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    LYST lysosomal trafficking regulator [ Homo sapiens (human) ]

    Gene ID: 1130, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LYSTprovided by HGNC
    Official Full Name
    lysosomal trafficking regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:1968
    See related
    Ensembl:ENSG00000143669 MIM:606897; AllianceGenome:HGNC:1968
    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
    mouse all
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    Genomic context

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    See LYST in Genome Data Viewer
    Location:
    1q42.3
    Exon count:
    59
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (235661031..235883713, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235057704..235280316, complement)
    RS_2024_09 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 H3K4me1 hESC enhancer GRCh37_chr1:235785967-235786467 Neighboring gene uncharacterized LOC124904560 Neighboring gene Sharpr-MPRA regulatory region 105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1989 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235814049-235814900 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:235832683-235833882 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:235871544-235872743 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:235884502-235885701 Neighboring gene MPRA-validated peak779 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1990 Neighboring gene lactate dehydrogenase A pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr1:235977481-235977982 Neighboring gene Sharpr-MPRA regulatory region 11090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2807 Neighboring gene microRNA 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1993 Neighboring gene uncharacterized LOC105373215 Neighboring gene RNA, U5E small nuclear 2, pseudogene Neighboring gene MPRA-validated peak780 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:236073306-236074505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236081529-236082028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2808 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1994 Neighboring gene MPRA-validated peak781 silencer Neighboring gene meiotic recombination hotspot NID3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2809 Neighboring gene MPRA-validated peak782 silencer Neighboring gene meiotic recombination hotspot NID2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236162526-236163725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:236164752-236165460 Neighboring gene nidogen 1 Neighboring gene meiotic recombination hotspot NID1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:236221449-236221986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1995

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Use of expression constructs to dissect the functional domains of the CHS/beige protein: identification of multiple phenotypes. Ward DM, et al. Traffic, 2003 Jun. PMID 12753649
    2. Chediak-Higashi syndrome: Lysosomal trafficking regulator domains regulate exocytosis of lytic granules but not cytokine secretion by natural killer cells. Gil-Krzewska A, et al. J Allergy Clin Immunol, 2016 Apr. PMID 26478006, Free PMC Article
    3. LYST controls the biogenesis of the endosomal compartment required for secretory lysosome function. Sepulveda FE, et al. Traffic, 2015 Feb. PMID 25425525
    4. LYST affects lysosome size and quantity, but not trafficking or degradation through autophagy or endocytosis. Holland P, et al. Traffic, 2014 Dec. PMID 25216107
    5. Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator gene mutation. Shimazaki H, et al. J Neurol Neurosurg Psychiatry, 2014 Sep. PMID 24521565

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lysosomal trafficking regulator restricts intracellular growth of Coxiella burnetii by inhibiting the expansion of Coxiella-containing vacuole and upregulating nos2 expression.
      Title: Lysosomal trafficking regulator restricts intracellular growth of Coxiella burnetii by inhibiting the expansion of Coxiella-containing vacuole and upregulating nos2 expression.
    2. Spectrum of LYST mutations in Chediak-Higashi syndrome: a report of novel variants and a comprehensive review of the literature.
      Title: Spectrum of LYST mutations in Chediak-Higashi syndrome: a report of novel variants and a comprehensive review of the literature.
    3. LYST deficiency impairs autophagic lysosome reformation in neurons and alters lysosome number and size.
      Title: LYST deficiency impairs autophagic lysosome reformation in neurons and alters lysosome number and size.
    4. Chediak-Higashi syndrome presenting as a hereditary spastic paraplegia.
      Title: Chédiak-Higashi syndrome presenting as a hereditary spastic paraplegia.
    5. A compound heterozygote in LYST gene, consisting of a missense mutation c.5719A > G and an intron mutation c.4863-4G > A, was identified from the patient by using amplicon sequencing. The missense mutation is reported for the first time.
      Title: Identification of a compound heterozygote in LYST gene: a case report on Chediak-Higashi syndrome.
    6. LYST mutation was found in a family
      Title: [A novel mutation of the LYST gene in a Chinese family with Chediak-Higashi syndrome].
    7. homozygous c.6077_6078insA (p.Tyr2026Terfs) mutation was detected in the LYST gene in both patients
      Title: [Analysis of clinical characteristics and genetic mutation in a pedigree affected with Chediak-Higashi syndrome].
    8. LYST mutations in sporadic chordoma
      Title: The driver landscape of sporadic chordoma.
    9. Pathway analysis of the genes associated with the 46 CpG sites revealed an enrichment of immune system process genes, including LYST (cg16962115, FDR = 1.24E-04), CADM1 (cg21933078, FDR = 1.22E-02) and NFATC1 (cg06784563, FDR = 1.46E-02)
      Title: DNA methylation signatures and coagulation factors in the peripheral blood leucocytes of epithelial ovarian cancer.
    10. Mutation in LYST gene is associated with hemophagocytic lymphohistiocytosis.
      Title: Clinical presentation and outcome of pediatric patients with hemophagocytic lymphohistiocytosis in China: A retrospective multicenter study.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Chediak-Higashi syndrome
    MedGen: C0007965 OMIM: 214500 GeneReviews: Chediak-Higashi Syndrome
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    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

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    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 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 transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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_000081.4 → NP_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
      O43274, Q5T2U9, Q96TD7, Q96TD8, Q99698, Q99709, Q9H133
      Related
      ENSP00000374443.2, ENST00000389793.7
      Conserved Domains (5) summary
      smart01026
      Location:3132 → 3422
      Beach; Beige/BEACH domain
      COG2319
      Location:3476 → 3783
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:3012 → 3117
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:3528 → 3565
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:3529 → 3778
      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_001301365.1 → NP_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
      O43274, Q5T2U9, Q96TD7, Q96TD8, Q99698, Q99709, Q9H133
      Conserved Domains (5) summary
      smart01026
      Location:3132 → 3422
      Beach; Beige/BEACH domain
      COG2319
      Location:3476 → 3783
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:3012 → 3117
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:3528 → 3565
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:3529 → 3778
      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
      Related
      ENST00000697181.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_011544032.2 → XP_011542334.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542334.1

      Conserved Domains (5) summary
      smart01026
      Location:3186 → 3476
      Beach; Beige/BEACH domain
      COG2319
      Location:3530 → 3837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:3066 → 3171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:3582 → 3619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:3583 → 3832
      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_011544031.2 → XP_011542333.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542333.1

      Conserved Domains (5) summary
      smart01026
      Location:3186 → 3476
      Beach; Beige/BEACH domain
      COG2319
      Location:3530 → 3837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:3066 → 3171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:3582 → 3619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:3583 → 3832
      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_011544033.3 → XP_011542335.1  lysosomal-trafficking regulator isoform X1

      See identical proteins and their annotated locations for XP_011542335.1

      Conserved Domains (5) summary
      smart01026
      Location:3186 → 3476
      Beach; Beige/BEACH domain
      COG2319
      Location:3530 → 3837
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:3066 → 3171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:3582 → 3619
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:3583 → 3832
      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 ...

    4. XM_047443026.1 → XP_047298982.1  lysosomal-trafficking regulator isoform X1

    5. XM_047443034.1 → XP_047298990.1  lysosomal-trafficking regulator isoform X5

    6. XM_011544036.3 → XP_011542338.1  lysosomal-trafficking regulator isoform X4

      Conserved Domains (5) summary
      smart01026
      Location:2407 → 2697
      Beach; Beige/BEACH domain
      COG2319
      Location:2751 → 3058
      WD40; WD40 repeat [General function prediction only]
      cd01201
      Location:2287 → 2392
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:2803 → 2840
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:2804 → 3053
      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_047443027.1 → XP_047298983.1  lysosomal-trafficking regulator isoform X3

    8. XM_011544035.3 → XP_011542337.1  lysosomal-trafficking regulator isoform X2

      Conserved Domains (2) summary
      cd01201
      Location:3066 → 3171
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cl10511
      Location:3186 → 3316
      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 ...

    9. XM_047443046.1 → XP_047299002.1  lysosomal-trafficking regulator isoform X9

    10. XM_047443040.1 → XP_047298996.1  lysosomal-trafficking regulator isoform X8

    11. XM_047443038.1 → XP_047298994.1  lysosomal-trafficking regulator isoform X7

    12. XM_011544037.3 → XP_011542339.1  lysosomal-trafficking regulator isoform X6

    13. XM_011544039.3 → XP_011542341.1  lysosomal-trafficking regulator isoform X10

    14. XM_047443064.1 → XP_047299020.1  lysosomal-trafficking regulator isoform X11

      Related
      ENSP00000513166.1, ENST00000489585.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      235057704..235280316 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334011.1 → XP_054189986.1  lysosomal-trafficking regulator isoform X1

    2. XM_054334010.1 → XP_054189985.1  lysosomal-trafficking regulator isoform X1

    3. XM_054334012.1 → XP_054189987.1  lysosomal-trafficking regulator isoform X1

    4. XM_054334016.1 → XP_054189991.1  lysosomal-trafficking regulator isoform X5

    5. XM_054334015.1 → XP_054189990.1  lysosomal-trafficking regulator isoform X4

    6. XM_054334014.1 → XP_054189989.1  lysosomal-trafficking regulator isoform X3

    7. XM_054334013.1 → XP_054189988.1  lysosomal-trafficking regulator isoform X2

    8. XM_054334020.1 → XP_054189995.1  lysosomal-trafficking regulator isoform X9

    9. XM_054334019.1 → XP_054189994.1  lysosomal-trafficking regulator isoform X8

    10. XM_054334018.1 → XP_054189993.1  lysosomal-trafficking regulator isoform X7

    11. XM_054334017.1 → XP_054189992.1  lysosomal-trafficking regulator isoform X6

    12. XM_054334021.1 → XP_054189996.1  lysosomal-trafficking regulator isoform X10

    13. XM_054334022.1 → XP_054189997.1  lysosomal-trafficking regulator isoform X11

    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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99698.3 GenPept UniProtKB/Swiss-Prot:Q99698

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