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

SYNGAP1 (synaptic Ras GTPase activating protein 1)

Identity

Alias_namessynaptic Ras GTPase activating protein 1 homolog (rat)
Alias_symbol (synonym)SYNGAP
RASA5
KIAA1938
Other aliasMRD5
RASA1
HGNC (Hugo) SYNGAP1
LocusID (NCBI) 8831
Atlas_Id 54681
Location 6p21.32  [Link to chromosome band 6p21]
Location_base_pair Starts at 33420070 and ends at 33453689 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)
SYNGAP1 (6p21.32) / HSP90AB1 (6p21.1)

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 ]
  SYNGAP1/HSP90AB1 (6p21)


External links

Nomenclature
HGNC (Hugo)SYNGAP1   11497
LRG (Locus Reference Genomic)LRG_1193
Cards
Entrez_Gene (NCBI)SYNGAP1  8831  synaptic Ras GTPase activating protein 1
AliasesMRD5; RASA1; RASA5; SYNGAP
GeneCards (Weizmann)SYNGAP1
Ensembl hg19 (Hinxton)ENSG00000197283 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000197283 [Gene_View]  ENSG00000197283 [Sequence]  chr6:33420070-33453689 [Contig_View]  SYNGAP1 [Vega]
ICGC DataPortalENSG00000197283
TCGA cBioPortalSYNGAP1
AceView (NCBI)SYNGAP1
Genatlas (Paris)SYNGAP1
WikiGenes8831
SOURCE (Princeton)SYNGAP1
Genetics Home Reference (NIH)SYNGAP1
Genomic and cartography
GoldenPath hg38 (UCSC)SYNGAP1  -     chr6:33420070-33453689 +  6p21.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SYNGAP1  -     6p21.32   [Description]    (hg19-Feb_2009)
EnsemblSYNGAP1 - 6p21.32 [CytoView hg19]  SYNGAP1 - 6p21.32 [CytoView hg38]
Mapping of homologs : NCBISYNGAP1 [Mapview hg19]  SYNGAP1 [Mapview hg38]
OMIM603384   612621   
Gene and transcription
Genbank (Entrez)AK094225 AK124666 AK307888 AL713634 BM354009
RefSeq transcript (Entrez)NM_001130066 NM_006772
RefSeq genomic (Entrez)NC_000006 NG_016137 NT_167249
Consensus coding sequences : CCDS (NCBI)SYNGAP1
Cluster EST : UnigeneHs.586264 [ NCBI ]
CGAP (NCI)Hs.586264
Alternative Splicing GalleryENSG00000197283
Gene ExpressionSYNGAP1 [ NCBI-GEO ]   SYNGAP1 [ EBI - ARRAY_EXPRESS ]   SYNGAP1 [ SEEK ]   SYNGAP1 [ MEM ]
Gene Expression Viewer (FireBrowse)SYNGAP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8831
GTEX Portal (Tissue expression)SYNGAP1
Human Protein AtlasENSG00000197283-SYNGAP1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96PV0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96PV0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96PV0
Splice isoforms : SwissVarQ96PV0
PhosPhoSitePlusQ96PV0
Domaine pattern : Prosite (Expaxy)PH_DOMAIN (PS50003)    RAS_GTPASE_ACTIV_1 (PS00509)    RAS_GTPASE_ACTIV_2 (PS50018)   
Domains : Interpro (EBI)C2_dom    C2_domain_sf    DUF3498    PH_domain    RasGAP_CS    RasGAP_dom    Rho_GTPase_activation_prot    SynGAP_PH   
Domain families : Pfam (Sanger)C2 (PF00168)    DUF3498 (PF12004)    RasGAP (PF00616)   
Domain families : Pfam (NCBI)pfam00168    pfam12004    pfam00616   
Domain families : Smart (EMBL)C2 (SM00239)  PH (SM00233)  RasGAP (SM00323)  
Conserved Domain (NCBI)SYNGAP1
DMDM Disease mutations8831
Blocks (Seattle)SYNGAP1
SuperfamilyQ96PV0
Human Protein Atlas [tissue]ENSG00000197283-SYNGAP1 [tissue]
Peptide AtlasQ96PV0
HPRD16018
IPIIPI00177884   IPI00337790   IPI00796859   IPI00847493   IPI00797957   IPI00924664   
Protein Interaction databases
DIP (DOE-UCLA)Q96PV0
IntAct (EBI)Q96PV0
FunCoupENSG00000197283
BioGRIDSYNGAP1
STRING (EMBL)SYNGAP1
ZODIACSYNGAP1
Ontologies - Pathways
QuickGOQ96PV0
Ontology : AmiGOMAPK cascade  GTPase activator activity  cytosol  plasma membrane  Ras protein signal transduction  pattern specification process  visual learning  postsynaptic density  dendrite development  SH3 domain binding  receptor clustering  dendritic shaft  regulation of MAPK cascade  negative regulation of neuron apoptotic process  positive regulation of GTPase activity  negative regulation of Ras protein signal transduction  regulation of synaptic plasticity  regulation of long-term neuronal synaptic plasticity  negative regulation of axonogenesis  regulation of synapse structure or activity  maintenance of postsynaptic specialization structure  glutamatergic synapse  
Ontology : EGO-EBIMAPK cascade  GTPase activator activity  cytosol  plasma membrane  Ras protein signal transduction  pattern specification process  visual learning  postsynaptic density  dendrite development  SH3 domain binding  receptor clustering  dendritic shaft  regulation of MAPK cascade  negative regulation of neuron apoptotic process  positive regulation of GTPase activity  negative regulation of Ras protein signal transduction  regulation of synaptic plasticity  regulation of long-term neuronal synaptic plasticity  negative regulation of axonogenesis  regulation of synapse structure or activity  maintenance of postsynaptic specialization structure  glutamatergic synapse  
Pathways : KEGGRas signaling pathway   
NDEx NetworkSYNGAP1
Atlas of Cancer Signalling NetworkSYNGAP1
Wikipedia pathwaysSYNGAP1
Orthology - Evolution
OrthoDB8831
GeneTree (enSembl)ENSG00000197283
Phylogenetic Trees/Animal Genes : TreeFamSYNGAP1
HOVERGENQ96PV0
HOGENOMQ96PV0
Homologs : HomoloGeneSYNGAP1
Homology/Alignments : Family Browser (UCSC)SYNGAP1
Gene fusions - Rearrangements
Fusion : MitelmanSYNGAP1/HSP90AB1 [6p21.32/6p21.1]  
Fusion : QuiverSYNGAP1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSYNGAP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SYNGAP1
dbVarSYNGAP1
ClinVarSYNGAP1
1000_GenomesSYNGAP1 
Exome Variant ServerSYNGAP1
ExAC (Exome Aggregation Consortium)ENSG00000197283
GNOMAD BrowserENSG00000197283
Varsome BrowserSYNGAP1
Genetic variants : HAPMAP8831
Genomic Variants (DGV)SYNGAP1 [DGVbeta]
DECIPHERSYNGAP1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSYNGAP1 
Mutations
ICGC Data PortalSYNGAP1 
TCGA Data PortalSYNGAP1 
Broad Tumor PortalSYNGAP1
OASIS PortalSYNGAP1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSYNGAP1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSYNGAP1
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)Mendelian genes
BioMutasearch SYNGAP1
DgiDB (Drug Gene Interaction Database)SYNGAP1
DoCM (Curated mutations)SYNGAP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SYNGAP1 (select a term)
intoGenSYNGAP1
Cancer3DSYNGAP1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603384    612621   
Orphanet18028   
DisGeNETSYNGAP1
MedgenSYNGAP1
Genetic Testing Registry SYNGAP1
NextProtQ96PV0 [Medical]
TSGene8831
GENETestsSYNGAP1
Target ValidationSYNGAP1
Huge Navigator SYNGAP1 [HugePedia]
snp3D : Map Gene to Disease8831
BioCentury BCIQSYNGAP1
ClinGenSYNGAP1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8831
Chemical/Pharm GKB GenePA36279
Clinical trialSYNGAP1
Miscellaneous
canSAR (ICR)SYNGAP1 (select the gene name)
Probes
Litterature
PubMed39 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSYNGAP1
EVEXSYNGAP1
GoPubMedSYNGAP1
iHOPSYNGAP1
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 : Tue Nov 6 11:43:14 CET 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.