Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SNX4 (sorting nexin 4)

Identity

Alias_symbol (synonym)ATG24B
Other alias
HGNC (Hugo) SNX4
LocusID (NCBI) 8723
Atlas_Id 54653
Location 3q21.2  [Link to chromosome band 3q21]
Location_base_pair Starts at 125446644 and ends at 125520214 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)
SNX4 (3q21.2) / EPC2 (2q23.1)SNX4 (3q21.2) / OSBPL11 (3q21.2)SNX4 (3q21.2) / PARD3B (2q33.3)
SNX4 (3q21.2) / SNX4 (3q21.2)

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(2;3)(q33;q21) SNX4/PARD3B

External links

Nomenclature
HGNC (Hugo)SNX4   11175
Cards
Entrez_Gene (NCBI)SNX4  8723  sorting nexin 4
AliasesATG24B
GeneCards (Weizmann)SNX4
Ensembl hg19 (Hinxton)ENSG00000114520 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000114520 [Gene_View]  chr3:125446644-125520214 [Contig_View]  SNX4 [Vega]
ICGC DataPortalENSG00000114520
TCGA cBioPortalSNX4
AceView (NCBI)SNX4
Genatlas (Paris)SNX4
WikiGenes8723
SOURCE (Princeton)SNX4
Genetics Home Reference (NIH)SNX4
Genomic and cartography
GoldenPath hg38 (UCSC)SNX4  -     chr3:125446644-125520214 -  3q21.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SNX4  -     3q21.2   [Description]    (hg19-Feb_2009)
EnsemblSNX4 - 3q21.2 [CytoView hg19]  SNX4 - 3q21.2 [CytoView hg38]
Mapping of homologs : NCBISNX4 [Mapview hg19]  SNX4 [Mapview hg38]
OMIM605931   
Gene and transcription
Genbank (Entrez)AF065485 AF130078 AI187416 AK001835 AK298972
RefSeq transcript (Entrez)NM_003794
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SNX4
Cluster EST : UnigeneHs.507243 [ NCBI ]
CGAP (NCI)Hs.507243
Alternative Splicing GalleryENSG00000114520
Gene ExpressionSNX4 [ NCBI-GEO ]   SNX4 [ EBI - ARRAY_EXPRESS ]   SNX4 [ SEEK ]   SNX4 [ MEM ]
Gene Expression Viewer (FireBrowse)SNX4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8723
GTEX Portal (Tissue expression)SNX4
Human Protein AtlasENSG00000114520-SNX4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95219   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO95219  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95219
Splice isoforms : SwissVarO95219
PhosPhoSitePlusO95219
Domaine pattern : Prosite (Expaxy)PX (PS50195)   
Domains : Interpro (EBI)Phox   
Domain families : Pfam (Sanger)PX (PF00787)   
Domain families : Pfam (NCBI)pfam00787   
Domain families : Smart (EMBL)PX (SM00312)  
Conserved Domain (NCBI)SNX4
DMDM Disease mutations8723
Blocks (Seattle)SNX4
SuperfamilyO95219
Human Protein Atlas [tissue]ENSG00000114520-SNX4 [tissue]
Peptide AtlasO95219
HPRD09334
IPIIPI00029403   IPI01009795   IPI00945903   IPI00946080   
Protein Interaction databases
DIP (DOE-UCLA)O95219
IntAct (EBI)O95219
FunCoupENSG00000114520
BioGRIDSNX4
STRING (EMBL)SNX4
ZODIACSNX4
Ontologies - Pathways
QuickGOO95219
Ontology : AmiGOepidermal growth factor receptor binding  insulin receptor binding  protein binding  cytoplasm  cytoplasmic dynein complex  plasma membrane  endocytosis  protein transport  membrane  vesicle organization  extrinsic component of membrane  SNARE complex  early endosome membrane  endocytic recycling  phosphatidylinositol binding  protein complex  positive regulation of histamine secretion by mast cell  transferrin receptor binding  leptin receptor binding  
Ontology : EGO-EBIepidermal growth factor receptor binding  insulin receptor binding  protein binding  cytoplasm  cytoplasmic dynein complex  plasma membrane  endocytosis  protein transport  membrane  vesicle organization  extrinsic component of membrane  SNARE complex  early endosome membrane  endocytic recycling  phosphatidylinositol binding  protein complex  positive regulation of histamine secretion by mast cell  transferrin receptor binding  leptin receptor binding  
NDEx NetworkSNX4
Atlas of Cancer Signalling NetworkSNX4
Wikipedia pathwaysSNX4
Orthology - Evolution
OrthoDB8723
GeneTree (enSembl)ENSG00000114520
Phylogenetic Trees/Animal Genes : TreeFamSNX4
HOVERGENO95219
HOGENOMO95219
Homologs : HomoloGeneSNX4
Homology/Alignments : Family Browser (UCSC)SNX4
Gene fusions - Rearrangements
Fusion : MitelmanSNX4/PARD3B [3q21.2/2q33.3]  
Fusion : QuiverSNX4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSNX4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNX4
dbVarSNX4
ClinVarSNX4
1000_GenomesSNX4 
Exome Variant ServerSNX4
ExAC (Exome Aggregation Consortium)ENSG00000114520
GNOMAD BrowserENSG00000114520
Genetic variants : HAPMAP8723
Genomic Variants (DGV)SNX4 [DGVbeta]
DECIPHERSNX4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSNX4 
Mutations
ICGC Data PortalSNX4 
TCGA Data PortalSNX4 
Broad Tumor PortalSNX4
OASIS PortalSNX4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSNX4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSNX4
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 SNX4
DgiDB (Drug Gene Interaction Database)SNX4
DoCM (Curated mutations)SNX4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SNX4 (select a term)
intoGenSNX4
Cancer3DSNX4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605931   
Orphanet
DisGeNETSNX4
MedgenSNX4
Genetic Testing Registry SNX4
NextProtO95219 [Medical]
TSGene8723
GENETestsSNX4
Target ValidationSNX4
Huge Navigator SNX4 [HugePedia]
snp3D : Map Gene to Disease8723
BioCentury BCIQSNX4
ClinGenSNX4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8723
Chemical/Pharm GKB GenePA36014
Clinical trialSNX4
Miscellaneous
canSAR (ICR)SNX4 (select the gene name)
Probes
Litterature
PubMed28 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSNX4
EVEXSNX4
GoPubMedSNX4
iHOPSNX4
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 13:38:52 CET 2018
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