VPS35

gene
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Also known as FLJ10752MEM3PARK17

Summary

VPS35 (VPS35 retromer complex component, HGNC:13487) is a protein-coding gene on chromosome 16q11.2, encoding Vacuolar protein sorting-associated protein 35 (Q96QK1). Acts as a component of the retromer cargo-selective complex (CSC). It is a selective cancer dependency (DepMap: 66.8% of cell lines).

This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex.

Source: NCBI Gene 55737 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Parkinson disease (Definitive, ClinGen) — +3 more curated relationships
  • Clinical variants (ClinVar): 288 total — 1 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 37
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 66.8% of screened cell lines
  • MANE Select transcript: NM_018206

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13487
Approved symbolVPS35
NameVPS35 retromer complex component
Location16q11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10752, MEM3, PARK17
Ensembl geneENSG00000069329
Ensembl biotypeprotein_coding
OMIM601501
Entrez55737

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 15 protein_coding, 6 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000299138, ENST00000562420, ENST00000563884, ENST00000563984, ENST00000565228, ENST00000568191, ENST00000568612, ENST00000568642, ENST00000568784, ENST00000569950, ENST00000647959, ENST00000904858, ENST00000904859, ENST00000904860, ENST00000904861, ENST00000904862, ENST00000904863, ENST00000904864, ENST00000904865, ENST00000921303, ENST00000921304, ENST00000921305, ENST00000940929, ENST00000940930, ENST00000940931

RefSeq mRNA: 1 — MANE Select: NM_018206 NM_018206

CCDS: CCDS10721

Canonical transcript exons

ENST00000299138 — 17 exons

ExonStartEnd
ENSE000013244674665613246660651
ENSE000013708844668913146689178
ENSE000034622954668067146680853
ENSE000034663774668207946682175
ENSE000034826084667894346679156
ENSE000035001894667431446674462
ENSE000035205154667226546672472
ENSE000035287004666298346663162
ENSE000035457144666893046669052
ENSE000035520954666224346662482
ENSE000035905054667170546671860
ENSE000036141174667731546677398
ENSE000036199924667658346676692
ENSE000036324614667456446674660
ENSE000036474104668350846683606
ENSE000036511004668137746681500
ENSE000036895274666171846661861

Expression profiles

Bgee: expression breadth ubiquitous, 149 present calls, max score 97.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.1671 / max 686.9537, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15719837.10641817
1571970.060715

Top tissues by expression

151 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305397.51gold quality
adrenal tissueUBERON:001830396.77gold quality
corpus callosumUBERON:000233696.65gold quality
embryoUBERON:000092296.56gold quality
ganglionic eminenceUBERON:000402396.56gold quality
superior frontal gyrusUBERON:000266196.20gold quality
cortical plateUBERON:000534396.20gold quality
duodenumUBERON:000211496.11gold quality
calcaneal tendonUBERON:000370196.05gold quality
islet of LangerhansUBERON:000000695.88gold quality
endometriumUBERON:000129595.83gold quality
monocyteCL:000057695.70gold quality
colonic epitheliumUBERON:000039795.61gold quality
leukocyteCL:000073895.51gold quality
tonsilUBERON:000237295.31gold quality
prefrontal cortexUBERON:000045195.20gold quality
smooth muscle tissueUBERON:000113595.04gold quality
rectumUBERON:000105294.83gold quality
placentaUBERON:000198794.55gold quality
urinary bladderUBERON:000125594.50gold quality
vermiform appendixUBERON:000115494.45gold quality
bloodUBERON:000017894.29gold quality
Brodmann (1909) area 9UBERON:001354094.29gold quality
bone marrow cellCL:000209294.15gold quality
gall bladderUBERON:000211093.89gold quality
stromal cell of endometriumCL:000225593.76gold quality
dorsolateral prefrontal cortexUBERON:000983493.76gold quality
frontal cortexUBERON:000187093.50gold quality
frontal lobeUBERON:001652593.50gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.43gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

TargetRegulation
DNM1LActivation
LAMP1Repression
LAMP2Activation
SNCARepression
VPS26AActivation

miRNA regulators (miRDB)

175 targeting VPS35, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4533100.0069.482758
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-5692A100.0074.406850
HSA-MIR-548AW99.9972.573559
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-477599.9875.006394
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AN99.9770.912817
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-302E99.9670.742669
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-144-3P99.9473.982698
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-145-5P99.9271.131836

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 66.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • These observations indicate that the mammalian retromer complex assembles by sequential association of SNX1/2 and Vps26-Vps29-Vps35 subcomplexes on endosomal membranes and that SNX1 and SNX2 play interchangeable but essential roles. (PMID:17101778)
  • crystal structure of a VPS29-VPS35 subcomplex showing how the metallophosphoesterase-fold subunit VPS29 acts as a scaffold for the carboxy-terminal half of VPS35 (PMID:17891154)
  • Membrane recruitment of the cargo-selective retromer subcomplex VPS35/29/26 is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. (PMID:19531583)
  • Depletion of the retromer by siRNA against Vps35 leads to mis-sorting of DMT1-II to LAMP2-positive structures, and expression of siRNA-resistant Vps35 can rescue this effect. (PMID:20164305)
  • Vps35 mediates vesicle transport between the mitochondria and peroxisomes. (PMID:20619655)
  • Knockdown of retromer protein VPS35 activity produces no change in the quantity or cellular distribution of total cellular amyloid precursor protein (APP) and has no affect on internalization of cell-surface APP. (PMID:21515373)
  • Frameshift mutations of VPS genes and losses of expression of Vps13A and Vps35 proteins are common in gastric cancers and colorectal cancers with high microsatellite instability. (PMID:21733561)
  • Disruption of VPS35 and retromer-mediated trans-membrane protein sorting, rescue, and recycling in the neurodegenerative process led to Parkinson disease. (PMID:21763482)
  • Only a single heterozygous variant in the VPS35 gene caused late-onset Parkinson disease in this family. (PMID:21763483)
  • The amino-terminal conserved, glutamate-rich sequence of herpesvirus saimiri Tip specifically interacts with the human retromer subunit Vps35 and inhibits retromer activity. (PMID:21849449)
  • The results of this study concluded that VPS35 c.1858G>A mutation is an uncommon cause of familial Parkinson’s disease. (PMID:22154191)
  • Failed to find any case of VPS35 pAsp620Asn mutation in a cohort of Italian patients with familial Parkinson disease. (PMID:22278960)
  • Hence, our data do not support a major role for VPS35 variations in the genetic etiology of Lewy body disorders in the Flanders-Belgian population. (PMID:22336192)
  • This study suggested that VPS35 Asp620Asn may be not associated with PD in Chinese population. (PMID:22410496)
  • Data show that a component of the WASH regulatory complex (SHRC), FAM21, directly interacts with the retromer CSC protein VPS35. (PMID:22513087)
  • We have extended the number of autosomal dominant PD families with VPS35 mutations to 13 families, worldwide; D620N is the most frequent. (PMID:22517097)
  • VPS35 variants are not associated with Parkinson’s disease in the mainland Chinese population. (PMID:22673036)
  • VPS35 mutations are a rare cause of PD in different populations. (PMID:22801713)
  • result suggests that mutation in the VPS35 coding region probably does not represent a major cause of late-onset Parkinson Disease in the Chinese Han population. (PMID:22891780)
  • This study reported that VPS35 mutation in Japanese patients with typical Parkinson’s disease. (PMID:22991136)
  • Our study apart from identifying the p.Asp620Asn variant in familial cases also identified it in idiopathic Parkinson disease cases, and thus provides genetic evidence for a role of p.Asp620Asn in Parkinson disease in different populations worldwide. (PMID:23125461)
  • Mutations in VPS35 were found to not play a role in Parkinson disease patients from Southwest China. (PMID:23261770)
  • There is no evidence for an overall contribution of genetic variability in VPS35 (or EIF4G1) to Parkinson disease development in this large family. (PMID:23408866)
  • Pathogenic mutation in VPS35 impairs its protection against MPP(+) cytotoxicity in dopaminergic neurons in Parkinson’s disease. (PMID:23411763)
  • Pathogenic VPS35 mutations provide important insights into novel molecular targets for parkinson disease. (PMID:23536430)
  • Its mutation causes Parkinson’s disease in Indian population. (PMID:23726718)
  • Dominant expression of Vps35 D620N mutation results in endosomal trafficking alterations that may underpin its role in PD. (PMID:24152121)
  • In 2011 two groups reported the identification of the same missense mutation (p.Asp620Asn) in the vacuolar protein sorting 35 (VPS35) gene, as a novel cause of autosomal dominant parkinson disease. (PMID:24262182)
  • dominant VPS35 mutations lead to neurodegeneration in Parkinson’s disease. (PMID:24740878)
  • D620N mutation in VPS35 restricts WASH complex recruitment to endosomes, inhibiting autophagy. The autophagy defects can be explained, at least in part, by abnormal trafficking of the autophagy protein ATG9A. (PMID:24819384)
  • Its mutation is not a common cause of familial Parkinson’s disease. (PMID:24854799)
  • the major defect of the D620N mutation in the retromer component VPS35 lies in the association to the actin-nucleating Wiskott-Aldrich syndrome and SCAR homolog (WASH) complex. (PMID:24980502)
  • provides molecular insights into the essential role of Vps26 and Vps35 in Rab7-mediated recruitment of the core retromer complex (PMID:25367362)
  • Mutagenesis studies coupled with coimmunoprecipitations revealed that retromer-mediated trafficking requires the Env cytoplasmic tail that we show binds directly to retromer components Vps35 and Vps26. (PMID:25393110)
  • VPS35 p.D620N is loss-of-function mutation with respect to VPS35 regulating synaptic transmission and AMPA-type glutamate receptors recycling in mouse cortical neurons and dopamine neuron-like cells produced from stem cells of human p.D620N carriers. (PMID:25416282)
  • This study demonstrated that Genetic variability of VPS35 in parkinsonism. (PMID:25475142)
  • Data indicate that vesicular transport proteins VPS35 and VPS29 influence the levels of the other subunit of retromer. (PMID:25937119)
  • findings provide evidence that the VPS35 D620N mutation likely confers pathogenicity through a partial loss of function mechanism and that this may be linked to other known pathogenic mechanisms such as mitochondrial dysfunction (PMID:26251041)
  • VPS35 D620N and EIF4G1 R1205H mutations are not a common cause of Parkinson disease in the Greek population. (PMID:26300542)
  • neither the R120W nor the N370S variant of the GBA gene nor D620N mutation of the VPS35 gene were detected among the Parkinson disease cases or the controls. (PMID:26547032)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriovps35ENSDARG00000008224
mus_musculusVps35ENSMUSG00000031696
rattus_norvegicusVps35ENSRNOG00000017612
drosophila_melanogasterVps35FBGN0034708
caenorhabditis_elegansWBGENE00006933

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 35Q96QK1 (reviewed: Q96QK1)

Alternative names: Maternal-embryonic 3, Vesicle protein sorting 35

All UniProt accessions (4): Q96QK1, A0A3B3ITD4, H3BRJ7, I3L4S0

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The CSC seems to associate with the cytoplasmic domain of cargo proteins predominantly via VPS35; however, these interactions seem to be of low affinity and retromer SNX proteins may also contribute to cargo selectivity thus questioning the classical function of the CSC. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required for retrograde transport of lysosomal enzyme receptor IGF2R and SLC11A2. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA). Required for endosomal localization of WASHC2C. Mediates the association of the CSC with the WASH complex via WASHC2. Required for the endosomal localization of TBC1D5. (Microbial infection) The heterotrimeric retromer cargo-selective complex (CSC) mediates the exit of human papillomavirus from the early endosome and the delivery to the Golgi apparatus.

Subunit / interactions. Component of the heterotrimeric retromer cargo-selective complex (CSC), also decribed as vacuolar protein sorting subcomplex (VPS), formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35. The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform. The CSC is believed to associate with variable sorting nexins to form functionally distinct retromer complex variants. The originally described retromer complex (also called SNX-BAR retromer) is a pentamer containing the CSC and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. The CSC associates with SNX3 to form a SNX3-retromer complex. The CSC associates with SNX27, the WASH complex and the SNX-BAR subcomplex to form the SNX27-retromer complex. Interacts with VPS26A, VPS26B, VPS29, SNX1, SNX2, IGF2R, SNX3, GOLPH3, LRRK2, SLC11A2, WASHC2A, WASHC2C, FKBP15, WASHC1, RAB7A, SNX27, WASHC5, EHD1. Interacts with MAGEL2; leading to recruitment of the TRIM27:MAGEL2 E3 ubiquitin ligase complex retromer-containing endosomes. Interacts with SORCS2. (Microbial infection) Interacts with human papillomavirus 16 minor capsid protein L2 (via C-terminus); this interaction mediates the transport of the capsid from the early endosome to the Golgi apparatus.

Subcellular location. Cytoplasm. Membrane. Endosome. Early endosome. Late endosome.

Tissue specificity. Ubiquitous. Highly expressed in heart, brain, placenta, skeletal muscle, spleen, thymus, testis, ovary, small intestine, kidney and colon.

Disease relevance. Parkinson disease 17 (PARK17) [MIM:614203] An autosomal dominant, adult-onset form of Parkinson disease. Parkinson disease is a complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability, as well as by a clinically significant response to treatment with levodopa. The pathology involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the VPS35 family.

RefSeq proteins (1): NP_060676* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005378Vps35Family
IPR016024ARM-type_foldHomologous_superfamily
IPR042491Vps35_CHomologous_superfamily

Pfam: PF03635

UniProt features (80 total): helix 44, sequence variant 11, sequence conflict 7, strand 5, region of interest 4, turn 3, modified residue 3, mutagenesis site 2, chain 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
8R0JX-RAY DIFFRACTION2.4
8R02X-RAY DIFFRACTION2.5
5OSIX-RAY DIFFRACTION2.52
5F0JX-RAY DIFFRACTION2.7
5F0PX-RAY DIFFRACTION2.78
2R17X-RAY DIFFRACTION2.8
5F0KX-RAY DIFFRACTION3.07
5F0MX-RAY DIFFRACTION3.1
8RKSX-RAY DIFFRACTION3.1
5F0LX-RAY DIFFRACTION3.2
5OSHX-RAY DIFFRACTION4.3
7BLNELECTRON MICROSCOPY8.9
7BLOELECTRON MICROSCOPY9.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96QK1-F191.400.74

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 7, 783, 791

Mutagenesis-validated functional residues (2):

PositionPhenotype
108disrupts interaction with vps26; no effect on interaction with vps29.
675disrupts interaction with vps29. does not effect interaction with vps26.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-3238698WNT ligand biogenesis and trafficking

MSigDB gene sets: 437 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOBP_PHENOL_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_POSITIVE_REGULATION_OF_MITOCHONDRIAL_FISSION, GOBP_PHENOL_CONTAINING_COMPOUND_BIOSYNTHETIC_PROCESS, GOBP_LYSOSOMAL_TRANSPORT, GOBP_BEHAVIOR, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_INFLAMMATORY_RESPONSE, GOBP_SYNAPSE_ASSEMBLY, GOCC_VACUOLAR_MEMBRANE

GO Biological Process (46): intracellular protein transport (GO:0006886), lysosome organization (GO:0007040), positive regulation of gene expression (GO:0010628), negative regulation of gene expression (GO:0010629), regulation of mitochondrion organization (GO:0010821), Wnt signaling pathway (GO:0016055), regulation of macroautophagy (GO:0016241), regulation of protein stability (GO:0031647), protein destabilization (GO:0031648), endocytic recycling (GO:0032456), negative regulation of protein homooligomerization (GO:0032463), protein localization to endosome (GO:0036010), retrograde transport, endosome to Golgi (GO:0042147), mitochondrial fragmentation involved in apoptotic process (GO:0043653), transcytosis (GO:0045056), positive regulation of protein catabolic process (GO:0045732), negative regulation of inflammatory response (GO:0050728), modulation of chemical synaptic transmission (GO:0050804), voluntary musculoskeletal movement (GO:0050882), regulation of protein metabolic process (GO:0051246), positive regulation of dopamine receptor signaling pathway (GO:0060161), positive regulation of Wnt protein secretion (GO:0061357), regulation of synapse maturation (GO:0090128), positive regulation of mitochondrial fission (GO:0090141), positive regulation of canonical Wnt signaling pathway (GO:0090263), positive regulation of locomotion involved in locomotory behavior (GO:0090326), neurotransmitter receptor transport, endosome to postsynaptic membrane (GO:0098887), vesicle-mediated transport in synapse (GO:0099003), mitochondrion to lysosome vesicle-mediated transport (GO:0099074), neurotransmitter receptor transport, endosome to plasma membrane (GO:0099639), regulation of postsynapse assembly (GO:0150052), negative regulation of late endosome to lysosome transport (GO:1902823), regulation of dendritic spine maintenance (GO:1902950), positive regulation of dopamine biosynthetic process (GO:1903181), negative regulation of protein localization (GO:1903828), positive regulation of protein localization to cell periphery (GO:1904377), negative regulation of lysosomal protein catabolic process (GO:1905166), regulation of presynapse assembly (GO:1905606), regulation of terminal button organization (GO:2000331), positive regulation of signal transduction (GO:0009967)

GO Molecular Function (2): D1 dopamine receptor binding (GO:0031748), protein binding (GO:0005515)

GO Cellular Component (24): lysosome (GO:0005764), lysosomal membrane (GO:0005765), endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), cytosol (GO:0005829), endosome membrane (GO:0010008), postsynaptic density (GO:0014069), retromer complex (GO:0030904), retromer, cargo-selective complex (GO:0030906), neuron projection (GO:0043005), neuronal cell body (GO:0043025), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), tubular endosome (GO:0097422), dopaminergic synapse (GO:0098691), presynapse (GO:0098793), glutamatergic synapse (GO:0098978), mitochondrion-derived vesicle (GO:0099073), cytoplasm (GO:0005737), mitochondrion (GO:0005739), membrane (GO:0016020), synapse (GO:0045202), postsynapse (GO:0098794)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by WNT1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
endosome4
synapse3
gene expression2
regulation of gene expression2
endosomal transport2
endomembrane system2
cytoplasmic vesicle2
cytoplasm2
membrane protein complex2
intracellular protein localization1
protein transport1
intracellular transport1
lytic vacuole organization1
positive regulation of macromolecule biosynthetic process1
negative regulation of macromolecule biosynthetic process1
mitochondrion organization1
regulation of organelle organization1
cell surface receptor signaling pathway1
regulation of autophagy1
macroautophagy1
regulation of biological quality1
regulation of protein stability1
vesicle-mediated transport to the plasma membrane1
negative regulation of protein oligomerization1
regulation of protein homooligomerization1
protein homooligomerization1
protein localization to organelle1
intercellular transport1
cytosolic transport1
apoptotic mitochondrial changes1
vesicle-mediated transport1
multicellular organismal process1
positive regulation of catabolic process1
protein catabolic process1
regulation of protein catabolic process1
positive regulation of protein metabolic process1
inflammatory response1
negative regulation of defense response1
negative regulation of response to external stimulus1

Protein interactions and networks

STRING

3056 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VPS35SNX1Q13596999
VPS35VPS26AO75436999
VPS35VPS26BQ4G0F5999
VPS35VPS29Q9UBQ0999
VPS35SNX2P82862997
VPS35SNX3O60493994
VPS35SNX5Q9Y5X3990
VPS35SNX6Q9UNH7964
VPS35SNX27Q96L92957
VPS35DNAJC13O75165904
VPS35PRKNO60260898
VPS35EIF4G1Q04637898
VPS35TBC1D5Q92609874
VPS35LRRK2Q5S007863
VPS35ATP13A2Q9NQ11853

IntAct

225 interactions, top by confidence:

ABTypeScore
VPS35VPS26Apsi-mi:“MI:0915”(physical association)0.980
VPS26AVPS35psi-mi:“MI:0915”(physical association)0.980
VPS35VPS26Apsi-mi:“MI:0914”(association)0.980
VPS35VPS26Apsi-mi:“MI:0407”(direct interaction)0.980
VPS35VPS29psi-mi:“MI:0915”(physical association)0.970
VPS29VPS35psi-mi:“MI:0915”(physical association)0.970
VPS29VPS35psi-mi:“MI:0407”(direct interaction)0.970
VPS35VPS29psi-mi:“MI:0407”(direct interaction)0.970
VPS29VPS26Apsi-mi:“MI:0914”(association)0.930
VPS26BVPS35psi-mi:“MI:0915”(physical association)0.910
VPS29TBC1D5psi-mi:“MI:0914”(association)0.860
VPS26ATBC1D5psi-mi:“MI:0914”(association)0.810
TBC1D5VPS26Apsi-mi:“MI:0914”(association)0.810
VPS29CCDC22psi-mi:“MI:0914”(association)0.790
VPS29VPS26Cpsi-mi:“MI:0914”(association)0.760

BioGRID (388): VPS35 (Two-hybrid), VPS35 (Affinity Capture-RNA), VPS35 (Affinity Capture-RNA), VPS35 (Affinity Capture-RNA), VPS35 (Affinity Capture-MS), VPS35 (Affinity Capture-MS), VPS35 (Affinity Capture-MS), VPS35 (Affinity Capture-MS), SNX3 (Reconstituted Complex), VPS35 (Reconstituted Complex), SLC11A2 (Reconstituted Complex), VPS26A (Reconstituted Complex), VPS29 (Reconstituted Complex), VPS35 (Affinity Capture-RNA), SAC3D1 (Co-fractionation)

ESM2 similar proteins: A0A0R4ITC5, A1L1F4, A4L9P7, E9Q8I9, F1MKX4, F1QFR9, F1R2X6, F8VPU6, O94915, P21359, P42345, P42346, P51593, P97526, Q04690, Q14997, Q29RF7, Q2HJG5, Q498H0, Q4KLU7, Q4QXM3, Q4VA53, Q5F3U9, Q5F3V3, Q5R6J0, Q5SSW2, Q5TBA9, Q5U241, Q5VYK3, Q6A026, Q6DDM4, Q6GP04, Q6NRP2, Q6P4S8, Q6PDI5, Q6TRW4, Q7PX35, Q7TMY8, Q7Z3U7, Q7Z6Z7

Diamond homologs: A8R7K9, F4I0P8, O74552, P34110, Q2HJG5, Q54C24, Q7X659, Q96QK1, Q9EQH3

SIGNOR signaling

1 interactions.

AEffectBMechanism
PTCHD1“up-regulates quantity”VPS35binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 152 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
endocytic recycling917.8×7e-07
retrograde transport, endosome to Golgi1015.2×6e-07
endosomal transport610.8×3e-03
protein transport227.2×5e-10
endocytosis96.3×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

288 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic3
Uncertain significance125
Likely benign86
Benign26

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
30196NM_018206.6(VPS35):c.1858G>A (p.Asp620Asn)Pathogenic
208774NM_018206.6(VPS35):c.1463A>G (p.Gln488Arg)Likely pathogenic
4278242NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu)Likely pathogenic
930214t(10;16)(q26;q11)Likely pathogenic

SpliceAI

2670 predictions. Top by Δscore:

VariantEffectΔscore
16:46660466:T:TAdonor_gain1.0000
16:46661711:CACT:Cdonor_loss1.0000
16:46661712:ACTT:Adonor_loss1.0000
16:46661713:CTT:Cdonor_loss1.0000
16:46661714:TTA:Tdonor_loss1.0000
16:46661715:T:TGdonor_loss1.0000
16:46661716:A:ACdonor_gain1.0000
16:46661716:A:Tdonor_loss1.0000
16:46661717:C:CAdonor_loss1.0000
16:46661717:C:CCdonor_gain1.0000
16:46661862:C:CCacceptor_gain1.0000
16:46662241:ACCT:Adonor_gain1.0000
16:46662242:CCTC:Cdonor_gain1.0000
16:46662244:T:TAdonor_gain1.0000
16:46662480:TGCCT:Tacceptor_loss1.0000
16:46662481:GCC:Gacceptor_loss1.0000
16:46662482:CCTAG:Cacceptor_loss1.0000
16:46663159:CATC:Cacceptor_gain1.0000
16:46663161:TCC:Tacceptor_loss1.0000
16:46663163:C:Aacceptor_loss1.0000
16:46663164:T:Cacceptor_loss1.0000
16:46668929:CCA:Cdonor_gain1.0000
16:46669065:CAT:Cacceptor_gain1.0000
16:46669067:T:Cacceptor_gain1.0000
16:46669067:T:TCacceptor_gain1.0000
16:46671701:ATAC:Adonor_gain1.0000
16:46671702:T:Cdonor_gain1.0000
16:46671703:A:ACdonor_gain1.0000
16:46671703:A:Cdonor_loss1.0000
16:46671704:C:CCdonor_gain1.0000

AlphaMissense

5286 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:46662331:A:GL660P1.000
16:46662431:C:GA627P1.000
16:46663050:C:TG587E1.000
16:46663051:C:GG587R1.000
16:46663051:C:TG587R1.000
16:46663056:A:GL585P1.000
16:46663062:A:GL583P1.000
16:46668961:A:GL539P1.000
16:46668991:A:GL529P1.000
16:46669006:C:GR524P1.000
16:46669036:C:GR514P1.000
16:46672431:A:GL401P1.000
16:46672440:A:GL398P1.000
16:46674356:A:GL373P1.000
16:46674401:G:TA358D1.000
16:46674402:C:GA358P1.000
16:46674404:A:GL357P1.000
16:46674413:A:GL354P1.000
16:46674600:A:CF325L1.000
16:46674600:A:TF325L1.000
16:46674602:A:GF325L1.000
16:46674656:C:GA307P1.000
16:46674658:A:GL306S1.000
16:46674660:T:AR305S1.000
16:46674660:T:GR305S1.000
16:46676583:C:AR305I1.000
16:46676583:C:GR305T1.000
16:46676584:T:CR305G1.000
16:46676649:A:GL283P1.000
16:46676670:A:GL276P1.000

dbSNP variants (sampled 300 via entrez): RS1000102437 (16:46657188 T>C), RS1000114746 (16:46670190 A>C,G), RS1000341322 (16:46678072 G>A,C), RS1000541108 (16:46656880 C>T), RS1000954989 (16:46675874 A>G), RS1000978565 (16:46664463 T>C), RS1001066360 (16:46687283 T>C), RS1001144196 (16:46689865 G>A,C,T), RS1001161056 (16:46686289 G>C), RS1001171055 (16:46678722 A>G), RS1001175364 (16:46690137 A>G), RS1001531520 (16:46663942 C>T), RS1001613992 (16:46661026 A>G), RS1001641725 (16:46660771 A>G), RS1001671530 (16:46670445 A>G)

Disease associations

OMIM: gene MIM:601501 | disease phenotypes: MIM:614203, MIM:168600

GenCC curated gene-disease

DiseaseClassificationInheritance
Parkinson diseaseDefinitiveAutosomal dominant
Parkinson disease 17StrongAutosomal dominant
hereditary late onset Parkinson diseaseSupportiveAutosomal dominant
intellectual disabilityLimitedAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Parkinson diseaseDefinitiveAD

Mondo (6): Parkinson disease 17 (MONDO:0013625), Parkinson disease (MONDO:0005180), glioma (MONDO:0021042), late-onset Parkinson disease (MONDO:0008199), intellectual disability (MONDO:0001071), (MONDO:0018466)

Orphanet (3): Hereditary late-onset Parkinson disease (Orphanet:411602), Glial tumor (Orphanet:182067), NON RARE IN EUROPE: Parkinson disease (Orphanet:319705)

HPO phenotypes

37 total (30 of 37 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000338Hypomimic face
HP:0000651Diplopia
HP:0000713Agitation
HP:0000716Depression
HP:0000726Dementia
HP:0000741Apathy
HP:0000744Low frustration tolerance
HP:0001268Mental deterioration
HP:0001300Parkinsonism
HP:0001332Dystonia
HP:0001337Tremor
HP:0001824Weight loss
HP:0002015Dysphagia
HP:0002063Rigidity
HP:0002067Bradykinesia
HP:0002120Cerebral cortical atrophy
HP:0002171Gliosis
HP:0002172Postural instability
HP:0002304Akinesia
HP:0002322Resting tremor
HP:0002359Frequent falls
HP:0002360Sleep disturbance
HP:0002362Shuffling gait
HP:0002367Visual hallucination
HP:0002548Parkinsonism with favorable response to dopaminergic medication
HP:0003394Muscle spasm
HP:0003581Adult onset
HP:0004409Hyposmia
HP:0004926Orthostatic hypotension due to autonomic dysfunction

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

DescriptorNameTree numbers
D005910GliomaC04.557.465.625.600.380; C04.557.470.670.380; C04.557.580.625.600.380
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D010300Parkinson DiseaseC10.228.140.079.862.500; C10.228.662.600.400; C10.574.928.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2216744 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

3 potent at pChembl≥5 of 6 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.59Kd25.61nMCHEMBL5653589
7.59ED5025.61nMCHEMBL5653589
5.24IC505760nMMOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 14 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149772: Binding affinity to human VPS35 incubated for 45 mins by Kinobead based pull down assaykd0.0256uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2178593: Inhibition of VPS35 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisic505.7600uM

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
sodium arsenitedecreases expression2
bisphenol Saffects expression, increases expression2
Nickeldecreases expression, decreases reaction, affects expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression, increases expression2
FR900359affects phosphorylation1
dicrotophosdecreases expression1
sodium arsenatedecreases expression1
titanium dioxideincreases expression1
pyrogallol 1,3-dimethyl etheraffects localization, affects cotreatment, decreases expression1
trichostatin Adecreases reaction, affects expression1
beta-lapachoneincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
ICG 001increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
pentabrominated diphenyl ether 100decreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Air Pollutants, Occupationaldecreases expression1
Atrazinedecreases expression1
Cadmiumincreases abundance, increases expression1
Caffeineaffects phosphorylation1

ChEMBL screening assays

11 unique, capped per target: 11 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2217171BindingBinding affinity to VPS35 in human HepG2 cell lysate after 1 hr by capture compound based LC/MS analysisDabigatran and dabigatran ethyl ester: potent inhibitors of ribosyldihydronicotinamide dehydrogenase (NQO2). — J Med Chem

Cellosaurus cell lines

10 cell lines: 5 cancer cell line, 4 induced pluripotent stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C0GDJUCGRMi001-AInduced pluripotent stem cellMale
CVCL_C0GEJUCGRMi001-BInduced pluripotent stem cellMale
CVCL_C0GFJUCGRMi001-CInduced pluripotent stem cellMale
CVCL_D9VPUbigene HEK293 VPS35 KOTransformed cell lineFemale
CVCL_TX53HAP1 VPS35 (-) 1Cancer cell lineMale
CVCL_TX54HAP1 VPS35 (-) 2Cancer cell lineMale
CVCL_TX55HAP1 VPS35 (-) 3Cancer cell lineMale
CVCL_TX56HAP1 VPS35 (-) 4Cancer cell lineMale
CVCL_TX57HAP1 VPS35 (-) 5Cancer cell lineMale
CVCL_YD64LCSBi001-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

497 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT00030979PHASE4COMPLETEDDonepezil to Treat Dementia in Parkinson’s Disease
NCT00043849PHASE4COMPLETEDTreatment of Agitation/Psychosis in Dementia/Parkinsonism (TAP/DAP)
NCT00095810PHASE4COMPLETEDAripiprazole in Patients With Psychosis Associated With Parkinson’s Disease
NCT00125567PHASE4COMPLETEDStalevo in Early Wearing-Off Patients
NCT00143026PHASE4COMPLETEDStudy to Compare the Effect of Treatment With Carbidopa/Levodopa/Entacapone on the Quality of Life of Patients With Parkinson’s Disease. This Study is Not Recruiting in the United States
NCT00144300PHASE4COMPLETEDOphthalmologic Safety Study of Pramipexole Immediate Release (IR) Versus Ropinirole in Early Parkinson’s Disease (PD) Patients
NCT00153972PHASE4COMPLETEDDopamine Turnover Rate as Surrogate Parameter for Diagnosis of Early Parkinson’s Disease
NCT00174239PHASE4TERMINATEDStudy Of Cabaser and Sinemet CR For The Treatment Of Nighttime Symptoms Associated With Parkinson’s Disease.
NCT00215904PHASE4COMPLETEDD-serine Adjuvant Treatment for Parkinson’s Disease
NCT00247247PHASE4COMPLETEDComtess® Versus Cabaseril® as Add-on to Levodopa in the Treatment of Parkinsonian Patients Suffering From Wearing- Off.
NCT00272688PHASE4COMPLETEDContinuous Delivery of Levodopa in Patients With Advanced Idiopathic Parkinsons Disease - Cost-benefit
NCT00297778PHASE4COMPLETEDPramipexole Versus Placebo in Parkinson’s Disease (PD) Patients With Depressive Symptoms
NCT00304161PHASE4COMPLETEDEffectiveness of Antidepressant Treatment for Depression in People With Parkinson’s Disease
NCT00307450PHASE4COMPLETEDEfficacy and Safety of Levetiracetam Versus Placebo on Levodopa-induced Dyskinesias in Advanced Parkinson’s Disease
NCT00321854PHASE4COMPLETEDStudy of (Mirapex) Pramipexole for the Early Treatment of Parkinsons Disease (PD)
NCT00354133PHASE4UNKNOWNControlled Trial With Deep Brain Stimulation in Patients With Early Parkinson’s Disease
NCT00373087PHASE4COMPLETEDCOMT Polymorphism and Entacapone Efficacy
NCT00391898PHASE4COMPLETEDEfficacy of Levodopa/Carbidopa/Entacapone vs Levodopa/Carbidopa in Parkinson’s Disease Patients With Early Wearing-off
NCT00399477PHASE4COMPLETEDA Non-Blinded Study Demonstrating the Effectiveness and Safety of Azilect Alone or in Combination Therapy in Parkinson’s Disease
NCT00402233PHASE4COMPLETEDA Randomized, Double-blind, Active (Pramipexole 0.5 mg Tid) and Placebo Controlled, Study of Pramipexole Given 0.5 mg and 0.75 mg Bid Over 12-week Treatment in Early Parkinson’s Disease (PD) Patients
NCT00437125PHASE4COMPLETEDStudy on the Tolerability of Duloxetine in Depressed Patients With Parkinson’s Disease
NCT00443872PHASE4COMPLETEDEfficacy of Orally Disintegrating Selegiline in Parkinson’s Patients Experiencing Adverse Effects With Dopamine Agonists
NCT00455143PHASE4TERMINATEDCognitive Protection - Dexmedetomidine and Cognitive Reserve
NCT00462007PHASE4COMPLETEDStudy to Evaluate Initiation of Stalevo in Early Wearing-off
NCT00462254PHASE4TERMINATEDRamelteon (ROZEREM) in the Treatment of Sleep Disturbances Associated With Parkinson’s Disease
NCT00477802PHASE4TERMINATEDBotulinum Toxin Type A (Botox) in the Management of Levodopa-Induced Peak-Dose Dyskinesias in Parkinson’s Disease
NCT00485069PHASE4COMPLETEDREQUIP (Ropinirole Hydrochloride) IR Long-Term Phase 4 Study
NCT00489255PHASE4COMPLETEDSafety/Efficacy of Tigan® to Control Nausea/Vomiting Experienced During Apokyn® Initiation and Treatment
NCT00526630PHASE4COMPLETEDMethylphenidate for the Treatment of Gait Impairment in Parkinson’s Disease
NCT00561678PHASE4COMPLETEDPerioperative Cognitive Function - Dexmedetomidine and Cognitive Reserve
NCT00571285PHASE4TERMINATEDClinical Effects of Vitamin D Repletion in Patients With Parkinson’s Disease
NCT00584025PHASE4WITHDRAWNKeppra IV for the Treatment of Motor Fluctuations in Parkinson’s Disease
NCT00584090PHASE4WITHDRAWNSolifenacin Succinate (VESIcare) for the Treatment of Urinary Incontinence in Parkinson’s Disease
NCT00590122PHASE4COMPLETEDParcopa Versus Carbidopa-levodopa in a Single Dose Cross-over Comparison Study
NCT00594464PHASE4COMPLETEDA Trial of Neupro® (Rotigotine Transdermal Patch) in Patients With Parkinson’s Disease Undergoing Surgery
NCT00601978PHASE4WITHDRAWNCarbidopa/Levodopa Versus Carbidopa/Levodopa/Entacapone on Markers of Event Related Potentials (ERPs) in Patients With Idiopathic Parkinson’s Disease (PD) and End-of-dose Wearing Off