom    Kinase-like_dom    PI3/4_kinase_cat_dom    PI3/4_kinase_CS    PIK_FAT    SMG1   
Domain families : Pfam (Sanger)FATC (PF02260)    PI3_PI4_kinase (PF00454)    SMG1 (PF15785)   
Domain families : Pfam (NCBI)pfam02260    pfam00454    pfam15785   
Domain families : Smart (EMBL)FATC (SM01343)  PI3Kc (SM00146)  
Conserved Domain (NCBI)SMG1
DMDM Disease mutations23049
Blocks (Seattle)SMG1
SuperfamilyQ96Q15
Human Protein Atlas [tissue]ENSG00000157106-SMG1 [tissue]
Peptide AtlasQ96Q15
HPRD06123
IPIIPI00939320   IPI00639874   IPI00183368   IPI00640955   IPI00747038   IPI00556369   IPI00978348   
Protein Interaction databases
DIP (DOE-UCLA)Q96Q15
IntAct (EBI)Q96Q15
FunCoupENSG00000157106
BioGRIDSMG1
STRING (EMBL)SMG1
ZODIACSMG1
Ontologies - Pathways
QuickGOQ96Q15
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  RNA binding  protein kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein binding  ATP binding  nucleus  nucleoplasm  cytoplasm  cytosol  DNA repair  mRNA export from nucleus  peptidyl-serine phosphorylation  peptidyl-serine phosphorylation  regulation of telomere maintenance  telomeric DNA binding  protein autophosphorylation  phosphatidylinositol phosphorylation  metal ion binding  regulation of response to DNA damage stimulus  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  RNA binding  protein kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein binding  ATP binding  nucleus  nucleoplasm  cytoplasm  cytosol  DNA repair  mRNA export from nucleus  peptidyl-serine phosphorylation  peptidyl-serine phosphorylation  regulation of telomere maintenance  telomeric DNA binding  protein autophosphorylation  phosphatidylinositol phosphorylation  metal ion binding  regulation of response to DNA damage stimulus  
NDEx NetworkSMG1
Atlas of Cancer Signalling NetworkSMG1
Wikipedia pathwaysSMG1
Orthology - Evolution
OrthoDB23049
GeneTree (enSembl)ENSG00000157106
Phylogenetic Trees/Animal Genes : TreeFamSMG1
HOVERGENQ96Q15
HOGENOMQ96Q15
Homologs : HomoloGeneSMG1
Homology/Alignments : Family Browser (UCSC)SMG1
Gene fusions - Rearrangements
Fusion : MitelmanSMG1/ANO3 [16p12.3/11p14.2]  
Fusion: TCGA_MDACCSMG1 16p12.3 ANO3 11p14.2 BRCA
Fusion PortalSMG1 16p12.3 ANO3 11p14.2 BRCA
Fusion : QuiverSMG1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMG1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMG1
dbVarSMG1
ClinVarSMG1
1000_GenomesSMG1 
Exome Variant ServerSMG1
ExAC (Exome Aggregation Consortium)ENSG00000157106
GNOMAD BrowserENSG00000157106
Genetic variants : HAPMAP23049
Genomic Variants (DGV)SMG1 [DGVbeta]
DECIPHERSMG1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMG1 
Mutations
ICGC Data PortalSMG1 
TCGA Data PortalSMG1 
Broad Tumor PortalSMG1
OASIS PortalSMG1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMG1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMG1
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
BioMutasearch SMG1
DgiDB (Drug Gene Interaction Database)SMG1
DoCM (Curated mutations)SMG1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMG1 (select a term)
intoGenSMG1
Cancer3DSMG1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607032   
Orphanet
DisGeNETSMG1
MedgenSMG1
Genetic Testing Registry SMG1
NextProtQ96Q15 [Medical]
TSGene23049
GENETestsSMG1
Target ValidationSMG1
Huge Navigator SMG1 [HugePedia]
snp3D : Map Gene to Disease23049
BioCentury BCIQSMG1
ClinGenSMG1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23049
Chemical/Pharm GKB GenePA164725852
Clinical trialSMG1
Miscellaneous
canSAR (ICR)SMG1 (select the gene name)
Probes
Litterature
PubMed59 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMG1
EVEXSMG1
GoPubMedSMG1
iHOPSMG1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Feb 28 13:38:32 CET 2018
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