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LYST Gene

protein-coding GIFtS: 55
GCID: GC01M235824

Lysosomal Trafficking Regulator

(Previous name: Chediak-Higashi syndrome 1)
(Previous symbol: CHS1)

See related diseases
at

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Lysosomal Trafficking Regulator¹ ²
CHS1¹ ² ³ ⁵
Chediak-Higashi Syndrome 1¹ ²
Beige Homolog² ³
CHS² ³
Lysosomal-Trafficking Regulator²

External Ids:	HGNC: 1968¹	Entrez Gene: 1130²	Ensembl: ENSG00000143669⁷	OMIM: 606897⁵	UniProtKB: Q99698³

Export aliases for LYST gene to outside databases

Previous GC identifers: GC01M232151 GC01M233890 GC01M206276

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 ch??diak-higashi syndrome. An important paralog of this gene is NSMAF.

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698

Function: May be required for sorting endosomal resident proteins into late multivesicular endosomes by a

mechanism involving microtubules

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:

NC_000001.11 NT_167186.2 NC_018912.2

Regulatory elements:

Regulatory transcription factor binding sites in the LYST gene promoter:
LHX3b/Lhx3b p53 FOXD1 POU6F1 (c2) Egr-4 AREB6 FOXO1a LHX3a/Lhx3a NF-kappaB1 FOXO1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LYST promoter sequence

Search Chromatin IP Primers for LYST

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LYST

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q42.1-q42.2 Ensembl cytogenetic band: 1q42.3 HGNC cytogenetic band: 1q42.1-q42.2

LYST Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYST gene location

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01M235824: view genomic region (about GC identifiers)

Start:	235,824,341 bp from pter	End:	236,046,940 bp from pter
Size:	222,600 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698 (See protein sequence)

Recommended Name: Lysosomal-trafficking regulator

Size: 3801 amino acids; 429139 Da

Subunit: Interacts with CENPJ, LIP8 and ZNF521

Secondary accessions: O43274 Q5T2U9 Q96TD7 Q96TD8 Q99709 Q9H133

Alternative splicing: 3 isoforms: Q99698-1 Q99698-2 Q99698-3 (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for LYST: NX_Q99698

Explore proteomics data for LYST at MOPED

Post-translational modifications:

Ubiquitination² at Lys1305, Lys3191

Modification sites at PhosphoSitePlus

See LYST Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_000072.2

ENSEMBL proteins:

ENSP00000374444 ENSP00000417168 ENSP00000374443 ENSP00000438315

LYST Human Recombinant Protein Products:

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	Novus Biologicals LYST Protein
	Browse Sino Biological Recombinant Proteins Browse Sino Biological Cell Lysates
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	Cloud-Clone Corp. Proteins for LYST

LYST Antibody Products:

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	Novus Biologicals LYST Antibody
	Abcam antibodies for LYST
	Cloud-Clone Corp. Antibodies for LYST
	Search ThermoFisher Antibodies for LYST
	LSBio Antibodies in human, mouse, rat for LYST

LYST Assay Products:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Assay Services for LYST
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	GenScript Custom Assay Services for LYST
	Browse Enzo Life Sciences for kits & assays
	Cloud-Clone Corp. ELISAs for LYST Cloud-Clone Corp. CLIAs for LYST

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

WDR: WD repeat domain containing

Selected InterPro protein domains (see all 7):

IPR000409 BEACH_dom

IPR019775 WD40_repeat_CS

IPR023362 PH-BEACH_dom

IPR001680 WD40_repeat

IPR017986 WD40_repeat_dom

Graphical View of Domain Structure for InterPro Entry Q99698

ProtoNet protein and cluster: Q99698

1 Blocks protein domain: IPB000409 Beige/BEACH domain

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698

Similarity: Contains 1 BEACH domain

Similarity: Contains 7 WD repeats

LYST for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: LYST_HUMAN, Q99698

Function: May be required for sorting endosomal resident proteins into late multivesicular endosomes by a

mechanism involving microtubules

Genatlas biochemistry entry for LYST:

putative lysosomal associated membrane protein,intracellular trafficking regulator,with two alternatively spliced

isoforms,homologous to mouse beige and yeast VPS15

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005488	binding	--	--
GO:0005515	protein binding	IPI	11984006

LYST for ontologies About GeneDecksing

Phenotypes:
1 GenomeRNAi human phenotype for LYST:

Synthetic lethal with Ras

Selected MGI mutant phenotypes (inferred from 15 alleles) (MGI details for Lyst) (see all 18):

behavior/neurological	cellular	craniofacial	growth/size/body	hearing/vestibular/ear
hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail
mortality/aging	nervous system	no phenotypic analysis	pigmentation	renal/urinary system

LYST for phenotypes About GeneDecksing

Animal Models:

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LYST

inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for LYST

genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LYST

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LYST

miRNA Products:		miRTarBase miRNAs that target LYST: hsa-mir-92b-3p (MIRT040614), hsa-mir-26a-5p (MIRT050104), hsa-mir-93-5p (MIRT028036), hsa-mir-335-5p (MIRT017524), hsa-mir-193a-3p (MIRT044888)

		Block miRNA regulation of human, mouse, rat LYST using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate LYST (see all 56):
		hsa-miR-26a-2* hsa-miR-3607-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-25 hsa-miR-374a

		SwitchGear 3'UTR luciferase reporter plasmid: LYST 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for LYST
		Predesigned siRNA for gene silencing in human, mouse, rat LYST

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for LYST

Clone Products:		OriGene clones in human, mouse for LYST (see all 4) OriGene ORF clones in mouse, rat for LYST OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: LYST (NM_000081)
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Cell Line Products:		GenScript Custom overexpressing Cell Line Services for LYST
		Browse ESI BIO Cell Lines and PureStem Progenitors for LYST

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYST

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

LYST_HUMAN, Q99698: Cytoplasm (Potential)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
cytoskeleton	5
cytosol	3
plasma membrane	3
endosome	2
lysosome	2
vacuole	2

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Gene Ontology (GO): 2 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005829	cytosol	IEA	--
GO:0015630	microtubule cytoskeleton	IDA	9606205

LYST for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Custom Pathway & Disease-focused RT² Profiler PCR Arrays for LYST
Interactions:

Search GeneGlobe Interaction Network for LYST

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for LYST (Q99698³ ENSP00000374443⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 36)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CSNK2B	P67870³, ENSP00000365025⁴	I2D: score=3 STRING: ENSP00000365025
ENSG00000224774	P67870³, ENSP00000415615⁴	I2D: score=3 STRING: ENSP00000415615
ENSG00000206406	P67870³	I2D: score=3
ENSG00000224398	P67870³	I2D: score=3
ENSG00000228875	P67870³	I2D: score=3

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Gene Ontology (GO): Selected biological process terms (see all 20): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0002446	neutrophil mediated immunity	IEA	--
GO:0002456	T cell mediated immunity	IEA	--
GO:0006644	phospholipid metabolic process	IEA	--
GO:0007017	microtubule-based process	IEA	--
GO:0007040	lysosome organization	IEA	--

LYST for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for LYST

7 Novoseek inferred chemical compound relationships for LYST gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
chalcone	78.7	10	9223265 (1), 20433752 (1), 17028970 (1), 9002621 (1) (see all 7)
chitin	68	17	17302816 (4), 12429521 (2), 17971081 (2), 10826699 (1) (see all 8)
anthocyanin	44.3	1	17028970 (1)
flavonoid	29.3	1	17028970 (1)
histidine	10.2	1	10690356 (1)
cholesterol	0	2	14657904 (1)
arginine	0	1	10690356 (1)

LYST for compounds About GeneDecksing

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for LYST gene (2 alternative transcripts):

NM_000081.3 NM_001005736.1

Unigene Cluster for LYST:

Lysosomal trafficking regulator

Hs.532411 [show with all ESTs]

Unigene Representative Sequence: NM_000081

13 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000389794 ENST00000473037(uc001hxi.2) ENST00000462376 ENST00000475277

ENST00000461526 ENST00000487530 ENST00000489585(uc009xgb.1) ENST00000492844

ENST00000465349(uc001hxl.1) ENST00000468107(uc001hxm.3) ENST00000468626(uc001hxn.1)

ENST00000389793(uc009xga.1 uc001hxj.2) ENST00000536965(uc010pxs.1)

miRNA Products:		Block miRNA regulation of human, mouse, rat LYST using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate LYST (see all 56):
		hsa-miR-26a-2* hsa-miR-3607-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-25 hsa-miR-374a

		SwitchGear 3'UTR luciferase reporter plasmid: LYST 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for LYST
		Predesigned siRNA for gene silencing in human, mouse, rat LYST

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		GenScript: all cDNA clones in your preferred vector: LYST (NM_000081)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for LYST
		Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat LYST

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for LYST
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat LYST
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		QuantiFast Probe-based Assays in human, mouse, rat LYST

Additional mRNA sequence:

AK307457.1 AK310790.1 AK311664.1 AL833100.1 BC020793.1 BC033098.1 BC144702.1 BX649113.1

L77889.1 U67615.1 U70064.1 U72192.1 U84744.1

19 DOTS entries:

DT.95364459 DT.95173157 DT.100777965 DT.216563 DT.216564 DT.91843611 DT.95173154 DT.100777966

DT.100777967 DT.91752927 DT.92427793 DT.95332360 DT.97771673 DT.97808809 DT.97813494 DT.101974170

DT.40128160 DT.92427792 DT.95257026

Selected AceView cDNA sequences (see all 149):

BU740347 CK904950 BM055408 AW236542 AI224922 AL598060 BU738023 AA424769

BX492438 AA360606 BQ006747 AI334317 AI698283 BX100814 BX105453 BQ214459

AI869371 AA417738 BQ011080 AA424902 BM700528 BX649113 BM055110 U67615

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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LYST expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

LYST expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 2) fully expand


Blood (Hematopoietic System) fully expand to see all 2 entries
Granulocytes Peripheral Blood

Thymus (Hematopoietic System)
Double Positive Thymocytes Thymus

LYST Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

LYST Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.532411

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698

Tissue specificity: Abundantly expressed in adult and fetal thymus, peripheral blood leukocytes, bone marrow and

several regions of the adult brain

Custom PCR Arrays for LYST

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		QuantiFast Probe-based Assays in human, mouse, rat LYST

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYST

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for LYST gene from Selected species (see all 13) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Lyst^{1 , 5}	lysosomal trafficking regulator^{1, 5}	85.2(n)¹ 85.64(a)¹		13 (5.28 cM)⁵ 17101¹ NM_010748.2¹ NP_034878.2¹ 13590409⁵
chicken (Gallus gallus)	Aves	LYST¹	lysosomal trafficking regulator	73.17(n) 73.77(a)		421514 XM_419558.4 XP_419558.4
lizard (Anolis carolinensis)	Reptilia	LYST⁶	lysosomal trafficking regulator	71(a)	1 ↔ 1	1(219274460-219378330)
tropical clawed frog (Xenopus tropicalis)	Amphibia	lyst¹	lysosomal trafficking regulator	67.36(n) 65.36(a)		779601 XM_002935831.2 XP_002935877.2
zebrafish (Danio rerio)	Actinopterygii	57097164²	--	74.91(n)		57097164
fruit fly (Drosophila melanogaster)	Insecta	CG42863⁶	--	25(a)	1 ↔ 1	3L(1950306-1964178)

ENSEMBL Gene Tree for LYST (if available)
TreeFam Gene Tree for LYST (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for LYST gene

NSMAF² NBEAL1² WDFY4² LRBA² NBEA² WDFY3² NBEAL2²

LYST for paralogs About GeneDecksing

1 Pseudogenes.org Pseudogene for LYST
PGOHUM00000248355

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs28942077^1,2,,4	C	Chediak-Higashi syndrome (CHS)⁴ pathogenic¹	206381059(-)	`AGAAGA/TCCTTG`	2	D V	mis¹ ese³		0	--	--	--	--
VAR_013556⁴		Chediak-Higashi syndrome (CHS)⁴	--	see VAR_013556	2	R H	mis⁴		0	--	--	--	--
rs80338657^1,2	C	pathogenic¹	206403555(-)	`CTTTCA/GGTATT`	2	H R	mis¹		0	--	--	--	--
rs80338652^1,2	C	pathogenic¹	206420671(-)	`GTATAC/TGACTT`	2	R *	stg¹		0	--	--	--	--
rs80338651^1,2	C	pathogenic¹	206420896(-)	`TTTCTC/TAACCT`	2	Q *	stg¹		0	--	--	--	--
rs80338643^1,2	C	pathogenic¹	206445113(-)	`ATGGTC/TGAGGA`	2	R *	stg¹		0	--	--	--	--
rs191165917^1,2		--	206275653(+)	`TGGCTC/TACACC`	1	--	ds500¹		0	--	--	--	--
rs12139320^1,2	C,F	--	206275656(+)	`ctcacG/Acctgt`	1	--	ds500¹		4		NA WA CSA	7
rs181492419^1,2		--	206275851(+)	`AGAATC/TGCTTG`	1	--	ds500¹		0	--	--	--	--
rs16832772^1,2	C	--	206276034(+)	`CCATCG/AATTTG`	1	--	ds500¹		3		NA	142

HapMap Linkage Disequilibrium report for LYST (235824341 - 236046940 bp)

Structural Variations
Database of Genomic Variants (DGV) 4 variations for LYST: About this table

Variant ID	Type	Subtype	PubMed ID
esv2661819	CNV	Deletion	23128226
nsv508701	CNV	Loss	20534489
nsv832936	CNV	Gain	17160897
nsv832947	CNV	Gain	17160897

Human Gene Mutation Database (HGMD): LYST
Locus Specific Mutation Databases (LSDB): LYST

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing LYST

DNA2.0 Custom Variant and Variant Library Synthesis for LYST

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 606897
OMIM disorders: 214500
UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698

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). Note=The

disease is caused by mutations affecting the gene represented in this entry

18 diseases for LYST:
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chediak-higashi syndrome attenuated ch??diak-higashi syndrome t lymphocyte deficiency exfoliation syndrome

platelet storage pool deficiency oculocutaneous albinism hemophagocytic lymphohistiocytosis hermansky-pudlak syndrome

albinism contact dermatitis hematopoietic stem cell transplantation neutropenia

dermatitis melanoma hiv-1 multiple myeloma

myeloma neuronitis

5 diseases from the University of Copenhagen DISEASES database for LYST:

Chediak-Higashi syndrome Oculocutaneous albinism Hemophagocytic lymphohistiocytosis Exfoliation syndrome

Platelet storage pool deficiency

LYST for disorders About GeneDecksing

2 Novoseek inferred disease relationships for LYST gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
chediak-higashi syndrome	95.7	14	10594238 (2), 17512928 (2), 16518687 (1), 9070932 (1) (see all 10)
tumors	3.9	1	11504836 (1)

GeneTests: LYST
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Human Genome Epidemiology (HuGE) Navigator: LYST (1 document)

Export disorders for LYST gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for LYST gene, integrated from 10 sources (see all 85):
(articles sorted by number of sources associating them with LYST)

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Identification of the homologous beige and Chediak-Higashi syndrome genes. (PubMed id 8717042)^{1, 2, 3, 9} Barbosa M.D.F.S.... Kingsmore S.F. (Nature 1996)
Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome. (PubMed id 8896560)^{1, 2, 3} Nagle D.L.... Moore K.J. (Nat. Genet. 1996)
The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. (PubMed id 11984006)^{1, 2, 9} Tchernev V.T.... Kingsmore S.F. (Mol. Med. 2002)
Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome. (PubMed id 11857544)^{1, 2, 9} Karim M.A.... Spritz R.A. (Am. J. Med. Genet. 2002)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (Nature 2006)
An unappreciated role for RNA surveillance. (PubMed id 14759258)^{1, 2} Hillman R.T.... Brenner S.E. (Genome Biol. 2004)
Identification of mutations in two major mRNA isoforms of the Chediak-Higashi syndrome gene in human and mouse. (PubMed id 9215680)^{1, 2} Barbosa M.D.F.S.... Kingsmore S.F. (Hum. Mol. Genet. 1997)
Two novel CHS1 (LYST) mutations: clinical correlations in an infant with Chediak-Higashi syndrome. (PubMed id 15896657)^{1, 9} Zarzour W....Gahl W.A. (Mol. Genet. Metab. 2005)
Chediak-Higashi syndrome associated with maternal uniparental isodisomy of chromosome 1. (PubMed id 10482950)^{1, 9} Dufourcq-Lagelouse R....de Saint Basile G. (Eur. J. Hum. Genet. 1999)
Protein truncation test of LYST reveals heterogenous mutations in patients with Chediak-Higashi syndrome. (PubMed id 10648412)^{1, 9} Certain S....de Saint Basile G. (Blood 2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 1130	HGNC: 1968	AceView: CHS1	Ensembl:ENSG00000143669	euGenes: HUgn1130
ECgene: LYST	H-InvDB: LYST

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for LYST	Pharmacogenomics, SNPs, Pathways
LYSTbase	http://bioinf.uta.fi/LYSTbase/
Mutations of the LYST gene	http://www.retina-international.org/files/sci-news/chsmut.htm
Albinism database (ADB)	http://albinismdb.med.umn.edu/chs1mut.html

Intellectual Property for LYST gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for LYST gene:
Search GeneIP for patents involving LYST

GeneCards and IP:
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