Seroatlas · Human Serome Atlas

VPS53

Vacuolar protein sorting-associated protein 53 homolog

Also known as: FLJ10979, HCCS1, VPS53_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q5VIR6
Gene: VPS53
Ensembl: ENSG00000141252
Chromosome: 17
Canonical length: 832 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Golgi apparatus,Vesicles,Cytosol

OverviewNCBI Gene

Involved in endocytic recycling and retrograde transport, endosome to Golgi. Acts upstream of or within lysosomal transport. Located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Part of EARP complex and GARP complex. Implicated in pontocerebellar hypoplasia type 2E. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

832 residues, UniProt reviewed canonical sequence.

>Q5VIR6|VPS53
     1  MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT LFPTEQSLAN
    61  IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA QKAIQQLFGK IKDIKDKAEK
   121  SEQMVKEITR DIKQLDHAKR HLTTSITTLN HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG
   181  VMNVLEHFHK YMGIPQIRQL SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD
   241  ACLVANILDP RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE
   301  KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR TTNFEGFLAK
   361  RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE KGDLDQPKKP KAPDNPFHGI
   421  VSKCFEPHLY VYIESQDKNL GELIDRFVAD FKAQGPPKPN TDEGGAVLPS CADLFVYYKK
   481  CMVQCSQLST GEPMIALTTI FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE
   541  VAKFTLEELC LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS
   601  SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP IIRDNLASTR
   661  KYFTQFCVKF ANSFIPKFIT HLFKCKPISM VGAEQLLLDT HSLKMVLLDL PSISSQVVRK
   721  APASYTKIVV KGMTRAEMIL KVVMAPHEPL VVFVDNYIKL LTDCNTETFQ KILDMKGLKR
   781  SEQSSMLELL RQRLPAPPSG AESSGSLSLT APTPEQESSR IRKLEKLIKK RL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS53 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: Other membrane
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.36
Highest tissue expression: 19 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 19 nTPM
testis: 18 nTPM
cerebellum: 13 nTPM
esophagus: 8.5 nTPM
retina: 7.8 nTPM
cerebral cortex: 7.3 nTPM

Single-cell type

early spermatids: 265 nCPM
late spermatids: 247 nCPM
ependymal cells: 245 nCPM
choroid plexus epithelial cells: 219 nCPM
brain excitatory neurons: 187 nCPM
renal collecting duct principal cells: 174 nCPM

Immune cell

basophil: 8 nTPM
neutrophil: 6.1 nTPM
non-classical monocyte: 5.6 nTPM
eosinophil: 4.4 nTPM
plasmacytoid DC: 3 nTPM
naive B-cell: 2.9 nTPM

Brain region

cerebellum: 88 nTPM
cerebral cortex: 64 nTPM
white matter: 60 nTPM
hippocampal formation: 60 nTPM
basal ganglia: 57 nTPM
amygdala: 55 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about VPS53.

Disease | AllUniProt

Conditions VPS53 is implicated in, by any mechanism.

Pontocerebellar hypoplasia 2E (PCH2E) MIM:615851

Disease | GeneticClinVar

16 pathogenic / likely-pathogenic of 704 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Pontocerebellar hypoplasia type 2E
Pontoneocerebellar hypoplasia
Melanoma

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): 0.61
gnomAD pLI: 0
gnomAD missense Z: 1.58
DepMap mean gene effect: -0.38
DepMap dependency class: selective

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

Cellular components

Protein domainsUniProt · Pfam · InterPro

Vps53, N-terminal
Vps53, C-terminal
Vps53, C-terminal domain superfamily
Vacuolar protein sorting-associated protein 53
Vps53, N-terminal
Vacuolar protein sorting-associated protein 53 C-terminus

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of VPS53 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads VPS53 as an antibody target. Whether an autoantibody or antibody against VPS53 could matter depends on whether native VPS53 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VPS53 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label VPS53 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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