Atlas of Genetics and Cytogenetics in Oncology and Haematology


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HPS4 (HPS4, biogenesis of lysosomal organelles complex 3 subunit 2)

Identity

Alias_namesHermansky-Pudlak syndrome 4
Alias_symbol (synonym)KIAA1667
LE
BLOC3S2
Other alias
HGNC (Hugo) HPS4
LocusID (NCBI) 89781
Atlas_Id 64418
Location 22q12.1  [Link to chromosome band 22q12]
Location_base_pair Starts at 26450883 and ends at 26483863 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)
KIF5B (10p11.22) / HPS4 (22q12.1)

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

 


External links

Nomenclature
HGNC (Hugo)HPS4   15844
LRG (Locus Reference Genomic)LRG_590
Cards
Entrez_Gene (NCBI)HPS4  89781  HPS4, biogenesis of lysosomal organelles complex 3 subunit 2
AliasesBLOC3S2; LE
GeneCards (Weizmann)HPS4
Ensembl hg19 (Hinxton)ENSG00000100099 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000100099 [Gene_View]  chr22:26450883-26483863 [Contig_View]  HPS4 [Vega]
ICGC DataPortalENSG00000100099
TCGA cBioPortalHPS4
AceView (NCBI)HPS4
Genatlas (Paris)HPS4
WikiGenes89781
SOURCE (Princeton)HPS4
Genetics Home Reference (NIH)HPS4
Genomic and cartography
GoldenPath hg38 (UCSC)HPS4  -     chr22:26450883-26483863 -  22q12.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HPS4  -     22q12.1   [Description]    (hg19-Feb_2009)
EnsemblHPS4 - 22q12.1 [CytoView hg19]  HPS4 - 22q12.1 [CytoView hg38]
Mapping of homologs : NCBIHPS4 [Mapview hg19]  HPS4 [Mapview hg38]
OMIM606682   614073   
Gene and transcription
Genbank (Entrez)AB051454 AK054717 AK057648 AK095406 AK097529
RefSeq transcript (Entrez)NM_001349896 NM_001349898 NM_001349899 NM_001349900 NM_001349901 NM_001349902 NM_001349903 NM_001349904 NM_001349905 NM_022081 NM_152840 NM_152841 NM_152842 NM_152843
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HPS4
Cluster EST : UnigeneHs.474436 [ NCBI ]
CGAP (NCI)Hs.474436
Alternative Splicing GalleryENSG00000100099
Gene ExpressionHPS4 [ NCBI-GEO ]   HPS4 [ EBI - ARRAY_EXPRESS ]   HPS4 [ SEEK ]   HPS4 [ MEM ]
Gene Expression Viewer (FireBrowse)HPS4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)89781
GTEX Portal (Tissue expression)HPS4
Human Protein AtlasENSG00000100099-HPS4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NQG7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NQG7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NQG7
Splice isoforms : SwissVarQ9NQG7
PhosPhoSitePlusQ9NQG7
Domains : Interpro (EBI)HPS4   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)HPS4
DMDM Disease mutations89781
Blocks (Seattle)HPS4
SuperfamilyQ9NQG7
Human Protein Atlas [tissue]ENSG00000100099-HPS4 [tissue]
Peptide AtlasQ9NQG7
HPRD05983
IPIIPI00152931   IPI00220743   IPI00375189   IPI00375190   IPI00877586   IPI00878650   IPI01010432   
Protein Interaction databases
DIP (DOE-UCLA)Q9NQG7
IntAct (EBI)Q9NQG7
FunCoupENSG00000100099
BioGRIDHPS4
STRING (EMBL)HPS4
ZODIACHPS4
Ontologies - Pathways
QuickGOQ9NQG7
Ontology : AmiGOguanyl-nucleotide exchange factor activity  protein binding  cytoplasm  lysosome  cytosol  protein targeting  lysosome organization  blood coagulation  hemostasis  membrane  Rab GTPase binding  melanocyte differentiation  BLOC-3 complex  melanosome  protein homodimerization activity  platelet dense granule  positive regulation of GTPase activity  protein dimerization activity  positive regulation of eye pigmentation  protein stabilization  membrane organization  melanosome assembly  positive regulation of protein targeting to mitochondrion  
Ontology : EGO-EBIguanyl-nucleotide exchange factor activity  protein binding  cytoplasm  lysosome  cytosol  protein targeting  lysosome organization  blood coagulation  hemostasis  membrane  Rab GTPase binding  melanocyte differentiation  BLOC-3 complex  melanosome  protein homodimerization activity  platelet dense granule  positive regulation of GTPase activity  protein dimerization activity  positive regulation of eye pigmentation  protein stabilization  membrane organization  melanosome assembly  positive regulation of protein targeting to mitochondrion  
NDEx NetworkHPS4
Atlas of Cancer Signalling NetworkHPS4
Wikipedia pathwaysHPS4
Orthology - Evolution
OrthoDB89781
GeneTree (enSembl)ENSG00000100099
Phylogenetic Trees/Animal Genes : TreeFamHPS4
HOVERGENQ9NQG7
HOGENOMQ9NQG7
Homologs : HomoloGeneHPS4
Homology/Alignments : Family Browser (UCSC)HPS4
Gene fusions - Rearrangements
Tumor Fusion PortalHPS4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHPS4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HPS4
dbVarHPS4
ClinVarHPS4
1000_GenomesHPS4 
Exome Variant ServerHPS4
ExAC (Exome Aggregation Consortium)ENSG00000100099
GNOMAD BrowserENSG00000100099
Genetic variants : HAPMAP89781
Genomic Variants (DGV)HPS4 [DGVbeta]
DECIPHERHPS4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHPS4 
Mutations
ICGC Data PortalHPS4 
TCGA Data PortalHPS4 
Broad Tumor PortalHPS4
OASIS PortalHPS4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHPS4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHPS4
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)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch HPS4
DgiDB (Drug Gene Interaction Database)HPS4
DoCM (Curated mutations)HPS4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HPS4 (select a term)
intoGenHPS4
Cancer3DHPS4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606682    614073   
Orphanet19195   
DisGeNETHPS4
MedgenHPS4
Genetic Testing Registry HPS4
NextProtQ9NQG7 [Medical]
TSGene89781
GENETestsHPS4
Target ValidationHPS4
Huge Navigator HPS4 [HugePedia]
snp3D : Map Gene to Disease89781
BioCentury BCIQHPS4
ClinGenHPS4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD89781
Chemical/Pharm GKB GenePA29434
Clinical trialHPS4
Miscellaneous
canSAR (ICR)HPS4 (select the gene name)
Probes
Litterature
PubMed28 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHPS4
EVEXHPS4
GoPubMedHPS4
iHOPHPS4
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 21 13:43:44 CET 2017

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