Seroatlas · Human Serome Atlas

VPS39

Vam6/Vps39-like protein

Also known as: KIAA0770, VAM6, VPS39_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q96JC1
Gene
VPS39
Ensembl
ENSG00000166887
Chromosome
15
Canonical length
886 aa
Protein class
Plasma proteins, Predicted intracellular proteins
Quaternary structure
Homooligomer

OverviewNCBI Gene

This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

Canonical amino-acid sequenceUniProt

886 residues, UniProt reviewed canonical sequence.

>Q96JC1|VPS39
     1  MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVVPAD VASPESGSCN
    61  RFEVTLEKSN KNFSKKIQQI HVVSQFKILV SLLENNIYVH DLLTFQQITT VSKAKGASLF
   121  TCDLQHTETG EEVLRMCVAV KKKLQLYFWK DREFHELQGD FSVPDVPKSM AWCENSICVG
   181  FKRDYYLIRV DGKGSIKELF PTGKQLEPLV APLADGKVAV GQDDLTVVLN EEGICTQKCA
   241  LNWTDIPVAM EHQPPYIIAV LPRYVEIRTF EPRLLVQSIE LQRPRFITSG GSNIIYVASN
   301  HFVWRLIPVP MATQIQQLLQ DKQFELALQL AEMKDDSDSE KQQQIHHIKN LYAFNLFCQK
   361  RFDESMQVFA KLGTDPTHVM GLYPDLLPTD YRKQLQYPNP LPVLSGAELE KAHLALIDYL
   421  TQKRSQLVKK LNDSDHQSST SPLMEGTPTI KSKKKLLQII DTTLLKCYLH TNVALVAPLL
   481  RLENNHCHIE ESEHVLKKAH KYSELIILYE KKGLHEKALQ VLVDQSKKAN SPLKGHERTV
   541  QYLQHLGTEN LHLIFSYSVW VLRDFPEDGL KIFTEDLPEV ESLPRDRVLG FLIENFKGLA
   601  IPYLEHIIHV WEETGSRFHN CLIQLYCEKV QGLMKEYLLS FPAGKTPVPA GEEEGELGEY
   661  RQKLLMFLEI SSYYDPGRLI CDFPFDGLLE ERALLLGRMG KHEQALFIYV HILKDTRMAE
   721  EYCHKHYDRN KDGNKDVYLS LLRMYLSPPS IHCLGPIKLE LLEPKANLQA ALQVLELHHS
   781  KLDTTKALNL LPANTQINDI RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ
   841  QVKCIITEEK VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNPADT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS39 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)
0.28
Highest tissue expression
41 nTPM

Expression across tissuesHPA

Tissue

  • parathyroid gland: 41 nTPM
  • skeletal muscle: 35 nTPM
  • tongue: 32 nTPM
  • thymus: 30 nTPM
  • skin: 28 nTPM
  • cerebral cortex: 27 nTPM

Single-cell type

  • neutrophil progenitors: 106 nCPM
  • sertoli cells: 96 nCPM
  • neutrophils: 89 nCPM
  • microglia: 75 nCPM
  • adrenal medulla cells: 75 nCPM
  • corticotrophs: 73 nCPM

Immune cell

  • basophil: 39 nTPM
  • NK-cell: 21 nTPM
  • total PBMC: 18 nTPM
  • eosinophil: 18 nTPM
  • neutrophil: 17 nTPM
  • intermediate monocyte: 16 nTPM

Brain region

  • hypothalamus: 47 nTPM
  • cerebral cortex: 44 nTPM
  • midbrain: 44 nTPM
  • pons: 43 nTPM
  • basal ganglia: 42 nTPM
  • thalamus: 42 nTPM

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)
0.68
gnomAD pLI
0
gnomAD missense Z
2.65
DepMap mean gene effect
-0.32
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

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of VPS39 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 VPS39 as an antibody target. Whether an autoantibody or antibody against VPS39 could matter depends on whether native VPS39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VPS39 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 VPS39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/VPS39. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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