LYST

Protein identityUniProt · HPA

UniProt accession

Q99698

Gene

LYST

Ensembl

ENSG00000143669

Chromosome

1

Canonical length

3801 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins

Subcellular location

Nucleoplasm,Plasma membrane,Centriolar satellite

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

3801 residues, UniProt reviewed canonical sequence.

>Q99698|LYST
     1  MSTDSNSLAR EFLTDVNRLC NAVVQRVEAR EEEEEETHMA TLGQYLVHGR GFLLLTKLNS
    61  IIDQALTCRE ELLTLLLSLL PLVWKIPVQE EKATDFNLPL SADIILTKEK NSSSQRSTQE
   121  KLHLEGSALS SQVSAKVNVF RKSRRQRKIT HRYSVRDARK TQLSTSDSEA NSDEKGIAMN
   181  KHRRPHLLHH FLTSFPKQDH PKAKLDRLAT KEQTPPDAMA LENSREIIPR QGSNTDILSE
   241  PAALSVISNM NNSPFDLCHV LLSLLEKVCK FDVTLNHNSP LAASVVPTLT EFLAGFGDCC
   301  SLSDNLESRV VSAGWTEEPV ALIQRMLFRT VLHLLSVDVS TAEMMPENLR KNLTELLRAA
   361  LKIRICLEKQ PDPFAPRQKK TLQEVQEDFV FSKYRHRALL LPELLEGVLQ ILICCLQSAA
   421  SNPFYFSQAM DLVQEFIQHH GFNLFETAVL QMEWLVLRDG VPPEASEHLK ALINSVMKIM
   481  STVKKVKSEQ LHHSMCTRKR HRRCEYSHFM HHHRDLSGLL VSAFKNQVSK NPFEETADGD
   541  VYYPERCCCI AVCAHQCLRL LQQASLSSTC VQILSGVHNI GICCCMDPKS VIIPLLHAFK
   601  LPALKNFQQH ILNILNKLIL DQLGGAEISP KIKKAACNIC TVDSDQLAQL EETLQGNLCD
   661  AELSSSLSSP SYRFQGILPS SGSEDLLWKW DALKAYQNFV FEEDRLHSIQ IANHICNLIQ
   721  KGNIVVQWKL YNYIFNPVLQ RGVELAHHCQ HLSVTSAQSH VCSHHNQCLP QDVLQIYVKT
   781  LPILLKSRVI RDLFLSCNGV SQIIELNCLN GIRSHSLKAF ETLIISLGEQ QKDASVPDID
   841  GIDIEQKELS SVHVGTSFHH QQAYSDSPQS LSKFYAGLKE AYPKRRKTVN QDVHINTINL
   901  FLCVAFLCVS KEAESDRESA NDSEDTSGYD STASEPLSHM LPCISLESLV LPSPEHMHQA
   961  ADIWSMCRWI YMLSSVFQKQ FYRLGGFRVC HKLIFMIIQK LFRSHKEEQG KKEGDTSVNE
  1021  NQDLNRISQP KRTMKEDLLS LAIKSDPIPS ELGSLKKSAD SLGKLELQHI SSINVEEVSA
  1081  TEAAPEEAKL FTSQESETSL QSIRLLEALL AICLHGARTS QQKMELELPN QNLSVESILF
  1141  EMRDHLSQSK VIETQLAKPL FDALLRVALG NYSADFEHND AMTEKSHQSA EELSSQPGDF
  1201  SEEAEDSQCC SFKLLVEEEG YEADSESNPE DGETQDDGVD LKSETEGFSA SSSPNDLLEN
  1261  LTQGEIIYPE ICMLELNLLS ASKAKLDVLA HVFESFLKII RQKEKNVFLL MQQGTVKNLL
  1321  GGFLSILTQD DSDFQACQRV LVDLLVSLMS SRTCSEELTL LLRIFLEKSP CTKILLLGIL
  1381  KIIESDTTMS PSQYLTFPLL HAPNLSNGVS SQKYPGILNS KAMGLLRRAR VSRSKKEADR
  1441  ESFPHRLLSS WHIAPVHLPL LGQNCWPHLS EGFSVSLWFN VECIHEAEST TEKGKKIKKR
  1501  NKSLILPDSS FDGTESDRPE GAEYINPGER LIEEGCIHII SLGSKALMIQ VWADPHNATL
  1561  IFRVCMDSND DMKAVLLAQV ESQENIFLPS KWQHLVLTYL QQPQGKRRIH GKISIWVSGQ
  1621  RKPDVTLDFM LPRKTSLSSD SNKTFCMIGH CLSSQEEFLQ LAGKWDLGNL LLFNGAKVGS
  1681  QEAFYLYACG PNHTSVMPCK YGKPVNDYSK YINKEILRCE QIRELFMTKK DVDIGLLIES
  1741  LSVVYTTYCP AQYTIYEPVI RLKGQMKTQL SQRPFSSKEV QSILLEPHHL KNLQPTEYKT
  1801  IQGILHEIGG TGIFVFLFAR VVELSSCEET QALALRVILS LIKYNQQRVH ELENCNGLSM
  1861  IHQVLIKQKC IVGFYILKTL LEGCCGEDII YMNENGEFKL DVDSNAIIQD VKLLEELLLD
  1921  WKIWSKAEQG VWETLLAALE VLIRADHHQQ MFNIKQLLKA QVVHHFLLTC QVLQEYKEGQ
  1981  LTPMPREVCR SFVKIIAEVL GSPPDLELLT IIFNFLLAVH PPTNTYVCHN PTNFYFSLHI
  2041  DGKIFQEKVR SIMYLRHSSS GGRSLMSPGF MVISPSGFTA SPYEGENSSN IIPQQMAAHM
  2101  LRSRSLPAFP TSSLLTQSQK LTGSLGCSID RLQNIADTYV ATQSKKQNSL GSSDTLKKGK
  2161  EDAFISSCES AKTVCEMEAV LSAQVSVSDV PKGVLGFPVV KADHKQLGAE PRSEDDSPGD
  2221  ESCPRRPDYL KGLASFQRSH STIASLGLAF PSQNGSAAVG RWPSLVDRNT DDWENFAYSL
  2281  GYEPNYNRTA SAHSVTEDCL VPICCGLYEL LSGVLLILPD VLLEDVMDKL IQADTLLVLV
  2341  NHPSPAIQQG VIKLLDAYFA RASKEQKDKF LKNRGFSLLA NQLYLHRGTQ ELLECFIEMF
  2401  FGRHIGLDEE FDLEDVRNMG LFQKWSVIPI LGLIETSLYD NILLHNALLL LLQILNSCSK
  2461  VADMLLDNGL LYVLCNTVAA LNGLEKNIPM SEYKLLACDI QQLFIAVTIH ACSSSGSQYF
  2521  RVIEDLIVML GYLQNSKNKR TQNMAVALQL RVLQAAMEFI RTTANHDSEN LTDSLQSPSA
  2581  PHHAVVQKRK SIAGPRKFPL AQTESLLMKM RSVANDELHV MMQRRMSQEN PSQATETELA
  2641  QRLQRLTVLA VNRIIYQEFN SDIIDILRTP ENVTQSKTSV FQTEISEENI HHEQSSVFNP
  2701  FQKEIFTYLV EGFKVSIGSS KASGSKQQWT KILWSCKETF RMQLGRLLVH ILSPAHAAQE
  2761  RKQIFEIVHE PNHQEILRDC LSPSLQHGAK LVLYLSELIH NHQGELTEEE LGTAELLMNA
  2821  LKLCGHKCIP PSASTKADLI KMIKEEQKKY ETEEGVNKAA WQKTVNNNQQ SLFQRLDSKS
  2881  KDISKIAADI TQAVSLSQGN ERKKVIQHIR GMYKVDLSAS RHWQELIQQL THDRAVWYDP
  2941  IYYPTSWQLD PTEGPNRERR RLQRCYLTIP NKYLLRDRQK SEDVVKPPLS YLFEDKTHSS
  3001  FSSTVKDKAA SESIRVNRRC ISVAPSRETA GELLLGKCGM YFVEDNASDT VESSSLQGEL
  3061  EPASFSWTYE EIKEVHKRWW QLRDNAVEIF LTNGRTLLLA FDNTKVRDDV YHNILTNNLP
  3121  NLLEYGNITA LTNLWYTGQI TNFEYLTHLN KHAGRSFNDL MQYPVFPFIL ADYVSETLDL
  3181  NDLLIYRNLS KPIAVQYKEK EDRYVDTYKY LEEEYRKGAR EDDPMPPVQP YHYGSHYSNS
  3241  GTVLHFLVRM PPFTKMFLAY QDQSFDIPDR TFHSTNTTWR LSSFESMTDV KELIPEFFYL
  3301  PEFLVNREGF DFGVRQNGER VNHVNLPPWA RNDPRLFILI HRQALESDYV SQNICQWIDL
  3361  VFGYKQKGKA SVQAINVFHP ATYFGMDVSA VEDPVQRRAL ETMIKTYGQT PRQLFHMAHV
  3421  SRPGAKLNIE GELPAAVGLL VQFAFRETRE QVKEITYPSP LSWIKGLKWG EYVGSPSAPV
  3481  PVVCFSQPHG ERFGSLQALP TRAICGLSRN FCLLMTYSKE QGVRSMNSTD IQWSAILSWG
  3541  YADNILRLKS KQSEPPVNFI QSSQQYQVTS CAWVPDSCQL FTGSKCGVIT AYTNRFTSST
  3601  PSEIEMETQI HLYGHTEEIT SLFVCKPYSI LISVSRDGTC IIWDLNRLCY VQSLAGHKSP
  3661  VTAVSASETS GDIATVCDSA GGGSDLRLWT VNGDLVGHVH CREIICSVAF SNQPEGVSIN
  3721  VIAGGLENGI VRLWSTWDLK PVREITFPKS NKPIISLTFS CDGHHLYTAN SDGTVIAWCR
  3781  KDQQRLKQPM FYSFLSSYAA G

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LYST can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0

Highest tissue expression

98 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LYST.

Disease | AllUniProt

Conditions LYST is implicated in, by any mechanism.

• Chediak-Higashi syndrome (CHS) MIM:214500

Disease | GeneticClinVar

274 pathogenic / likely-pathogenic of 4,066 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Chédiak-Higashi syndrome
• CHEDIAK-HIGASHI SYNDROME, CHILDHOOD TYPE
• LYST-related disorder
• CHEDIAK-HIGASHI SYNDROME, ADULT TYPE
• Inborn genetic diseases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.31

gnomAD pLI

0.02

gnomAD missense Z

1.41

DepMap mean gene effect

-0.07

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• defense response to bacterium
• defense response to protozoan
• defense response to virus
• endosome to lysosome transport via multivesicular body sorting pathway
• leukocyte chemotaxis
• mast cell secretory granule organization
• melanosome organization
• natural killer cell mediated cytotoxicity
• phagocytosis
• pigmentation
• protein transport

Cellular components

• cytoplasm
• microtubule cytoskeleton

Protein domainsUniProt · Pfam · InterPro

• BEACH domain
• WD40 repeat
• PH-like domain superfamily
• WD40/YVTN repeat-like-containing domain superfamily
• Armadillo-type fold
• WD40 repeat, conserved site
• PH-BEACH domain
• WD40-repeat-containing domain superfamily
• BEACH domain superfamily
• BEACH Domain-Containing
• WD domain, G-beta repeat
• Beige/BEACH domain
• PH domain associated with Beige/BEACH

KeywordsUniProt

• Cytoplasm
• Phagocytosis
• Phosphoprotein
• Protein transport
• Repeat
• Transport
• WD repeat

InteractionsUniProt · HPA

Protein binding partners of LYST in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• CPAP
• LIP8
• ZNF521
• CNTROB
• CSNK2B