VPS35 VPS35 retromer complex component [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS35provided by HGNC
Official Full Name: VPS35 retromer complex componentprovided by HGNC
Primary source: HGNC:HGNC:13487
See related: Ensembl:ENSG00000069329 MIM:601501; AllianceGenome:HGNC:13487
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MEM3; PARK17
Summary: 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. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in small intestine (RPKM 28.7), urinary bladder (RPKM 22.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q11.2

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (46656132..46689178, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (52452996..52486052, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (46690044..46723090, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The impact of VPS35 D620N mutation on alternative autophagy and its reversal by estrogen in Parkinson's disease.
Title: The impact of VPS35 D620N mutation on alternative autophagy and its reversal by estrogen in Parkinson's disease.
VPS35 and retromer dysfunction in Parkinson's disease.
Title: VPS35 and retromer dysfunction in Parkinson's disease.
VPS35 promotes gastric cancer progression through integrin/FAK/SRC signalling-mediated IL-6/STAT3 pathway activation in a YAP-dependent manner.
Title: VPS35 promotes gastric cancer progression through integrin/FAK/SRC signalling-mediated IL-6/STAT3 pathway activation in a YAP-dependent manner.
VPS35 promotes cell proliferation via EGFR recycling and enhances EGFR inhibitors response in gastric cancer.
Title: VPS35 promotes cell proliferation via EGFR recycling and enhances EGFR inhibitors response in gastric cancer.
Structural and Functional Impact of Damaging Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) on Human VPS35 Protein Using Computational Approaches.
Title: Structural and Functional Impact of Damaging Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) on Human VPS35 Protein Using Computational Approaches.
Mutant VPS35-D620N induces motor dysfunction and impairs DAT-mediated dopamine recycling pathway.
Title: Mutant VPS35-D620N induces motor dysfunction and impairs DAT-mediated dopamine recycling pathway.
ITRAQ-based quantitative proteomic analysis reveals that VPS35 promotes the expression of MCM2-7 genes in HeLa cells.
Title: ITRAQ-based quantitative proteomic analysis reveals that VPS35 promotes the expression of MCM2-7 genes in HeLa cells.
Endosomal traffic and glutamate synapse activity are increased in VPS35 D620N mutant knock-in mouse neurons, and resistant to LRRK2 kinase inhibition.
Title: Endosomal traffic and glutamate synapse activity are increased in VPS35 D620N mutant knock-in mouse neurons, and resistant to LRRK2 kinase inhibition.
Impaired neurogenesis in the hippocampus of an adult VPS35 mutant mouse model of Parkinson's disease through interaction with APP.
Title: Impaired neurogenesis in the hippocampus of an adult VPS35 mutant mouse model of Parkinson's disease through interaction with APP.
VPS35 Downregulation Alters Degradation Pathways in Neuronal Cells.
Title: VPS35 Downregulation Alters Degradation Pathways in Neuronal Cells.

Submit: New GeneRIF Correction See all GeneRIFs (75)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Parkinson disease 17 MedGen: C3280133 OMIM: 614203 GeneReviews: Parkinson Disease Overview, VPS35-Related Parkinson Disease	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope transmembrane glycoprotein gp41	env	The gp41 cytoplasmic tail binds directly to retromer components VPS26 and VPS35 in HIV-1-infected cells	PubMed
Tat	tat	Expression of HIV-1 Tat upregulates the abundance of vacuolar protein sorting 35 homolog (VPS35) in the nucleoli of Jurkat T-cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH79844 (e-PCR)
- UniSTS:88933

D16S3222 (e-PCR)
- UniSTS:26099

Clone Names

FLJ10752, FLJ13588, FLJ20388, DKFZp434E1211, DKFZp434P1672

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables D1 dopamine receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosome organization	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial fragmentation involved in apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrion to lysosome vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of inflammatory response	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of late endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of lysosomal protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein homooligomerization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter receptor transport, endosome to plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of Wnt protein secretion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dopamine biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dopamine receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of locomotion involved in locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mitochondrial fission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of protein localization to cell periphery	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to cell periphery	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	IEA Inferred from Electronic Annotation more info
involved_in protein localization to endosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of dendritic spine maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of macroautophagy	TAS Traceable Author Statement more info	PubMed
involved_in regulation of mitochondrion organization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of postsynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynapse assembly	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of protein metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of protein stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse maturation	IEA Inferred from Electronic Annotation more info
involved_in regulation of terminal button organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	NAS Non-traceable Author Statement more info	PubMed
involved_in transcytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in vesicle-mediated transport in synapse	IEA Inferred from Electronic Annotation more info
involved_in voluntary musculoskeletal movement	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in dopaminergic synapse	IEA Inferred from Electronic Annotation more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info
colocalizes_with mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion-derived vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
part_of retromer complex	IBA Inferred from Biological aspect of Ancestor more info
part_of retromer complex	IDA Inferred from Direct Assay more info	PubMed
part_of retromer complex	NAS Non-traceable Author Statement more info	PubMed
part_of retromer complex	TAS Traceable Author Statement more info	PubMed
part_of retromer, cargo-selective complex	IDA Inferred from Direct Assay more info	PubMed
part_of retromer, cargo-selective complex	NAS Non-traceable Author Statement more info	PubMed
located_in tubular endosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 35

Names: hVPS35; maternal-embryonic 3; vacuolar protein sorting 35 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029970.2 RefSeqGene

Range

5000..38046

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_018206.6 → NP_060676.2 vacuolar protein sorting-associated protein 35

See identical proteins and their annotated locations for NP_060676.2

Status: REVIEWED

Source sequence(s)

AC007225, AC012186

Consensus CDS

CCDS10721.1

UniProtKB/Swiss-Prot

Q561W2, Q96QK1, Q9H016, Q9H096, Q9H4P3, Q9H8J0, Q9NRS7, Q9NVG2, Q9NX80, Q9NZK2

UniProtKB/TrEMBL

Q53FR4

Related

ENSP00000299138.7, ENST00000299138.12

Conserved Domains (1) summary

pfam03635
Location:15 → 752

Vps35; Vacuolar protein sorting-associated protein 35

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

46656132..46689178 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011523227.4 → XP_011521529.1 vacuolar protein sorting-associated protein 35 isoform X1

See identical proteins and their annotated locations for XP_011521529.1

UniProtKB/TrEMBL

Q53FR4

Conserved Domains (1) summary

pfam03635
Location:1 → 723

Vps35; Vacuolar protein sorting-associated protein 35
XM_005256045.4 → XP_005256102.1 vacuolar protein sorting-associated protein 35 isoform X2

See identical proteins and their annotated locations for XP_005256102.1

UniProtKB/TrEMBL

Q53FR4

Conserved Domains (1) summary

pfam03635
Location:1 → 685

Vps35; Vacuolar protein sorting-associated protein 35

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

52452996..52486052 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054313466.1 → XP_054169441.1 vacuolar protein sorting-associated protein 35 isoform X1
XM_054313467.1 → XP_054169442.1 vacuolar protein sorting-associated protein 35 isoform X2