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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LYST Gene

protein-coding   GIFtS: 52
GCID: GC01M235824

Lysosomal Trafficking Regulator

(Previous name: Chediak-Higashi syndrome 1)
(Previous symbol: CHS1)
  14 related diseases
at
MalaCards
 

Aliases
for LYST gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section
Aliases
Lysosomal Trafficking Regulator1 2
CHS11 2 3 5
Chediak-Higashi Syndrome 11 2
Beige Homolog2 3
CHS2 3
Lysosomal-Trafficking Regulator2

External Ids:    HGNC: 19681   Entrez Gene: 11302   Ensembl: ENSG000001436697   OMIM: 6068975   UniProtKB: Q996983   

Export aliases for LYST gene to outside databases

Previous GC identifers: GC01M232151 GC01M233890 GC01M206276


Summaries
for LYST gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for LYST Gene:
This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in
pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder.
Alternative splicing results in multiple transcript variants, though the full-length nature of some of these
variants has not been determined. (provided by RefSeq, Apr 2013)

GeneCards Summary for LYST Gene: 
LYST (lysosomal trafficking regulator) is a protein-coding gene. Diseases associated with LYST include chediak-higashi syndrome, and t lymphocyte deficiency. GO annotations related to this gene include protein binding. An important paralog of this gene is NSMAF.

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
Function: May be required for sorting endosomal resident proteins into late multivesicular endosomes by a
mechanism involving microtubules




Genomic Views
for LYST gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NT_167186.1  NC_018912.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LYST gene promoter:
         LHX3b/Lhx3b   p53   FOXD1   POU6F1 (c2)   Egr-4   AREB6   FOXO1a   LHX3a/Lhx3a   NF-kappaB1   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LYST promoter sequence
   Search SABiosciences Chromatin IP Primers for LYST

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LYST


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q42.1-q42.2   Ensembl cytogenetic band:  1q42.3   HGNC cytogenetic band: 1q42.1-q42.2

LYST Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYST gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M235824:  view genomic region     (about GC identifiers)

Start:
 235,824,341 bp from pter      End:
 236,046,940 bp from pter
Size:
 222,600 bases      Orientation:
 minus strand

Proteins
for LYST gene

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section
UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698 (See protein sequence)
Recommended Name: Lysosomal-trafficking regulator  
Size: 3801 amino acids; 429139 Da
Subunit: Interacts with CENPJ, LIP8 and ZNF521
Subcellular location: Cytoplasm (Potential)
Secondary accessions: O43274 Q5T2U9 Q96TD7 Q96TD8 Q99709 Q9H133
Alternative splicing: 3 isoforms:  Q99698-1   Q99698-2   Q99698-3   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for LYST: NX_Q99698

Explore proteomics data for LYST at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q99698

    • LYST Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    LYST Protein Expression
    REFSEQ proteins: NP_000072.2  
    ENSEMBL proteins: 
     ENSP00000374444   ENSP00000417168   ENSP00000374443   ENSP00000438315  

    Human Recombinant Protein Products for LYST: 
    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
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    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec 
    OriGene Custom Protein Services for LYST
    GenScript Custom Purified and Recombinant Proteins Services for LYST
    Novus Biologicals LYST Protein
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for LYST 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol IEA--
    GO:0015630microtubule cytoskeleton IDA9606205

    LYST for ontologies           About GeneDecksing



    LYST Antibody Products: 
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    Novus Biologicals LYST Antibody
    Abcam antibodies for LYST
    Cloud-Clone Corp. Antibodies for LYST 
    Search ThermoFisher Antibodies for LYST
    Search LSBio for Antibodies for LYST 

    Assay Products for LYST: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for LYST
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for LYST
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for LYST 
    Cloud-Clone Corp. CLIAs for LYST

    Protein Domains /
    Families
    for LYST gene

    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    		 HGNC Gene Families: 
    WDR: WD repeat domain containing

    5/6 InterPro protein domains (see all 6):
     IPR000409 BEACH_dom
     IPR019775 WD40_repeat_CS
     IPR023362 PH-BEACH_dom
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom

    Graphical View of Domain Structure for InterPro Entry Q99698

    ProtoNet protein and cluster: Q99698

    1 Blocks protein domain: IPB000409 Beige/BEACH domain

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
    Similarity: Contains 1 BEACH domain
    Similarity: Contains 7 WD repeats


    LYST for domains           About GeneDecksing


    Function
    for LYST gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section
    Molecular Function:

         UniProtKB/Swiss-Prot Summary: LYST_HUMAN, Q99698
    Function: May be required for sorting endosomal resident proteins into late multivesicular endosomes by a
    mechanism involving microtubules

         Genatlas biochemistry entry for LYST:
    putative lysosomal associated membrane protein,intracellular trafficking regulator,with two alternatively spliced
    isoforms,homologous to mouse beige and yeast VPS15

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005488binding ----
    GO:0005515protein binding IPI11984006
         
    LYST for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for LYST:
     Synthetic lethal with Ras 

         15/18 MGI mutant phenotypes (inferred from 15 alleles) (MGI details for Lyst) (see all 18):
     behavior/neurological  cellular  craniofacial  growth/size  hearing/vestibular/ear 
     hematopoietic system  homeostasis/metabolism  immune system  integument  limbs/digits/tail 
     mortality/aging  nervous system  no phenotypic analysis  pigmentation  renal/urinary system 

    LYST for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for LYST 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for LYST

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LYST 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LYST 

    miRNA
    Products:            		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LYST
    8/56 QIAGEN miScript miRNA Assays for microRNAs that regulate LYST (see all 56):
    hsa-miR-26a-2* hsa-miR-3607-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-25 hsa-miR-374a
    SwitchGear 3'UTR luciferase reporter plasmid: LYST 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for LYST
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LYST

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for LYST


    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for LYST (see all 4)
    OriGene ORF clones in mouse, rat for LYST
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: LYST (NM_000081)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LYST
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat LYST

    Cell Line
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    Search LifeMap BioReagents cell lines for LYST
    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYST


    Pathways & Interactions
    for LYST gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LYST

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/33 Interacting proteins for LYST (Q996983 ENSP000003744434) via UniProtKB, MINT, STRING, and/or I2D (see all 33)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CSNK2BP678703, ENSP000003650254I2D: score=3 STRING: ENSP00000365025
    ENSG00000224774P678703, ENSP000004156154I2D: score=3 STRING: ENSP00000415615
    ENSG00000206406P678703I2D: score=3 
    ENSG00000224398P678703I2D: score=3 
    ENSG00000228875P678703I2D: score=3 
    About this table

    Gene Ontology (GO): 5/20 biological process terms (GO ID links to tree view) (see all 20):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002446neutrophil mediated immunity IEA--
    GO:0002456T cell mediated immunity IEA--
    GO:0006644phospholipid metabolic process IEA--
    GO:0007017microtubule-based process IEA--
    GO:0007040lysosome organization IEA--

    LYST for ontologies           About GeneDecksing



    Drugs & Compounds
    for LYST gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    LYST for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LYST

    7 Novoseek inferred chemical compound relationships for LYST gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chalcone 78.7 10 9223265 (1), 20433752 (1), 17028970 (1), 9002621 (1) (see all 7)
    chitin 68 17 17302816 (4), 12429521 (2), 17971081 (2), 10826699 (1) (see all 8)
    anthocyanin 44.3 1 17028970 (1)
    flavonoid 29.3 1 17028970 (1)
    histidine 10.2 1 10690356 (1)
    cholesterol 0 2 14657904 (1)
    arginine 0 1 10690356 (1)

    Search CenterWatch for drugs/clinical trials and news about LYST

    Transcripts
    for LYST gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for LYST gene (2 alternative transcripts): 
    NM_000081.3  NM_001005736.1  

    Unigene Cluster for LYST:

    Lysosomal trafficking regulator
    Hs.532411  [show with all ESTs]
    Unigene Representative Sequence: NM_000081
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000389794 ENST00000473037(uc001hxi.2) ENST00000462376 ENST00000475277
    ENST00000461526 ENST00000487530 ENST00000489585(uc009xgb.1) ENST00000492844
    ENST00000465349(uc001hxl.1) ENST00000468107(uc001hxm.3) ENST00000468626(uc001hxn.1)
    ENST00000389793(uc009xga.1 uc001hxj.2) ENST00000536965(uc010pxs.1)

    miRNA
    Products:             		 QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LYST
    8/56 QIAGEN miScript miRNA Assays for microRNAs that regulate LYST (see all 56):
    hsa-miR-26a-2* hsa-miR-3607-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-25 hsa-miR-374a
    SwitchGear 3'UTR luciferase reporter plasmid: LYST 3' UTR sequence
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for LYST
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LYST
    Clone
    Products:             		 OriGene clones in human, mouse for LYST (see all 4)
    OriGene ORF clones in mouse, rat for LYST
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: LYST (NM_000081)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LYST
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat LYST
    Primer
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    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat LYST
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LYST
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LYST

    Additional mRNA sequence: 

    AK307457.1 AK310790.1 AK311664.1 AL833100.1 BC020793.1 BC033098.1 BC144702.1 BX649113.1 
    L77889.1 U67615.1 U70064.1 U72192.1 U84744.1 

    19 DOTS entries:

    DT.95364459  DT.95173157  DT.100777965  DT.216563  DT.216564  DT.91843611  DT.95173154  DT.100777966 
    DT.100777967  DT.91752927  DT.92427793  DT.95332360  DT.97771673  DT.97808809  DT.97813494  DT.101974170 
    DT.40128160  DT.92427792  DT.95257026 

    24/149 AceView cDNA sequences (see all 149):

    BU740347 CK904950 BM055408 AW236542 AI224922 AL598060 BU738023 AA424769 
    BX492438 AA360606 BQ006747 AI334317 AI698283 BX100814 BX105453 BQ214459 
    AI869371 AA417738 BQ011080 AA424902 BM700528 BX649113 BM055110 U67615 

    GeneLoc Exon Structure


    Expression
    for LYST gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LYST expression in normal human tissues (normalized intensities)      LYST embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    LYST Expression
    About this image


    LYST expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/8 selected tissues (see all 8) fully expand
     
     Blood (Hematopoietic System)    fully expand to see all 6 entries
             Double Positive Thymocytes Thymus
             neutrophils   
     
     Paraxial Mesoderm (Gastrulation Derivatives)
             skeleton/axial skeleton   
     
     Thymus (Hematopoietic System)
             Double Positive Thymocytes Thymus
     
     Pancreas (Endocrine System)
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Bone (Muscoskeletal System)
             bone marrow   

    See LYST Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LYST

    SOURCE GeneReport for Unigene cluster: Hs.532411

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
    Tissue specificity: Abundantly expressed in adult and fetal thymus, peripheral blood leukocytes, bone marrow and
    several regions of the adult brain

        SABiosciences Custom PCR Arrays for LYST
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LYST
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYST

    Orthologs
    for LYST gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals and fungi.

    Orthologs for LYST gene from 7/14 species (see all 14)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Lyst1 , 5 lysosomal trafficking regulator1, 5 85.2(n)1
    85.64(a)1    		   13 (5.28 cM)5
    171011  NM_010748.21  NP_034878.21 
     135904095 
    chicken
    (Gallus gallus)    		 Aves LYST1 lysosomal trafficking regulator 73.22(n)
    73.81(a)    		   421514  XM_419558.3  XP_419558.3 
    lizard
    (Anolis carolinensis)    		 Reptilia LYST6
    		 Uncharacterized protein
    		 71(a)
    		 1 ↔ 1
    		 1(219274460-219378330)
    zebrafish
    (Danio rerio)    		 Actinopterygii 570971642   -- 74.91(n)    57097164 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG428636
    		 --
    		 25(a)
    		 1 ↔ 1
    		 3L(1950306-1964178)
    worm
    (Caenorhabditis elegans)    		 Secernentea T01H10.86
    		 Protein T01H10.8
    		 14(a)
    		 1 ↔ 1
    		 X(12128143-12141151)
    baker's yeast
    (Saccharomyces cerevisiae)    		 Saccharomycetes BPH16
    		 PProtein homologous to human Chediak-Higashi syndr...
    		 17(a)
    		 1 → many
    		 III(179520-186023)


    ENSEMBL Gene Tree for LYST (if available)
    TreeFam Gene Tree for LYST (if available)

    Paralogs
    for LYST gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LYST gene
    NSMAF2  NBEAL12  WDFY42  LRBA2  NBEA2  WDFY32  NBEAL22  

    LYST for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for LYST
    PGOHUM00000248355


    Genomic Variants
    for LYST gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/4433 SNPs in LYST are shown (see all 4433)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    VAR_0135564
    		Chediak-Higashi syndrome (CHS)4--see VAR_0135562 R H mis40--------
    rs289420771,2,4
    		CChediak-Higashi syndrome (CHS)4 pathogenic1206381059(-) AGAAGA/TCCTTG 2 D V mis1 ese30--------
    rs803386571,2
    		Cpathogenic1206403555(-) CTTTCA/GGTATT 2 H R mis10--------
    rs803386521,2
    		Cpathogenic1206420671(-) GTATAC/TGACTT 2 R * stg10--------
    rs803386511,2
    		Cpathogenic1206420896(-) TTTCTC/TAACCT 2 Q * stg10--------
    rs803386431,2
    		Cpathogenic1206445113(-) ATGGTC/TGAGGA 2 R * stg10--------
    rs1911659171,2
    		--206275653(+) TGGCTC/TACACC 1 -- ds50010--------
    rs121393201,2
    		C,F--206275656(+) ctcacG/Acctgt 1 -- ds50014Minor allele frequency- A:0.29NA WA CSA 7
    rs1814924191,2
    		--206275851(+) AGAATC/TGCTTG 1 -- ds50010--------
    rs168327721,2
    		C--206276034(+) CCATCG/AATTTG 1 -- ds50013Minor allele frequency- A:0.01NA 142

    HapMap Linkage Disequilibrium report for LYST (235824341 - 236046940 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for LYST:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2661819CNV Deletion23128226
    nsv508701CNV Loss20534489
    nsv832936CNV Gain17160897
    nsv832947CNV Gain17160897


    Human Gene Mutation Database (HGMD): LYST

    Locus Specific Mutation Databases (LSDB): LYST
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing LYST
    DNA2.0 Custom Variant and Variant Library Synthesis for LYST

    Disorders / Diseases
    for LYST gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    		 OMIM gene information: 606897   
    OMIM disorders: 214500  
    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
  • Chediak-Higashi syndrome (CHS) [MIM:214500]: A rare autosomal recessive disorder characterized by
    hypopigmentation, severe immunologic deficiency, a bleeding tendency, neurologic abnormalities, abnormal
    intracellular transport to and from the lysosome, and giant inclusion bodies in a variety of cell types. Most
    patients die at an early age unless they receive an allogeneic hematopoietic stem cell transplant (SCT). Note=The
    disease is caused by mutations affecting the gene represented in this entry

    • 14 diseases for LYST:    About MalaCards
    chediak-higashi syndrome    t lymphocyte deficiency    exfoliation syndrome    platelet storage pool deficiency
    oculocutaneous albinism    hemophagocytic lymphohistiocytosis    hermansky-pudlak syndrome    albinism
    contact dermatitis    hematopoietic stem cell transplantation    neutropenia    dermatitis
    melanoma    neuronitis

    5 diseases from the University of Copenhagen DISEASES database for LYST:
    Chediak-Higashi syndrome     Oculocutaneous albinism     Hemophagocytic lymphohistiocytosis     Exfoliation syndrome
    Platelet storage pool deficiency

    LYST for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for LYST gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chediak-higashi syndrome 95.7 14 10594238 (2), 17512928 (2), 16518687 (1), 9070932 (1) (see all 10)
    tumors 3.9 1 11504836 (1)

    GeneTests: LYST
    GeneReviews: LYST
    Genetic Association Database (GAD): LYST
    Human Genome Epidemiology (HuGE) Navigator: LYST (1 document)

    Export disorders for LYST gene to outside databases

    Publications
    for LYST gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LYST gene, integrated from 9 sources (see all 85):
    (articles sorted by number of sources associating them with LYST)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of the homologous beige and Chediak-Higashi syndrome genes. (PubMed id 8717042)1, 2, 3, 9 Barbosa M.D.F.S.... Kingsmore S.F. (1996)
    2. Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome. (PubMed id 8896560)1, 2, 3 Nagle D.L....Moore K.J. (1996)
    3. The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. (PubMed id 11984006)1, 2, 9 Tchernev V.T....Kingsmore S.F. (2002)
    4. Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome. (PubMed id 11857544)1, 2, 9 Karim M.A.... Spritz R.A. (2002)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    6. An unappreciated role for RNA surveillance. (PubMed id 14759258)1, 2 Hillman R.T.... Brenner S.E. (2004)
    7. Identification of mutations in two major mRNA isoforms of the Chediak-Higashi syndrome gene in human and mouse. (PubMed id 9215680)1, 2 Barbosa M.D.F.S.... Kingsmore S.F. (1997)
    8. Two novel CHS1 (LYST) mutations: clinical correlations in an infant with Chediak-Higashi syndrome. (PubMed id 15896657)1, 9 Zarzour W....Gahl W.A. (2005)
    9. Chediak-Higashi syndrome associated with maternal uniparental isodisomy of chromosome 1. (PubMed id 10482950)1, 9 Dufourcq-Lagelouse R....de Saint Basile G. (1999)
    10. Protein truncation test of LYST reveals heterogenous mutations in patients with Chediak-Higashi syndrome. (PubMed id 10648412)1, 9 Certain S....de Saint Basile G. (2000)

    External Searches for LYST gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing LYST gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1130 HGNC: 1968 AceView: CHS1 Ensembl:ENSG00000143669 euGenes: HUgn1130
    ECgene: LYST H-InvDB: LYST

    Other Databases showing LYST gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing LYST gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for LYST Pharmacogenomics, SNPs, Pathways
    LYSTbasehttp://bioinf.uta.fi/LYSTbase/
    Mutations of the LYST genehttp://www.retina-international.org/files/sci-news/chsmut.htm
    Albinism database (ADB)http://albinismdb.med.umn.edu/chs1mut.html

    Intellectual Property
    for LYST gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for LYST gene:
    Search GeneIP for patents involving LYST

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

     
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