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    LYST lysosomal trafficking regulator [ Homo sapiens ]

    Gene ID: 1130, updated on 11-May-2012
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    Summary

    Official Symbol
    LYSTprovided by HGNC
    Official Full Name
    lysosomal trafficking regulatorprovided by HGNC
    Primary source
    HGNC:1968
    See related
    Ensembl:ENSG00000143669; HPRD:06060; MIM:606897; Vega:OTTHUMG00000040527
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CHS; CHS1
    Summary
    This gene is thought to encode a protein that regulates intracellular protein trafficking to and from the lysosome. Mutations in this gene are associated with Chediak-Higashi syndrome, a rare lysosomal storage disorder. Alternatively spliced transcript variants have been described but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
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    Genomic context

    Location :
    1q42.1-q42.2
    Sequence :
    Chromosome: 1; NC_000001.10 (235824343..236030220, complement)
    See LYST in Epigenomics, MapViewer

    Chromosome 1 - NC_000001.10Genomic Context describing neighboring genes Neighboring gene tubulin folding cofactor E Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2 Neighboring gene solute carrier family 39 (zinc transporter), member 14 pseudogene Neighboring gene guanine nucleotide binding protein (G protein), gamma 4 Neighboring gene lactate dehydrogenase A pseudogene 2 Neighboring gene microRNA 1537 Neighboring gene nidogen 1 Neighboring gene aconitase 2, mitochondrial pseudogene

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, et al. Mol Cell Proteomics, 2011 Oct. PMID 21890473.
    2. A novel single point mutation of the LYST gene in two siblings with different phenotypic features of Chediak Higashi syndrome. Kaya Z, et al. Pediatr Blood Cancer, 2011 Jul 1. PMID 21488161.
    3. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Danielsen JM, et al. Mol Cell Proteomics, 2011 Mar. PMID 21139048.
    4. Digital quantification of human eye color highlights genetic association of three new loci. Liu F, et al. PLoS Genet, 2010 May 6. PMID 20463881.
    5. Chediak-Higashi Syndrome Introne WJ, et al. , 1993. PMID 20301751.

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. R1836X mutation in the LYST gene is associated with Chediak Higashi syndrome.
      Title: A novel single point mutation of the LYST gene in two siblings with different phenotypic features of Chediak Higashi syndrome.
    2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Digital quantification of human eye color highlights genetic association of three new loci.
    3. CHS1/LYST protein is involved in either vesicle fusion or fission. CHS1/LYST affects hematologic, immunologic and neurologic processes. Review.
      Title: Chediak-Higashi syndrome.
    4. two newly described nonsense mutations are expected to give rise to a severe phenotype and the patient had absolutely no cytotoxicity by natural killer cells or cytotoxic lymphocytes
      Title: Two novel CHS1 (LYST) mutations: clinical correlations in an infant with Chediak-Higashi syndrome.
    5. Childhood, adolescent, and adult forms of Chediak-Higashi syndrome correlate with different genotypes.
      Title: Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome.
    6. results suggest that the Beige protein interacts with at least two different partners and that the Beige protein affects cellular events, such as nuclear PtdIns(4,5)P2 localization, in addition to lysosome size
      Title: Use of expression constructs to dissect the functional domains of the CHS/beige protein: identification of multiple phenotypes.
    7. The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins.
      Title: The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins.
    Submit: New GeneRIF Correction
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    Phenotypes

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Chediak-Higashi syndrome

    Summary from GeneReviews: Go to GeneReviews

    Disease Characteristics
    Chediak-Higashi syndrome (CHS) is characterized by partial oculocutaneous albinism (OCA), immunodeficiency, and a mild bleeding tendency. Approximately 85% of affected individuals develop the accelerated phase, a lymphoproliferative infiltration of the bone marrow and reticuloendothelial system. Adolescents and adults with atypical CHS and children with classic CHS who have successfully undergone allogenic hematopoietic stem cell transplantation (HSCT) develop neurologic findings during early adulthood.
    Diagnosis Testing
    Diagnosis is based on ophthalmologic findings, identification of abnormal WBC granules on blood smear, and platelet aggregation studies in questionable cases. Molecular genetic testing of LYST, the only gene known to be associated with CHS, is available.
    Genetic Counseling
    CHS is inherited in an autosomal recessive manner. When both parents are heterozygous, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Prenatal diagnosis of CHS is available.
    References
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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    Q99698 P54259 ATN1    HPRD  PubMed  
    Q99698 Calmodulin 1 CALM1    HPRD  PubMed  
    Q99698 Q8N137 CNTROB    HPRD  PubMed  
    Q99698 P67870 CSNK2B    HPRD  PubMed  
    Q99698 Q96DF8 DGCR14    HPRD  PubMed  
    Q99698 Q6Y2X3 DNAJC14    HPRD  PubMed  
    Q99698 P11474 ESRRA    HPRD  PubMed  
    Q99698 O14964 HGS    HPRD  PubMed  
    Q99698 P52272 HNRNPM    HPRD  PubMed  
    Q99698 Q14974 KPNB1    HPRD  PubMed  
    Q99698 Q93074 MED12    HPRD  PubMed  
    Q99698 Q9NRX2 MRPL17    HPRD  PubMed  
    Q99698 Neurochondrin NCDN    HPRD  PubMed  
    Q99698 P31946 YWHAB    HPRD  PubMed  
    Q99698 P27348 YWHAQ    HPRD  PubMed  
    BioGRID:107552 BioGRID:108156 ATN1    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:121213 CELF4    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:120939 CENPJ    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:125533 CNTROB    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:107843 CSNK2B    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:107552 BioGRID:113855 DGCR14    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:124515 DNAJC14    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:115567 EFS    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:108405 ESRRA    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:114593 HGS    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:107552 BioGRID:110751 HNRNPM    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:110035 KPNB1    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:115293 MED12    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:121968 MRPL17    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:115534 MRPS31    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:116768 NCDN    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:121351 PCBP4    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:112991 TNNI3    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107552 BioGRID:119595 VTA1    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:113361 YWHAB    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:116168 YWHAQ    BioGRID  PubMed Two-hybrid 
    BioGRID:107552 BioGRID:113366 YWHAZ    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107552 BioGRID:117425 ZNF521    BioGRID  PubMed Two-hybrid 
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    General gene information

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    defense response to bacterium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    defense response to protozoan ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    defense response to virus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    endosome to lysosome transport via multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    leukocyte chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    mast cell secretory granule organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    melanosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    natural killer cell mediated cytotoxicity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    pigmentation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
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    General protein information

    Preferred Names
    lysosomal-trafficking regulator
    Names
    lysosomal-trafficking regulator
    beige homolog
    beige protein
    Chediak-Higashi syndrome 1
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    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_007397.1 RefSeqGene

      Range
      21721..227598
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000081.2 → NP_000072.2  lysosomal-trafficking regulator

      Status: REVIEWED

      Source sequence(s)
      BI031463, BX649113, U67615
      Consensus CDS
      CCDS31062.1
      UniProtKB/Swiss-Prot
      Q99698
      Related
      ENSP00000374443, ENST00000389793
      Conserved Domains (2) summary
      cd06071
      Location:3132 – 3422
      Blast Score: 1017
      Beach; BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor ...
      cl02567
      Location:3477 – 3778
      Blast Score: 265
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RefSeqs of Annotated Genomes: Build 37.3

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000001.10 Reference GRCh37.p5 Primary Assembly

      Range
      235824343..236030220, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000133.1 Alternate HuRef

      Range
      206276090..206481681, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001005736.1: Suppressed sequence

      Description
      NM_001005736.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AL121997.7 CAI18987.1
    genomic AL133286.9 (100..49259) None
    genomic AL390765.17 CAI14952.1
    genomic CH471098.1 EAW70034.1
      EAW70035.1
      EAW70036.1
      EAW70037.1
      EAW70038.1
    mRNA AK307457.1 None
    mRNA AK310790.1 None
    mRNA BC033098.1 None
    mRNA BC144702.1 AAI44703.1
    mRNA BI031463.1 None
    mRNA BX649113.1 None
    mRNA CD702969.1 None
    mRNA L77889.1 AAB51608.1
    mRNA U67615.1 AAB41309.1
    mRNA U70064.1 AAB41533.1
    mRNA U72192.1 AAB39697.1
    mRNA U84744.1 AAB87737.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99698.3 GenPept UniProtKB/Swiss-Prot:Q99698
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    Additional Links

    Additional Links

    • Epigenomics
    • MIM 606897
    • LYSTbase: Mutation registry for Chediak-Higashi syndrome (previously known as CHS1base) LYSTbase/
    • Retina International Mutations of the Chediak Higashi Syndrome chsmut.htm
    • Albinism Database Mutations of the Chediak-Higashi Syndrome gene chs1mut.html
    • GeneTests for MIM: 606897
    • Resource of Asian Primary Immunodeficiency Diseases (RAPID) AGID_90
    • UCSC UCSC
    • UniGene Hs.532411

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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