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Aliases for LYST Gene

Aliases for LYST Gene

  • Lysosomal Trafficking Regulator 2 3 5
  • Chediak-Higashi Syndrome 1 2 3
  • Beige Homolog 3 4
  • CHS1 3 4
  • CHS 3 4
  • Lysosomal-Trafficking Regulator 3

External Ids for LYST Gene

Previous HGNC Symbols for LYST Gene

  • CHS1

Previous GeneCards Identifiers for LYST Gene

  • GC01M232151
  • GC01M233890
  • GC01M235824
  • GC01M206276

Summaries for LYST Gene

Entrez Gene Summary for LYST Gene

  • 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]

GeneCards Summary for LYST Gene

LYST (Lysosomal Trafficking Regulator) is a Protein Coding gene. Diseases associated with LYST include Chediak-Higashi Syndrome and Attenuated Chédiak-Higashi Syndrome. Gene Ontology (GO) annotations related to this gene include binding and phospholipid binding. An important paralog of this gene is NBEAL2.

UniProtKB/Swiss-Prot for LYST Gene

  • May be required for sorting endosomal resident proteins into late multivesicular endosomes by a mechanism involving microtubules.

Additional gene information for LYST Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYST Gene

Genomics for LYST Gene

GeneHancer (GH) Regulatory Elements for LYST Gene

Promoters and enhancers for LYST Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J235862 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 673.3 +18.1 18058 7 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A FEZF1 ZNF2 YY1 LYST ENSG00000273058 ARID4B MTR ENSG00000230325 RPS21P1 GGPS1 HEATR1 RNU6-968P LDHAP2
GH01J235878 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 666.4 +2.5 2492 6.3 HDGF PKNOX1 NFIB ZSCAN4 BMI1 BATF RAD21 YY1 EGR1 ZNF366 LYST RNU6-968P GGPS1 RNU5E-2P
GH01J235944 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 33.8 -62.6 -62593 3.4 FOXA2 ZSCAN4 DMAP1 RAD21 RARA YY1 THAP11 RXRA REST SP1 LYST RNU6-968P RNU5E-2P ENSG00000237845 ENSG00000229291 LOC105373212 LOC105373215
GH01J235324 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.7 +555.4 555374 7.5 FEZF1 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF263 SP3 NFYC ZNF610 ARID4B GGPS1 PIR53063 RPS21P1 LYST LDHAP2 B3GALNT2 TARBP1 IRF2BP2
GH01J235916 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 25.5 -36.8 -36767 8.6 PKNOX1 SMAD1 SIN3A FEZF1 ZNF2 ZNF207 FOS JUNB REST GLIS1 LYST ARID4B RNU5E-2P ENSG00000229291 TOMM20 GPR137B EDARADD RNU6-968P ENSG00000237845 LOC105373215
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYST on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LYST gene promoter:
  • p53
  • NF-kappaB1
  • Egr-4
  • FOXO1a
  • FOXO1
  • FOXD1
  • AREB6
  • LHX3b
  • Lhx3a
  • POU6F1 (c2)

Genomic Locations for LYST Gene

Genomic Locations for LYST Gene
222,678 bases
Minus strand
222,600 bases
Minus strand

Genomic View for LYST Gene

Genes around LYST on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYST Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYST Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYST Gene

Proteins for LYST Gene

  • Protein details for LYST Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Lysosomal-trafficking regulator
    Protein Accession:
    Secondary Accessions:
    • O43274
    • Q5T2U9
    • Q96TD7
    • Q96TD8
    • Q99709
    • Q9H133

    Protein attributes for LYST Gene

    3801 amino acids
    Molecular mass:
    429139 Da
    Quaternary structure:
    • Interacts with CENPJ, LIP8 and ZNF521.

    Alternative splice isoforms for LYST Gene


neXtProt entry for LYST Gene

Post-translational modifications for LYST Gene

  • Ubiquitination at posLast=31913191 and isoforms=2, 31305
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LYST Gene

Domains & Families for LYST Gene

Gene Families for LYST Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for LYST Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYST: view

No data available for UniProtKB/Swiss-Prot for LYST Gene

Function for LYST Gene

Molecular function for LYST Gene

UniProtKB/Swiss-Prot Function:
May be required for sorting endosomal resident proteins into late multivesicular endosomes by a mechanism involving microtubules.
GENATLAS Biochemistry:
putative lysosomal associated membrane protein,intracellular trafficking regulator,with two alternatively spliced isoforms,homologous to mouse beige and yeast VPS15

Phenotypes From GWAS Catalog for LYST Gene

Gene Ontology (GO) - Molecular Function for LYST Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11984006
genes like me logo Genes that share ontologies with LYST: view
genes like me logo Genes that share phenotypes with LYST: view

Human Phenotype Ontology for LYST Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LYST Gene

MGI Knock Outs for LYST:
  • Lyst Lyst<tm1b(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for LYST

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LYST Gene

Localization for LYST Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYST Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LYST gene
Compartment Confidence
cytoskeleton 5
plasma membrane 4
nucleus 3
cytosol 3
lysosome 2
endosome 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubule organizing center (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LYST Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0015630 microtubule cytoskeleton IDA 9606205
genes like me logo Genes that share ontologies with LYST: view

Pathways & Interactions for LYST Gene

No Data Available

Gene Ontology (GO) - Biological Process for LYST Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007040 lysosome organization IEA --
GO:0015031 protein transport IEA --
GO:0030595 leukocyte chemotaxis ISS --
GO:0032438 melanosome organization ISS --
GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway IMP 9606205
genes like me logo Genes that share ontologies with LYST: view

No data available for Pathways by source and SIGNOR curated interactions for LYST Gene

Drugs & Compounds for LYST Gene

(5) Drugs for LYST Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for LYST Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LYST: view

Transcripts for LYST Gene

Unigene Clusters for LYST Gene

Lysosomal trafficking regulator:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYST Gene

No ASD Table

Relevant External Links for LYST Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LYST Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYST Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LYST Gene

This gene is overexpressed in Whole Blood (x5.6).

Protein differential expression in normal tissues from HIPED for LYST Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (17.2), Breast (13.6), and Peripheral blood mononuclear cells (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LYST Gene

NURSA nuclear receptor signaling pathways regulating expression of LYST Gene:


SOURCE GeneReport for Unigene cluster for LYST Gene:


mRNA Expression by UniProt/SwissProt for LYST Gene:

Tissue specificity: Abundantly expressed in adult and fetal thymus, peripheral blood leukocytes, bone marrow and several regions of the adult brain.

Evidence on tissue expression from TISSUES for LYST Gene

  • Liver(4.2)
  • Blood(2.7)
  • Bone marrow(2.3)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LYST Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
  • tooth
  • liver
  • spleen
  • lower limb
  • shin
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with LYST: view

No data available for Protein tissue co-expression partners for LYST Gene

Orthologs for LYST Gene

This gene was present in the common ancestor of animals.

Orthologs for LYST Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LYST 34 33
  • 99.43 (n)
(Canis familiaris)
Mammalia LYST 34 33
  • 90.61 (n)
(Bos Taurus)
Mammalia LYST 34 33
  • 90.03 (n)
(Rattus norvegicus)
Mammalia Lyst 33
  • 85.32 (n)
(Mus musculus)
Mammalia Lyst 16 34 33
  • 85.2 (n)
(Monodelphis domestica)
Mammalia LYST 34
  • 79 (a)
(Ornithorhynchus anatinus)
Mammalia LYST 34
  • 74 (a)
(Gallus gallus)
Aves LYST 34 33
  • 73.17 (n)
(Anolis carolinensis)
Reptilia LYST 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lyst 33
  • 67.36 (n)
(Danio rerio)
Actinopterygii lyst 33
  • 61.63 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG42863 34
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
Species where no ortholog for LYST was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LYST Gene

Gene Tree for LYST (if available)
Gene Tree for LYST (if available)
Evolutionary constrained regions (ECRs) for LYST: view image

Paralogs for LYST Gene

Paralogs for LYST Gene Pseudogenes for LYST Gene

genes like me logo Genes that share paralogs with LYST: view

Variants for LYST Gene

Sequence variations from dbSNP and Humsavar for LYST Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1013780006 uncertain-significance, Ch\u00e9diak-Higashi syndrome 235,866,876(-) C/G 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant
rs10465613 benign, conflicting-interpretations-of-pathogenicity, not specified, Ch\u00e9diak-Higashi syndrome 235,806,086(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1046600348 uncertain-significance, Ch\u00e9diak-Higashi syndrome 235,662,116(-) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1056514391 uncertain-significance, Ch\u00e9diak-Higashi syndrome 235,833,676(-) A/C genic_upstream_transcript_variant, intron_variant
rs1063128 benign, not specified, Ch\u00e9diak-Higashi syndrome 235,809,567(-) T/C coding_sequence_variant, genic_downstream_transcript_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, synonymous_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LYST Gene

Variant ID Type Subtype PubMed ID
dgv588n100 CNV gain 25217958
dgv589n100 CNV gain 25217958
esv2661819 CNV deletion 23128226
esv3589199 CNV loss 21293372
nsv1011288 CNV gain 25217958
nsv1012436 CNV loss 25217958
nsv472320 CNV novel sequence insertion 20440878
nsv508701 CNV deletion 20534489
nsv549394 CNV gain 21841781
nsv832936 CNV gain 17160897
nsv832947 CNV gain 17160897
nsv945383 CNV duplication 23825009

Variation tolerance for LYST Gene

Residual Variation Intolerance Score: 10.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.40; 81.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYST Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYST Gene

Disorders for LYST Gene

MalaCards: The human disease database

(10) MalaCards diseases for LYST Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LYST in MalaCards View complete list of genes associated with diseases


  • Chediak-Higashi syndrome (CHS) [MIM:214500]: A rare autosomal recessive disorder characterized by hypopigmentation, severe immunologic deficiency, a bleeding tendency, neurologic abnormalities, abnormal intracellular transport to and from the lysosome, and giant inclusion bodies in a variety of cell types. Most patients die at an early age unless they receive an allogeneic hematopoietic stem cell transplant (SCT). {ECO:0000269 PubMed:11857544, ECO:0000269 PubMed:24521565}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LYST

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LYST: view

No data available for Genatlas for LYST Gene

Publications for LYST Gene

  1. Identification of the homologous beige and Chediak-Higashi syndrome genes. (PMID: 8717042) Barbosa MD … Kingsmore SF (Nature 1996) 2 3 4 22 58
  2. Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome. (PMID: 11857544) Karim MA … Spritz RA (American journal of medical genetics 2002) 3 4 22 58
  3. The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. (PMID: 11984006) Tchernev VT … Kingsmore SF (Molecular medicine (Cambridge, Mass.) 2002) 3 4 22 58
  4. Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome. (PMID: 8896560) Nagle DL … Moore KJ (Nature genetics 1996) 2 3 4 58
  5. Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator gene mutation. (PMID: 24521565) Shimazaki H … Takiyama Y (Journal of neurology, neurosurgery, and psychiatry 2014) 3 4 58

Products for LYST Gene

Sources for LYST Gene

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