Seroatlas · Human Serome Atlas

VPS50

Syndetin

Also known as: CCDC132, DKFZp313I2429, FLJ20097, KIAA1861, VPS50_HUMAN, VPS54L

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

Protein identityUniProt · HPA

UniProt accession: Q96JG6
Gene: VPS50
Ensembl: ENSG00000004766
Chromosome: 7
Canonical length: 964 aa
Protein class: Disease related genes, Predicted intracellular proteins
Subcellular location: Plasma membrane,Primary cilium,Basal body,Cytosol,Mid piece,Principal piece,End piece

OverviewNCBI Gene

Enables SNARE binding activity. Acts upstream of or within endocytic recycling. Located in recycling endosome. Part of EARP complex. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

964 residues, UniProt reviewed canonical sequence.

>Q96JG6|VPS50
     1  MQKIKSLMTR QGLKSPQESL SDLGAIESLR VPGKEEFREL REQPSDPQAE QELINSIEQV
    61  YFSVDSFDIV KYELEKLPPV LNLQELEAYR DKLKQQQAAV SKKVADLILE KQPAYVKELE
   121  RVTSLQTGLQ LAAVICTNGR RHLNIAKEGF TQASLGLLAN QRKRQLLIGL LKSLRTIKTL
   181  QRTDVRLSEM LEEEDYPGAI QLCLECQKAA STFKHYSCIS ELNSKLQDTL EQIEEQLDVA
   241  LSKICKNFDI NHYTKVQQAY RLLGKTQTAM DQLHMHFTQA IHNTVFQVVL GYVELCAGNT
   301  DTKFQKLQYK DLCTHVTPDS YIPCLADLCK ALWEVMLSYY RTMEWHEKHD NEDTASASEG
   361  SNMIGTEETN FDRGYIKKKL EHGLTRIWQD VQLKVKTYLL GTDLSIFKYD DFIFVLDIIS
   421  RLMQVGEEFC GSKSEVLQES IRKQSVNYFK NYHRTRLDEL RMFLENETWE LCPVKSNFSI
   481  LQLHEFKFME QSRSPSVSPS KQPVSTSSKT VTLFEQYCSG GNPFEIQANH KDEETEDVLA
   541  SNGYESDEQE KSAYQEYDSD SDVPEELKRD YVDEQTGDGP VKSVSRETLK SRKKSDYSLN
   601  KVNAPILTNT TLNVIRLVGK YMQMMNILKP IAFDVIHFMS QLFDYYLYAI YTFFGRNDSL
   661  ESTGLGLSSS RLRTTLNRIQ ESLIDLEVSA DPTATLTAAE ERKEKVPSPH LSHLVVLTSG
   721  DTLYGLAERV VATESLVFLA EQFEFLQPHL DAVMPAVKKP FLQQFYSQTV STASELRKPI
   781  YWIVAGKALD YEQMLLLMAN VKWDVKEIMS QHNIYVDALL KEFEQFNRRL NEVSKRVRIP
   841  LPVSNILWEH CIRLANRTIV EGYANVKKCS NEGRALMQLD FQQFLMKLEK LTDIRPIPDK
   901  EFVETYIKAY YLTENDMERW IKEHREYSTK QLTNLVNVCL GSHINKKARQ KLLAAIDDID
   961  RPKR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VPS50 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): 0.35
Highest tissue expression: 6.6 nTPM

Expression across tissuesHPA

Tissue

breast: 6.6 nTPM
parathyroid gland: 5.6 nTPM
rectum: 4.9 nTPM
cerebral cortex: 4.7 nTPM
pancreas: 4.7 nTPM
retina: 4.7 nTPM

Single-cell type

choroid plexus epithelial cells: 168 nCPM
distal convoluted tubule cells: 166 nCPM
microglia: 131 nCPM
thyrotrophs: 128 nCPM
brain excitatory neurons: 127 nCPM
corticotrophs: 124 nCPM

Immune cell

MAIT T-cell: 4.5 nTPM
myeloid DC: 4.5 nTPM
intermediate monocyte: 3.4 nTPM
classical monocyte: 3.2 nTPM
basophil: 3 nTPM
T-reg: 2.9 nTPM

Brain region

cerebellum: 14 nTPM
cerebral cortex: 14 nTPM
white matter: 13 nTPM
choroid plexus: 12 nTPM
basal ganglia: 12 nTPM
spinal cord: 12 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about VPS50.

Disease | AllUniProt

Conditions VPS50 is implicated in, by any mechanism.

Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis (NEDMSC) MIM:619685

Disease | GeneticClinVar

8 pathogenic / likely-pathogenic of 153 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis

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: 0.81
DepMap mean gene effect: -0.2
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 10% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

SNARE binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

Vacuolar protein sorting-associated protein 54, N-terminal
Vacuolar-sorting protein 54, of GARP complex
Syndetin, C-terminal
Syndetin
Syndetin, C-terminal

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of VPS50 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 VPS50 as an antibody target. Whether an autoantibody or antibody against VPS50 could matter depends on whether native VPS50 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VPS50 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 VPS50 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...