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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret jlhuret@AtlasGeneticsOncology.org
Donations are also welcome
If each casual visitor gives 3 Euros or Dollars, the Atlas is saved in a week !
If each professional gives 100 Euros or Dollars once a year (now), the Atlas is saved in 2 weeks !
Don't let the Atlas imminent demise
Note: we send fiscal receipts for donations equal or above 50 Euros or Dollars

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SCN9A (sodium channel, voltage gated, type IX alpha subunit)

Identity

Other namesETHA
FEB3B
GEFSP7
HSAN2D
NE-NA
NENA
Nav1.7
PN1
SFNP
HGNC (Hugo) SCN9A
LocusID (NCBI) 6335
Location 2q24.3
Location_base_pair Starts at 167051697 and ends at 167232497 bp from pter ( according to hg19-Feb_2009)
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

 

External links

Nomenclature
HGNC (Hugo)SCN9A   10597
Cards
Entrez_Gene (NCBI)SCN9A  6335  sodium channel, voltage gated, type IX alpha subunit
GeneCards (Weizmann)SCN9A
Ensembl hg19 (Hinxton)ENSG00000169432 [Gene_View]  chr2:167051697-167232497 [Contig_View]  SCN9A [Vega]
Ensembl hg38 (Hinxton)ENSG00000169432 [Gene_View]  chr2:167051697-167232497 [Contig_View]  SCN9A [Vega]
ICGC DataPortalENSG00000169432
cBioPortalSCN9A
AceView (NCBI)SCN9A
Genatlas (Paris)SCN9A
WikiGenes6335
SOURCE (Princeton)SCN9A
Genomic and cartography
GoldenPath hg19 (UCSC)SCN9A  -     chr2:167051697-167232497 -  2q24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SCN9A  -     2q24.3   [Description]    (hg38-Dec_2013)
EnsemblSCN9A - 2q24.3 [CytoView hg19]  SCN9A - 2q24.3 [CytoView hg38]
Mapping of homologs : NCBISCN9A [Mapview hg19]  SCN9A [Mapview hg38]
OMIM133020   167400   201300   243000   603415   607208   613863   
Gene and transcription
Genbank (Entrez)AJ277393 AJ310882 AJ310883 AJ310897 AK307549
RefSeq transcript (Entrez)NM_002977
RefSeq genomic (Entrez)NC_000002 NC_018913 NG_012798 NT_005403 NW_004929305
Consensus coding sequences : CCDS (NCBI)SCN9A
Cluster EST : UnigeneHs.439145 [ NCBI ]
CGAP (NCI)Hs.439145
Alternative Splicing : Fast-db (Paris)GSHG0018127
Alternative Splicing GalleryENSG00000169432
Gene ExpressionSCN9A [ NCBI-GEO ]     SCN9A [ SEEK ]   SCN9A [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15858 (Uniprot)
NextProtQ15858  [Medical]
With graphics : InterProQ15858
Splice isoforms : SwissVarQ15858 (Swissvar)
Domains : Interpro (EBI)Channel_four-helix_dom    DUF3451    Ion_trans_dom    IQ_motif_EF-hand-BS    Na_channel_asu    Na_trans_assoc    SCN9A   
Related proteins : CluSTrQ15858
Domain families : Pfam (Sanger)DUF3451 (PF11933)    Ion_trans (PF00520)    Na_trans_assoc (PF06512)   
Domain families : Pfam (NCBI)pfam11933    pfam00520    pfam06512   
Domain families : Smart (EMBL)IQ (SM00015)  
DMDM Disease mutations6335
Blocks (Seattle)Q15858
Human Protein AtlasENSG00000169432
Peptide AtlasQ15858
HPRD04565
IPIIPI00745570   IPI00154944   IPI00479414   IPI00917567   
Protein Interaction databases
DIP (DOE-UCLA)Q15858
IntAct (EBI)Q15858
FunCoupENSG00000169432
BioGRIDSCN9A
IntegromeDBSCN9A
STRING (EMBL)SCN9A
Ontologies - Pathways
QuickGOQ15858
Ontology : AmiGOvoltage-gated sodium channel complex  voltage-gated sodium channel activity  plasma membrane  sodium ion transport  inflammatory response  response to toxic substance  post-embryonic development  neuronal action potential  sodium ion binding  regulation of ion transmembrane transport  sodium ion transmembrane transport  behavioral response to pain  membrane depolarization during action potential  
Ontology : EGO-EBIvoltage-gated sodium channel complex  voltage-gated sodium channel activity  plasma membrane  sodium ion transport  inflammatory response  response to toxic substance  post-embryonic development  neuronal action potential  sodium ion binding  regulation of ion transmembrane transport  sodium ion transmembrane transport  behavioral response to pain  membrane depolarization during action potential  
Protein Interaction DatabaseSCN9A
DoCM (Curated mutations)SCN9A
Wikipedia pathwaysSCN9A
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSCN9A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SCN9A
dbVarSCN9A
ClinVarSCN9A
1000_GenomesSCN9A 
Exome Variant ServerSCN9A
SNP (GeneSNP Utah)SCN9A
SNP : HGBaseSCN9A
Genetic variants : HAPMAPSCN9A
Genomic Variants (DGV)SCN9A [DGVbeta]
Mutations
ICGC Data PortalENSG00000169432 
Somatic Mutations in Cancer : COSMICSCN9A 
CONAN: Copy Number AnalysisSCN9A 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)2:167051697-167232497
Mutations and Diseases : HGMDSCN9A
OMIM133020    167400    201300    243000    603415    607208    613863   
MedgenSCN9A
NextProtQ15858 [Medical]
GENETestsSCN9A
Disease Genetic AssociationSCN9A
Huge Navigator SCN9A [HugePedia]  SCN9A [HugeCancerGEM]
snp3D : Map Gene to Disease6335
DGIdb (Drug Gene Interaction db)SCN9A
General knowledge
Homologs : HomoloGeneSCN9A
Homology/Alignments : Family Browser (UCSC)SCN9A
Phylogenetic Trees/Animal Genes : TreeFamSCN9A
Chemical/Protein Interactions : CTD6335
Chemical/Pharm GKB GenePA35010
Clinical trialSCN9A
Cancer Resource (Charite)ENSG00000169432
Other databases
Probes
Litterature
PubMed108 Pubmed reference(s) in Entrez
CoreMineSCN9A
GoPubMedSCN9A
iHOPSCN9A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated02-2015Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Mar 28 17:14:14 CET 2015

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