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LYST (lysosomal trafficking regulator)

Identity

Alias_namesCHS1
Chediak-Higashi syndrome 1
Alias_symbol (synonym)CHS
Other alias
HGNC (Hugo) LYST
LocusID (NCBI) 1130
Atlas_Id 56541
Location 1q42.3  [Link to chromosome band 1q42]
Location_base_pair Starts at 235824331 and ends at 236030227 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
FAM19A1 (3p14.1) / LYST (1q42.3)LYST (1q42.3) / DISC1 (1q42.2)LYST (1q42.3) / NID1 (1q42.3)
LYST (1q42.3) / SFTPB (2p11.2)LYST (1q42.3) / TRAF3IP1 (2q37.3)PWWP2B (10q26.3) / LYST (1q42.3)
RPS6KC1 (1q32.3) / LYST (1q42.3)TAPT1 (4p15.32) / LYST (1q42.3)

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 Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Chediak-Higashi Syndrome


External links

Nomenclature
HGNC (Hugo)LYST   1968
LRG (Locus Reference Genomic)LRG_143
Cards
Entrez_Gene (NCBI)LYST  1130  lysosomal trafficking regulator
AliasesCHS; CHS1
GeneCards (Weizmann)LYST
Ensembl hg19 (Hinxton)ENSG00000143669 [Gene_View]  chr1:235824331-236030227 [Contig_View]  LYST [Vega]
Ensembl hg38 (Hinxton)ENSG00000143669 [Gene_View]  chr1:235824331-236030227 [Contig_View]  LYST [Vega]
ICGC DataPortalENSG00000143669
TCGA cBioPortalLYST
AceView (NCBI)LYST
Genatlas (Paris)LYST
WikiGenes1130
SOURCE (Princeton)LYST
Genetics Home Reference (NIH)LYST
Genomic and cartography
GoldenPath hg19 (UCSC)LYST  -     chr1:235824331-236030227 -  1q42.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LYST  -     1q42.3   [Description]    (hg38-Dec_2013)
EnsemblLYST - 1q42.3 [CytoView hg19]  LYST - 1q42.3 [CytoView hg38]
Mapping of homologs : NCBILYST [Mapview hg19]  LYST [Mapview hg38]
OMIM214500   606897   
Gene and transcription
Genbank (Entrez)-
RefSeq transcript (Entrez)NM_000081 NM_001005736 NM_001301365
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LYST
Cluster EST : UnigeneHs.532411 [ NCBI ]
CGAP (NCI)Hs.532411
Alternative Splicing GalleryENSG00000143669
Gene ExpressionLYST [ NCBI-GEO ]   LYST [ EBI - ARRAY_EXPRESS ]   LYST [ SEEK ]   LYST [ MEM ]
Gene Expression Viewer (FireBrowse)LYST [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1130
GTEX Portal (Tissue expression)LYST
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99698   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ99698  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ99698
Splice isoforms : SwissVarQ99698
PhosPhoSitePlusQ99698
Domaine pattern : Prosite (Expaxy)BEACH (PS50197)    PH_BEACH (PS51783)    WD_REPEATS_1 (PS00678)    WD_REPEATS_2 (PS50082)    WD_REPEATS_REGION (PS50294)   
Domains : Interpro (EBI)ARM-type_fold    BEACH_dom    LYST    PH-BEACH_dom    PH_dom-like    WD40/YVTN_repeat-like_dom    WD40_repeat    WD40_repeat_CS    WD40_repeat_dom   
Domain families : Pfam (Sanger)Beach (PF02138)    PH_BEACH (PF14844)    WD40 (PF00400)   
Domain families : Pfam (NCBI)pfam02138    pfam14844    pfam00400   
Domain families : Smart (EMBL)Beach (SM01026)  WD40 (SM00320)  
Conserved Domain (NCBI)LYST
DMDM Disease mutations1130
Blocks (Seattle)LYST
SuperfamilyQ99698
Human Protein AtlasENSG00000143669
Peptide AtlasQ99698
HPRD06060
IPIIPI00796450   IPI00220899   IPI00017094   IPI01010045   IPI00946891   
Protein Interaction databases
DIP (DOE-UCLA)Q99698
IntAct (EBI)Q99698
FunCoupENSG00000143669
BioGRIDLYST
STRING (EMBL)LYST
ZODIACLYST
Ontologies - Pathways
QuickGOQ99698
Ontology : AmiGOprotein binding  cytoplasm  lysosome organization  protein transport  microtubule cytoskeleton  leukocyte chemotaxis  melanosome organization  endosome to lysosome transport via multivesicular body sorting pathway  mast cell secretory granule organization  natural killer cell mediated cytotoxicity  defense response to bacterium  defense response to protozoan  pigmentation  defense response to virus  
Ontology : EGO-EBIprotein binding  cytoplasm  lysosome organization  protein transport  microtubule cytoskeleton  leukocyte chemotaxis  melanosome organization  endosome to lysosome transport via multivesicular body sorting pathway  mast cell secretory granule organization  natural killer cell mediated cytotoxicity  defense response to bacterium  defense response to protozoan  pigmentation  defense response to virus  
NDEx NetworkLYST
Atlas of Cancer Signalling NetworkLYST
Wikipedia pathwaysLYST
Orthology - Evolution
OrthoDB1130
GeneTree (enSembl)ENSG00000143669
Phylogenetic Trees/Animal Genes : TreeFamLYST
HOVERGENQ99698
HOGENOMQ99698
Homologs : HomoloGeneLYST
Homology/Alignments : Family Browser (UCSC)LYST
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLYST [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LYST
dbVarLYST
ClinVarLYST
1000_GenomesLYST 
Exome Variant ServerLYST
ExAC (Exome Aggregation Consortium)LYST (select the gene name)
Genetic variants : HAPMAP1130
Genomic Variants (DGV)LYST [DGVbeta]
DECIPHER (Syndromes)1:235824331-236030227  ENSG00000143669
CONAN: Copy Number AnalysisLYST 
Mutations
ICGC Data PortalLYST 
TCGA Data PortalLYST 
Broad Tumor PortalLYST
OASIS PortalLYST [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLYST  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLYST
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)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch LYST
DgiDB (Drug Gene Interaction Database)LYST
DoCM (Curated mutations)LYST (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LYST (select a term)
intoGenLYST
Cancer3DLYST(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM214500    606897   
Orphanet249    22107   
MedgenLYST
Genetic Testing Registry LYST
NextProtQ99698 [Medical]
TSGene1130
GENETestsLYST
Huge Navigator LYST [HugePedia]
snp3D : Map Gene to Disease1130
BioCentury BCIQLYST
ClinGenLYST
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1130
Chemical/Pharm GKB GenePA26500
Clinical trialLYST
Miscellaneous
canSAR (ICR)LYST (select the gene name)
Probes
Litterature
PubMed40 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLYST
EVEXLYST
GoPubMedLYST
iHOPLYST
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Mar 30 15:08:08 CEST 2017

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