Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SNX1 (sorting nexin 1)

Identity

Other namesHsT17379
VPS5
HGNC (Hugo) SNX1
LocusID (NCBI) 6642
Location 15q22.31
Location_base_pair Starts at 64388083 and ends at 64436433 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)SNX1   11172
Cards
Entrez_Gene (NCBI)SNX1  6642  sorting nexin 1
GeneCards (Weizmann)SNX1
Ensembl hg19 (Hinxton)ENSG00000028528 [Gene_View]  chr15:64388083-64436433 [Contig_View]  SNX1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000028528 [Gene_View]  chr15:64388083-64436433 [Contig_View]  SNX1 [Vega]
ICGC DataPortalENSG00000028528
cBioPortalSNX1
AceView (NCBI)SNX1
Genatlas (Paris)SNX1
WikiGenes6642
SOURCE (Princeton)SNX1
Genomic and cartography
GoldenPath hg19 (UCSC)SNX1  -     chr15:64388083-64436433 +  15q22.31   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SNX1  -     15q22.31   [Description]    (hg38-Dec_2013)
EnsemblSNX1 - 15q22.31 [CytoView hg19]  SNX1 - 15q22.31 [CytoView hg38]
Mapping of homologs : NCBISNX1 [Mapview hg19]  SNX1 [Mapview hg38]
OMIM601272   
Gene and transcription
Genbank (Entrez)AB209013 AF065483 AF065484 AF131792 AK128179
RefSeq transcript (Entrez)NM_001242933 NM_003099 NM_148955 NM_152826
RefSeq genomic (Entrez)AC_000147 NC_000015 NC_018926 NG_029708 NT_010194 NW_001838218 NW_004929398
Consensus coding sequences : CCDS (NCBI)SNX1
Cluster EST : UnigeneHs.188634 [ NCBI ]
CGAP (NCI)Hs.188634
Alternative Splicing : Fast-db (Paris)GSHG0009928
Alternative Splicing GalleryENSG00000028528
Gene ExpressionSNX1 [ NCBI-GEO ]     SNX1 [ SEEK ]   SNX1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13596 (Uniprot)
NextProtQ13596  [Medical]
With graphics : InterProQ13596
Splice isoforms : SwissVarQ13596 (Swissvar)
Domaine pattern : Prosite (Expaxy)PX (PS50195)   
Domains : Interpro (EBI)Phox    SNX1    Sorting_nexin_N    Vps5_C   
Related proteins : CluSTrQ13596
Domain families : Pfam (Sanger)PX (PF00787)    Sorting_nexin (PF03700)    Vps5 (PF09325)   
Domain families : Pfam (NCBI)pfam00787    pfam03700    pfam09325   
Domain families : Smart (EMBL)PX (SM00312)  
DMDM Disease mutations6642
Blocks (Seattle)Q13596
PDB (SRS)2I4K    4FZS   
PDB (PDBSum)2I4K    4FZS   
PDB (IMB)2I4K    4FZS   
PDB (RSDB)2I4K    4FZS   
Human Protein AtlasENSG00000028528
Peptide AtlasQ13596
HPRD03171
IPIIPI00220527   IPI00183274   IPI00556082   IPI00183530   
Protein Interaction databases
DIP (DOE-UCLA)Q13596
IntAct (EBI)Q13596
FunCoupENSG00000028528
BioGRIDSNX1
IntegromeDBSNX1
STRING (EMBL)SNX1
Ontologies - Pathways
QuickGOQ13596
Ontology : AmiGOprotein binding  cytoplasm  Golgi apparatus  cytosol  intracellular protein transport  endocytosis  endosome membrane  cytoplasmic membrane-bounded vesicle  retromer complex  early endosome membrane  early endosome to Golgi transport  phosphatidylinositol binding  intracellular membrane-bounded organelle  positive regulation of protein catabolic process  
Ontology : EGO-EBIprotein binding  cytoplasm  Golgi apparatus  cytosol  intracellular protein transport  endocytosis  endosome membrane  cytoplasmic membrane-bounded vesicle  retromer complex  early endosome membrane  early endosome to Golgi transport  phosphatidylinositol binding  intracellular membrane-bounded organelle  positive regulation of protein catabolic process  
Protein Interaction DatabaseSNX1
DoCM (Curated mutations)SNX1
Wikipedia pathwaysSNX1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSNX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNX1
dbVarSNX1
ClinVarSNX1
1000_GenomesSNX1 
Exome Variant ServerSNX1
SNP (GeneSNP Utah)SNX1
SNP : HGBaseSNX1
Genetic variants : HAPMAPSNX1
Genomic VariantsSNX1  SNX1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000028528 
Somatic Mutations in Cancer : COSMICSNX1 
CONAN: Copy Number AnalysisSNX1 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)15:64388083-64436433
Mutations and Diseases : HGMDSNX1
OMIM601272   
MedgenSNX1
NextProtQ13596 [Medical]
GENETestsSNX1
Disease Genetic AssociationSNX1
Huge Navigator SNX1 [HugePedia]  SNX1 [HugeCancerGEM]
snp3D : Map Gene to Disease6642
DGIdb (Drug Gene Interaction db)SNX1
General knowledge
Homologs : HomoloGeneSNX1
Homology/Alignments : Family Browser (UCSC)SNX1
Phylogenetic Trees/Animal Genes : TreeFamSNX1
Chemical/Protein Interactions : CTD6642
Chemical/Pharm GKB GenePA36011
Clinical trialSNX1
Cancer Resource (Charite)ENSG00000028528
Other databases
Probes
Litterature
PubMed48 Pubmed reference(s) in Entrez
CoreMineSNX1
GoPubMedSNX1
iHOPSNX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sun Dec 21 01:39:25 CET 2014

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