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LYST lysosomal trafficking regulator [ Homo sapiens (human) ]

Gene ID: 1130, updated on 14-Nov-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
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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: HPA RNA-seq normal tissues 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

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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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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
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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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