VPS54

Protein identityUniProt · HPA

UniProt accession

Q9P1Q0

Gene

VPS54

Ensembl

ENSG00000143952

Chromosome

2

Canonical length

977 aa

Protein class

Predicted intracellular proteins

Subcellular location

Nucleoplasm,Golgi apparatus

OverviewNCBI Gene

This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

977 residues, UniProt reviewed canonical sequence.

>Q9P1Q0|VPS54
     1  MASSHSSSPV PQGSSSDVFF KIEVDPSKHI RPVPSLPDVC PKEPTGDSHS LYVAPSLVTD
    61  QHRWTVYHSK VNLPAALNDP RLAKRESDFF TKTWGLDFVD TEVIPSFYLP QISKEHFTVY
   121  QQEISQREKI HERCKNICPP KDTFERTLLH THDKSRTDLE QVPKIFMKPD FALDDSLTFN
   181  SVLPWSHFNT AGGKGNRDAA SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE
   241  LQDYLRKTSQ AVKMLRDKIA QIDKVMCEGS LHILRLALTR NNCVKVYNKL KLMATVHQTQ
   301  PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI DKMMIAEFST
   361  YSHSDLNRPL EDDCQVLEEE RLISLVFGLL KQRKLNFLEI YGEKMVITAK NIIKQCVINK
   421  VSQTEEIDTD VVVKLADQMR MLNFPQWFDL LKDIFSKFTI FLQRVKATLN IIHSVVLSVL
   481  DKNQRTRELE EISQQKNAAK DNSLDTEVAY LIHEGMFISD AFGEGELTPI AVDTTSQRNA
   541  SPNSEPCSSD SVSEPECTTD SSSSKEHTSS SAIPGGVDIM VSEDMKLTDS ELGKLANNIQ
   601  ELLYSASDIC HDRAVKFLMS RAKDGFLEKL NSMEFITLSR LMETFILDTE QICGRKSTSL
   661  LGALQSQAIK FVNRFHEERK TKLSLLLDNE RWKQADVPAE FQDLVDSLSD GKIALPEKKS
   721  GATEERKPAE VLIVEGQQYA VVGTVLLLIR IILEYCQCVD NIPSVTTDML TRLSDLLKYF
   781  NSRSCQLVLG AGALQVVGLK TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQYSML
   841  RHFDHITKDY HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSACFRNI CKQMTKMHEA
   901  IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA FYTGNLQALK
   961  GLKDLDLNMA EIWEQKR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS54 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)

0.4

Highest tissue expression

35 nTPM

Expression across tissuesHPA

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)

0.25

gnomAD pLI

1

gnomAD missense Z

0.95

DepMap mean gene effect

-0.52

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• apoptotic DNA fragmentation
• astrocyte differentiation
• cellular response to progesterone stimulus
• gene expression
• Golgi to vacuole transport
• homeostasis of number of cells within a tissue
• in utero embryonic development
• intracellular calcium ion homeostasis
• L-glutamate import
• lysosomal transport
• microglia differentiation
• mitochondrion organization
• motor behavior
• motor neuron apoptotic process
• musculoskeletal movement
• negative regulation of motor neuron apoptotic process
• neural tissue regeneration
• neurofilament cytoskeleton organization
• neuroinflammatory response
• neuromuscular synaptic transmission
• neuron projection morphogenesis
• post-embryonic forelimb morphogenesis
• protein localization to cell surface
• protein targeting to ER
• protein targeting to lysosome
• regulation of growth
• respiratory electron transport chain
• response to antibiotic
• response to calcium ion
• retrograde transport, endosome to Golgi
• skeletal muscle tissue growth
• spermatid differentiation
• sphingolipid catabolic process
• striated muscle contraction
• synaptic transmission, GABAergic
• synaptic transmission, glutamatergic
• thrombin-activated receptor signaling pathway
• ubiquitin recycling
• vacuole organization
• vesicle-mediated cholesterol transport

Molecular functions

• syntaxin binding

Cellular components

• cytosol
• GARP complex
• Golgi apparatus
• membrane
• mitochondrion
• nucleoplasm
• perinuclear region of cytoplasm
• synapse
• trans-Golgi network
• trans-Golgi network membrane

Protein domainsUniProt · Pfam · InterPro

• Vacuolar protein sorting-associated protein 54, N-terminal
• Vacuolar-sorting protein 54, of GARP complex
• Vacuolar protein sorting-associated protein 54, C-terminal
• Vacuolar protein sorting-associated protein 54
• Vps54-like protein

KeywordsUniProt

• Coiled coil
• Golgi apparatus
• Membrane
• Phosphoprotein
• Protein transport
• Transport

InteractionsUniProt · HPA

Protein binding partners of VPS54 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• VPS51
• VPS53