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    LYST lysosomal trafficking regulator [ Homo sapiens (human) ]

    Gene ID: 1130, updated on 11-Jun-2021

    Summary

    Official Symbol
    LYSTprovided by HGNC
    Official Full Name
    lysosomal trafficking regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:1968
    See related
    Ensembl:ENSG00000143669 MIM:606897
    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; Mauve
    Summary
    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]
    Expression
    Broad expression in bone marrow (RPKM 12.2), skin (RPKM 4.6) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LYST in Genome Data Viewer
    Location:
    1q42.3
    Exon count:
    61
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (235661031..235883713, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235824331..236047013, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 4 Neighboring gene solute carrier family 39 member 14 pseudogene Neighboring gene Sharpr-MPRA regulatory region 105 Neighboring gene lactate dehydrogenase A pseudogene 2 Neighboring gene microRNA 1537 Neighboring gene RNA, U5E small nuclear 2, pseudogene Neighboring gene uncharacterized LOC105373215 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene meiotic recombination hotspot NID3

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Nef-triggered MHCII endocytosis requires Rab5 activity and lyst function, whereas lysosomal trafficking of internalized MHCII molecules requires Rab7 activity PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in defense response to bacterium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in defense response to protozoan ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in defense response to virus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endosome to lysosome transport via multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in leukocyte chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lysosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mast cell secretory granule organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in melanosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in natural killer cell mediated cytotoxicity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phagocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pigmentation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    lysosomal-trafficking regulator
    Names
    Chediak-Higashi syndrome 1
    beige homolog

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      4933..227610
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_143

    mRNA and Protein(s)

    1. NM_000081.4NP_000072.2  lysosomal-trafficking regulator

      See identical proteins and their annotated locations for NP_000072.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the functional protein. Variants 1 and 3 encode the same protein.
      Source sequence(s)
      AA486745, BI031463, BX649113, U67615
      Consensus CDS
      CCDS31062.1
      UniProtKB/Swiss-Prot
      Q99698
      Related
      ENSP00000374443.2, ENST00000389793.7
      Conserved Domains (5) summary
      smart01026
      Location:31323422
      Beach; Beige/BEACH domain
      COG2319
      Location:34763783
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30123117
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35283565
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35293778
      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 ...
    2. NM_001301365.1NP_001288294.1  lysosomal-trafficking regulator

      See identical proteins and their annotated locations for NP_001288294.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) variant differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same protein.
      Source sequence(s)
      AL121997, AL133286, AL390765
      Consensus CDS
      CCDS31062.1
      UniProtKB/Swiss-Prot
      Q99698
      Conserved Domains (5) summary
      smart01026
      Location:31323422
      Beach; Beige/BEACH domain
      COG2319
      Location:34763783
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30123117
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35283565
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35293778
      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 ...

    RNA

    1. NR_102436.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains multiple differences at the 5' and 3' ends, including the lack of multiple 3' exons. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
      Source sequence(s)
      AL121997, AL133286, BC033098, BF692337

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      235661031..235883713 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544032.1XP_011542334.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542334.1

      Conserved Domains (5) summary
      smart01026
      Location:31863476
      Beach; Beige/BEACH domain
      COG2319
      Location:35303837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30663171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35823619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35833832
      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 ...
    2. XM_011544034.1XP_011542336.1  lysosomal-trafficking regulator isoform X2

      Conserved Domains (5) summary
      smart01026
      Location:31403430
      Beach; Beige/BEACH domain
      COG2319
      Location:34843791
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30203125
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35363573
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35373786
      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 ...
    3. XM_017000150.1XP_016855639.1  lysosomal-trafficking regulator isoform X3

    4. XM_011544031.1XP_011542333.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542333.1

      Conserved Domains (5) summary
      smart01026
      Location:31863476
      Beach; Beige/BEACH domain
      COG2319
      Location:35303837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30663171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35823619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35833832
      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 ...
    5. XM_011544033.2XP_011542335.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542335.1

      Conserved Domains (5) summary
      smart01026
      Location:31863476
      Beach; Beige/BEACH domain
      COG2319
      Location:35303837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:30663171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:35823619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35833832
      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 ...
    6. XM_011544036.2XP_011542338.1  lysosomal-trafficking regulator isoform X5

      Conserved Domains (5) summary
      smart01026
      Location:24072697
      Beach; Beige/BEACH domain
      COG2319
      Location:27513058
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:22872392
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:28032840
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:28043053
      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 ...
    7. XM_011544035.2XP_011542337.1  lysosomal-trafficking regulator isoform X4

      Conserved Domains (2) summary
      cd01201
      Location:30663171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cl10511
      Location:31863316
      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 ...
    8. XM_011544037.2XP_011542339.1  lysosomal-trafficking regulator isoform X6

    9. XM_011544039.2XP_011542341.1  lysosomal-trafficking regulator isoform X7

    10. XM_017000151.1XP_016855640.1  lysosomal-trafficking regulator isoform X8

    RNA

    1. XR_001736947.1 RNA Sequence

    2. XR_001736946.2 RNA Sequence

    3. XR_001736948.1 RNA Sequence

    4. XR_002959252.1 RNA Sequence

      Related
      ENST00000489585.5

    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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