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LYST lysosomal trafficking regulator [ Homo sapiens (human) ]

Gene ID: 1130, updated on 17-Feb-2019

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
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

Genomic context

See LYST in Genome Data Viewer
Location:
1q42.3
Exon count:
61
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (235661031..235883708, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235824331..236047008, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MT-CO3 pseudogene 46 Neighboring gene G protein subunit gamma 4 Neighboring gene solute carrier family 39 member 14 pseudogene 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 uncharacterized LOC105373212 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 FunctionsWhat'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
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
 
lysosome organization IEA
Inferred from Electronic Annotation
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 

General protein information

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

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

mRNA and Protein(s)

  1. NM_000081.3NP_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, DB265889, U67615
    Consensus CDS
    CCDS31062.1
    UniProtKB/Swiss-Prot
    Q99698
    Related
    ENSP00000374443.2, ENST00000389793.6
    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_102436.2 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, BC033098, BF692337

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    235661031..235883708 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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