Seroatlas · Human Serome Atlas

VPS4B

Vacuolar protein sorting-associated protein 4B

Also known as: SKD1, SKD1B, VPS4-2, VPS4B_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
O75351
Gene
VPS4B
Ensembl
ENSG00000119541
Chromosome
18
Canonical length
444 aa
Protein class
Enzymes, Plasma proteins, Predicted intracellular proteins
Subcellular location
Vesicles,Intermediate filaments

OverviewNCBI Gene

The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. Mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be a yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 18; the gene for the other resides on chromosome 16. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

444 residues, UniProt reviewed canonical sequence.

>O75351|VPS4B
     1  MSSTSPNLQK AIDLASKAAQ EDKAGNYEEA LQLYQHAVQY FLHVVKYEAQ GDKAKQSIRA
    61  KCTEYLDRAE KLKEYLKNKE KKAQKPVKEG QPSPADEKGN DSDGEGESDD PEKKKLQNQL
   121  QGAIVIERPN VKWSDVAGLE GAKEALKEAV ILPIKFPHLF TGKRTPWRGI LLFGPPGTGK
   181  SYLAKAVATE ANNSTFFSIS SSDLVSKWLG ESEKLVKNLF QLARENKPSI IFIDEIDSLC
   241  GSRSENESEA ARRIKTEFLV QMQGVGVDND GILVLGATNI PWVLDSAIRR RFEKRIYIPL
   301  PEPHARAAMF KLHLGTTQNS LTEADFRELG RKTDGYSGAD ISIIVRDALM QPVRKVQSAT
   361  HFKKVRGPSR ADPNHLVDDL LTPCSPGDPG AIEMTWMDVP GDKLLEPVVS MSDMLRSLSN
   421  TKPTVNEHDL LKLKKFTEDF GQEG

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS4B 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)
0.32
Highest tissue expression
71 nTPM

Expression across tissuesHPA

Tissue

  • esophagus: 71 nTPM
  • bone marrow: 50 nTPM
  • colon: 40 nTPM
  • tonsil: 37 nTPM
  • rectum: 35 nTPM
  • small intestine: 34 nTPM

Single-cell type

  • esophageal apical cells: 1,139 nCPM
  • ocular epithelial cells: 427 nCPM
  • neutrophils: 357 nCPM
  • esophageal suprabasal cells: 240 nCPM
  • endometrial glandular cells: 218 nCPM
  • suprabasal keratinocytes: 209 nCPM

Immune cell

  • neutrophil: 187 nTPM
  • basophil: 165 nTPM
  • eosinophil: 125 nTPM
  • non-classical monocyte: 77 nTPM
  • naive B-cell: 74 nTPM
  • NK-cell: 69 nTPM

Brain region

  • midbrain: 35 nTPM
  • white matter: 33 nTPM
  • hypothalamus: 31 nTPM
  • pons: 31 nTPM
  • medulla oblongata: 29 nTPM
  • cerebellum: 29 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)
0.48
gnomAD pLI
0.23
gnomAD missense Z
2.41
DepMap mean gene effect
-0.18
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% 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 VPS4B 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 VPS4B as an antibody target. Whether an autoantibody or antibody against VPS4B could matter depends on whether native VPS4B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VPS4B 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 VPS4B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/VPS4B. 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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