VPS13D

Protein identityUniProt · HPA

UniProt accession

Q5THJ4

Gene

VPS13D

Ensembl

ENSG00000048707

Chromosome

1

Canonical length

4388 aa

Protein class

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

Subcellular location

Nucleoplasm,Vesicles,Cytosol

OverviewNCBI Gene

This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

4388 residues, UniProt reviewed canonical sequence.

>Q5THJ4|VPS13D
     1  MLEGLVAWVL NTYLGKYVNN LNTDQLSVAL LKGAVELENL PLKKDALKEL ELPFEVKAGF
    61  IGKVTLQIPF YRPHVDPWVI SISSLHLIGA PEKIQDFNDE KEKLLERERK KALLQALEEK
   121  WKNDRQQKGE SYWYSVTASV VTRIVENIEL KIQDVHLRFE DGVTNPSHPF AFGICIKNVS
   181  MQNAVNEPVQ KLMRKKQLDV AEFSIYWDVD CTLLGDLPQM ELQEAMARSM ESRSHHYVLE
   241  PVFASALLKR NCSKKPLRSR HSPRIDCDIQ LETIPLKLSQ LQYRQIMEFL KELERKERQV
   301  KFRRWKPKVA ISKNCREWWY FALNANLYEI REQRKRCTWD FMLHRARDAV SYTDKYFNKL
   361  KGGLLSTDDK EEMCRIEEEQ SFEELKILRE LVHDRFHKQE ELAESLREPQ FDSPGACPGA
   421  PEPGGGSGML QYLQSWFPGW GGWYGQQTPE GNVVEGLSAE QQEQWIPEEI LGTEEFFDPT
   481  ADASCMNTYT KRDHVFAKLN LQLQRGTVTL LHKEQGTPQM NESAFMQLEF SDVKLLAESL
   541  PRRNSSLLSV RLGGLFLRDL ATEGTMFPLL VFPNPQKEVG RVSQSFGLQT TSADRSDHYP
   601  AADPDGPVFE MLYERNPAHS HFERRLNVST RPLNIIYNPQ AIKKVADFFY KGKVHTSGFG
   661  YQSELELRVA EAARRQYNKL KMQTKAEIRQ TLDRLLVGDF IEESKRWTVR LDISAPQVIF
   721  PDDFKFKNPV LVVVDLGRML LTNTQDNSRR KSRDGSASEE TQFSDDEYKT PLATPPNTPP
   781  PESSSSNGEK TPPFSGVEFS EEQLQAHLMS TKMYERYSLS FMDLQIMVGR VKDNWKHVQD
   841  IDVGPTHVVE KFNVHLQLER RLIYTSDPKY PGAVLSGNLP DLKIHINEDK ISALKNCFAL
   901  LTTPEMKTSD TQIKEKIFPQ EEQRGSLQDS VMNLTQSIVL LEQHTREVLV ESQLLLAEFK
   961  VNCMQLGVES NGRYISVLKV FGTNAHFVKR PYDAEVSLTV HGLLLVDTMQ TYGADFDLLM
  1021  ASHKNLSFDI PTGSLRDSRA QSPVSGPNVA HLTDGATLND RSATSVSLDK ILTKEQESLI
  1081  KLEYQFVSSE CPSMNLDSTL QVISLQVNNL DIILNPETIV ELIGFLQKSF PKEKDDLSPQ
  1141  PLMTDFERSF REQGTYQSTY EQNTEVAVEI HRLNLLLLRT VGMANREKYG RKIATASIGG
  1201  TKVNVSMGST FDMNGSLGCL QLMDLTQDNV KNQYVVSIGN SVGYENIISD IGYFESVFVR
  1261  MEDAALTEAL SFTFVERSKQ ECFLNLKMAS LHYNHSAKFL KELTLSMDEL EENFRGMLKS
  1321  AATKVTTVLA TKTAEYSEMV SLFETPRKTR EPFILEENEI YGFDLASSHL DTVKLILNIN
  1381  IESPVVSIPR KPGSPELLVG HLGQIFIQNF VAGDDESRSD RLQVEIKDIK LYSLNCTQLA
  1441  GREAVGSEGS RMFCPPSGSG SANSQEEAHF TRHDFFESLH RGQAFHILNN TTIQFKLEKI
  1501  PIERESELTF SLSPDDLGTS SIMKIEGKFV NPVQVVLAKH VYEQVLQTLD NLVYSEDLNK
  1561  YPASATSSPC PDSPLPPLST CGESSVERKE NGLFSHSSLS NTSQKSLSVK EVKSFTQIQA
  1621  TFCISELQVQ LSGDLTLGAQ GLVSLKFQDF EVEFSKDHPQ TLSIQIALHS LLMEDLLEKN
  1681  PDSKYKNLMV SRGAPKPSSL AQKEYLSQSC PSVSNVEYPD MPRSLPSHME EAPNVFQLYQ
  1741  RPTSASRKKQ KEVQDKDYPL TPPPSPTVDE PKILVGKSKF DDSLVHINIF LVDKKHPEFS
  1801  SSYNRVNRSI DVDFNCLDVL ITLQTWVVIL DFFGIGSTAD NHAMRLPPEG ILHNVKLEPH
  1861  ASMESGLQDP VNTKLDLKVH SLSLVLNKTT SELAKANVSK LVAHLEMIEG DLALQGSIGS
  1921  LSLSDLTCHG EFYRERFTTS GEEALIFQTF KYGRPDPLLR REHDIRVSLR MASVQYVHTQ
  1981  RFQAEVVAFI QHFTQLQDVL GRQRAAIEGQ TVRDQAQRCS RVLLDIEAGA PVLLIPESSR
  2041  SNNLIVANLG KLKVKNKFLF AGFPGTFSLQ DKESVPSASP TGIPKHSLRK TTSTEEPRGT
  2101  HSQGQFTMPL AGMSLGSLKS EFVPSTSTKQ QGPQPTLSVG QESSSPEDHV CLLDCVVVDL
  2161  QDMDIFAAER HPREYSKAPE DSSGDLIFPS YFVRQTGGSL LTEPCRLKLQ VERNLDKEIS
  2221  HTVPDISIHG NLSSVHCSLD LYKYKLIRGL LENNLGEPIE EFMRPYDLQD PRIHTVLSGE
  2281  VYTCMCFLID MVNVSLELKD PKRKEGAGSL ARFDFKKCKL LYESFSNQTK SINLVSHSMM
  2341  AFDTRYAGQK TSPGMTNVFS CIFQPAKNSS TTQGSIQIEL HFRSTKDSSC FTVVLNNLRV
  2401  FLIFDWLLLV HDFLHTPSDI KKQNHVTPSR HRNSSSESAI VPKTVKSGVV TKRSSLPVSN
  2461  ERHLEVKVNV TGTEFVVIED VSCFDTNAII LKGTTVLTYK PRFVDRPFSG SLFGIEVFSC
  2521  RLGNEHDTAL SIVDPVQIQM ELVGNSSYQN SSGLMDAFNS EDFPPVLEIQ LQALDIRLSY
  2581  NDVQLFLAIA KSIPEQANAA VPDSVALESD SVGTYLPGAS RVGEEIREGT RHTLDPVLEL
  2641  QLARLQELGF SMDDCRKALL ACQGQLKKAA SWLFKNAEPL KSLSLASTSR DSPGAVAAPL
  2701  ISGVEIKAES VCICFIDDCM DCDVPLAELT FSRLNFLQRV RTSPEGYAHF TLSGDYYNRA
  2761  LSGWEPFIEP WPCSVSWQQQ AASRLHPPRL KLEAKAKPRL DINITSVLID QYVSTKESWM
  2821  ADYCKDDKDI ESAKSEDWMG SSVDPPCFGQ SLPLVYLRTR STASLTNLEH QIYARAEVKT
  2881  PKRRQPFVPF ALRNHTGCTL WFATLTTTPT RAALSHSGSP GVVPEGNGTF LDDTHNVSEW
  2941  REVLTGEEIP FEFEARGKLR HRHTHDLRIH QLQVRVNGWE QVSPVSVDKV GTFFRYAAPD
  3001  KNSSSSTIGS PSSRTNIIHP QVYFSSLPPV RVVFAVTMEG SARKVITVRS ALIVRNRLET
  3061  PMELRLDSPS APDKPVVLPA IMPGDSFAVP LHLTSWRLQA RPKGLGVFFC KAPIHWTNVV
  3121  KTAEISSSKR ECHSMDTEKS RFFRFCVAIK KENYPDYMPS NIFSDSAKQI FRQPGHTIYL
  3181  LPTVVICNLL PCELDFYVKG MPINGTLKPG KEAALHTADT SQNIELGVSL ENFPLCKELL
  3241  IPPGTQNYMV RMRLYDVNRR QLNLTIRIVC RAEGSLKIFI SAPYWLINKT GLPLIFRQDN
  3301  AKTDAAGQFE EHELARSLSP LLFCYADKEQ PNLCTMRIGR GIHPEGMPGW CQGFSLDGGS
  3361  GVRALKVIQQ GNRPGLIYNI GIDVKKGRGR YIDTCMVIFA PRYLLDNKSS HKLAFAQREF
  3421  ARGQGTANPE GYISTLPGSS VVFHWPRNDY DQLLCVRLMD VPNCIWSGGF EVNKNNSFHI
  3481  NMRDTLGKCF FLRVEITLRG ATYRISFSDT DQLPPPFRID NFSKVPVVFT QHGVAEPRLR
  3541  TEVKPMTSLD YAWDEPTLPP FITLTVKGAG SSEINCNMND FQDNRQLYYE NFIYIAATYT
  3601  FSGLQEGTGR PVASNKAITC AELVLDVSPK TQRVILKKKE PGKRSQLWRM TGTGMLAHEG
  3661  SSVPHNPNKP SAARSTEGSA ILDIAGLAAV TDNRYEPLML RKPDRRRSTT QTWSFREGKL
  3721  TCGLHGLVVQ AKGGLSGLFD GAEVVLGPDT SMELLGPVPP EQQFINQKMR PGSGMLSIRV
  3781  IPDGPTRALQ ITDFCHRKSS RSYEVDELPV TEQELQKLKN PDTEQELEVL VRLEGGIGLS
  3841  LINKVPEELV FASLTGINVH YTQLATSHML ELSIQDVQVD NQLIGTTQPF MLYVTPLSNE
  3901  NEVIETGPAV QVNAVKFPSK SALTNIYKHL MITAQRFTVQ IEEKLLLKLL SFFGYDQAES
  3961  EVEKYDENLH EKTAEQGGTP IRYYFENLKI SIPQIKLSVF TSNKLPLDLK ALKSTLGFPL
  4021  IRFEDAVINL DPFTRVHPYE TKEFIINDIL KHFQEELLSQ AARILGSVDF LGNPMGLLND
  4081  VSEGVTGLIK YGNVGGLIRN VTHGVSNSAA KFAGTLSDGL GKTMDNRHQS EREYIRYHAA
  4141  TSGEHLVAGI HGLAHGIIGG LTSVITSTVE GVKTEGGVSG FISGLGKGLV GTVTKPVAGA
  4201  LDFASETAQA VRDTATLSGP RTQAQRVRKP RCCTGPQGLL PRYSESQAEG QEQLFKLTDN
  4261  IQDEFFIAVE NIDSYCVLIS SKAVYFLKSG DYVDREAIFL EVKYDDLYHC LVSKDHGKVY
  4321  VQVTKKAVST SSGVSIPGPS HQKPMVHVKS EVLAVKLSQE INYAKSLYYE QQLMLRLSEN
  4381  REQLELDS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS13D 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

25 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about VPS13D.

Disease | AllUniProt

Conditions VPS13D is implicated in, by any mechanism.

• Spinocerebellar ataxia, autosomal recessive 4 (SCAR4) MIM:607317

Disease | GeneticClinVar

77 pathogenic / likely-pathogenic of 1,835 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
• VPS13D-related disorder
• Spinocerebellar ataxia type 4
• Leigh syndrome
• 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)

0.33

gnomAD pLI

0

gnomAD missense Z

2.5

DepMap mean gene effect

-0.72

DepMap dependency class

common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• lipid transport
• mitochondrion organization
• positive regulation of mitophagy
• protein retention in Golgi apparatus
• protein targeting to vacuole

Cellular components

• extracellular exosome
• mitochondrion

Protein domainsUniProt · Pfam · InterPro

• UBA-like superfamily
• Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain
• Ubiquitin-associated domain
• Vacuolar protein sorting-associated protein 13
• Vacuolar protein sorting-associated protein 13, N-terminal domain
• VPS13-like, middle region
• VPS13-like family N-terminal region
• VPS13-like family middle region
• Vacuolar-sorting associated protein 13, adaptor binding domain
• Intermembrane lipid transfer protein VPS13D, UBA domain

KeywordsUniProt

• Acetylation
• Lipid transport
• Neurodegeneration
• Phosphoprotein
• Transport