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Aliases for VPS29 Gene

Aliases for VPS29 Gene

  • VPS29, Retromer Complex Component 2 3 5
  • Vesicle Protein Sorting 29 3 4
  • PEP11 Homolog 3 4
  • HVPS29 3 4
  • Vacuolar Protein Sorting 29 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting-Associated Protein 29 3
  • Vacuolar Sorting Protein VPS29/PEP11 3
  • Vacuolar Protein Sorting 29 Homolog 3
  • Retromer Protein 3
  • X 007 Protein 3
  • PEP11 3
  • DC15 3
  • DC7 3

External Ids for VPS29 Gene

Previous GeneCards Identifiers for VPS29 Gene

  • GC12M109953
  • GC12M110725
  • GC12M110771
  • GC12M109341
  • GC12M109392
  • GC12M110929
  • GC12M107947

Summaries for VPS29 Gene

Entrez Gene Summary for VPS29 Gene

  • This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]

GeneCards Summary for VPS29 Gene

VPS29 (VPS29, Retromer Complex Component) is a Protein Coding gene. Diseases associated with VPS29 include Spastic Paraplegia 36, Autosomal Dominant. Among its related pathways are Signaling by Wnt and Neuroscience. Gene Ontology (GO) annotations related to this gene include protein transporter activity and phosphoserine phosphatase activity.

UniProtKB/Swiss-Prot for VPS29 Gene

  • Acts as 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 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 to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514).

Gene Wiki entry for VPS29 Gene

Additional gene information for VPS29 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS29 Gene

Genomics for VPS29 Gene

GeneHancer (GH) Regulatory Elements for VPS29 Gene

Promoters and enhancers for VPS29 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J110499 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +1.1 1104 4 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ENSG00000278993 VPS29 RAD9B IFT81 ARPC3 FAM216A ENSG00000257268 ANAPC7 GPN3 RNU4-32P
GH12J110542 Enhancer 1.3 Ensembl ENCODE dbSUPER 0.3 -42.8 -42830 5 HDGF PKNOX1 SMAD1 FEZF1 ZNF2 IRF4 YY1 ATF7 FOS RUNX3 HVCN1 TCTN1 FAM216A PPTC7 VPS29
GH12J110536 Enhancer 1.2 Ensembl ENCODE dbSUPER 0.3 -35.9 -35879 3 INSM2 FEZF1 RAD21 YY1 ZNF335 ZNF366 SCRT2 EGR2 ZNF362 RXRA ARPC3 GLTP GPN3 VPS29 PPTC7
GH12J110574 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 0.2 -75.0 -75034 6.2 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B DMAP1 YBX1 IRF4 YY1 FAM216A GPN3 ARPC3 TCTN1 GLTP PPTC7 ATP2A2 VPS29
GH12J110512 Enhancer 0.8 Ensembl ENCODE 0.4 -10.4 -10381 0.2 HDGF CTCF ZNF654 L3MBTL2 TRIM22 REST RAD21 RFX5 GTF3C2 PRDM6 GPN3 RNU4-32P HSPA8P14 PHETA1 RAD9B VPS29 PPTC7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS29 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS29 gene promoter:
  • AREB6
  • AML1a
  • Evi-1
  • Egr-2
  • FOXJ2
  • FOXJ2 (long isoform)
  • RSRFC4
  • GATA-1
  • GR-alpha
  • GR

Genomic Locations for VPS29 Gene

Genomic Locations for VPS29 Gene
chr12:110,491,097-110,502,142
(GRCh38/hg38)
Size:
11,046 bases
Orientation:
Minus strand
chr12:110,928,902-110,939,922
(GRCh37/hg19)
Size:
11,021 bases
Orientation:
Minus strand

Genomic View for VPS29 Gene

Genes around VPS29 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS29 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS29 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS29 Gene

Proteins for VPS29 Gene

  • Protein details for VPS29 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBQ0-VPS29_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 29
    Protein Accession:
    Q9UBQ0
    Secondary Accessions:
    • Q502Y5
    • Q6FIF8
    • Q6IAH3
    • Q9H0W0
    • Q9NRP1
    • Q9NRU7

    Protein attributes for VPS29 Gene

    Size:
    182 amino acids
    Molecular mass:
    20506 Da
    Quaternary structure:
    • Component of the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting subcomplex (VPS), formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35 (PubMed:11102511, PubMed:16737443, PubMed:17891154). The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform (By similarity). 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 (Probable). Interacts with VPS26A, VPS35, SNX1, SNX2, SNX27, WASHC5, TBC1D5 (PubMed:11102511, PubMed:20923837, PubMed:23331060, PubMed:23563491). Interacts with VPS26B and ANKRD27 (By similarity).

    Three dimensional structures from OCA and Proteopedia for VPS29 Gene

    Alternative splice isoforms for VPS29 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS29 Gene

Post-translational modifications for VPS29 Gene

  • Ubiquitination at posLast=5050 and posLast=3030
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS29 Gene

Domains & Families for VPS29 Gene

Gene Families for VPS29 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q9UBQ0

UniProtKB/Swiss-Prot:

VPS29_HUMAN :
  • Belongs to the VPS29 family.
Family:
  • Belongs to the VPS29 family.
genes like me logo Genes that share domains with VPS29: view

Function for VPS29 Gene

Molecular function for VPS29 Gene

UniProtKB/Swiss-Prot Function:
Acts as 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 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 to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514).

Gene Ontology (GO) - Molecular Function for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11102511
GO:0008270 zinc ion binding IBA --
GO:0008565 contributes_to protein transporter activity IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with VPS29: view
genes like me logo Genes that share phenotypes with VPS29: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VPS29

CRISPR Products

miRNA for VPS29 Gene

miRTarBase miRNAs that target VPS29

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS29

Clone Products

  • Addgene plasmids for VPS29

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS29 Gene

Localization for VPS29 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS29 Gene

Cytoplasm. Membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Early endosome. Late endosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS29 gene
Compartment Confidence
extracellular 5
cytosol 5
endosome 5
mitochondrion 2
nucleus 2
lysosome 2
golgi apparatus 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IDA --
GO:0005769 early endosome IEA --
GO:0005770 late endosome IEA --
GO:0005829 cytosol TAS,IEA --
genes like me logo Genes that share ontologies with VPS29: view

Pathways & Interactions for VPS29 Gene

genes like me logo Genes that share pathways with VPS29: view

Pathways by source for VPS29 Gene

1 KEGG pathway for VPS29 Gene
1 Cell Signaling Technology pathway for VPS29 Gene

Gene Ontology (GO) - Biological Process for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0010506 NOT regulation of autophagy IMP 24603492
GO:0015031 protein transport IEA --
GO:0016055 Wnt signaling pathway TAS --
GO:0042147 retrograde transport, endosome to Golgi NAS,IEA 26220253
genes like me logo Genes that share ontologies with VPS29: view

No data available for SIGNOR curated interactions for VPS29 Gene

Drugs & Compounds for VPS29 Gene

(2) Drugs for VPS29 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
genes like me logo Genes that share compounds with VPS29: view

Transcripts for VPS29 Gene

Unigene Clusters for VPS29 Gene

Vacuolar protein sorting 29 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS29

Clone Products

  • Addgene plasmids for VPS29

Alternative Splicing Database (ASD) splice patterns (SP) for VPS29 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8a · 8b
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - -
SP5: - - -
SP6:
SP7: - - - -
SP8:
SP9: - - -
SP10:

Relevant External Links for VPS29 Gene

GeneLoc Exon Structure for
VPS29
ECgene alternative splicing isoforms for
VPS29

Expression for VPS29 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS29 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS29 Gene



Protein tissue co-expression partners for VPS29 Gene

NURSA nuclear receptor signaling pathways regulating expression of VPS29 Gene:

VPS29

SOURCE GeneReport for Unigene cluster for VPS29 Gene:

Hs.600114

mRNA Expression by UniProt/SwissProt for VPS29 Gene:

Q9UBQ0-VPS29_HUMAN
Tissue specificity: Ubiquitous. Highly expressed in heart, lung, placenta, spleen, peripheral blood leukocytes, thymus, colon skeletal muscle, kidney and brain.

Evidence on tissue expression from TISSUES for VPS29 Gene

  • Lung(4.7)
  • Nervous system(4.7)
  • Liver(4.4)
  • Lymph node(4.4)
  • Spleen(4.4)
  • Thyroid gland(4.4)
  • Blood(4.3)
  • Intestine(2.2)
  • Pancreas(2.2)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with VPS29: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS29 Gene

Orthologs for VPS29 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS29 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS29 34 33
  • 99.69 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS29 34
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS29 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS29 34 33
  • 96.01 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS29 34 33
  • 95.47 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps29 33
  • 91.11 (n)
mouse
(Mus musculus)
Mammalia Vps29 16 34 33
  • 90.19 (n)
chicken
(Gallus gallus)
Aves VPS29 34 33
  • 85.33 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 97 (a)
OneToMany
-- 34
  • 90 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vps29 33
  • 82.41 (n)
Str.3938 33
zebrafish
(Danio rerio)
Actinopterygii vps29 34 33
  • 79.07 (n)
OneToOne
wufb06g05 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9310 33
fruit fly
(Drosophila melanogaster)
Insecta CG4764 34 35 33
  • 70.93 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002338 33
  • 70 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-29 34 33
  • 61.51 (n)
OneToOne
ZK1128.8 35
  • 60 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS29 36 34
  • 29 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons MAG1 33
  • 62.06 (n)
rice
(Oryza sativa)
Liliopsida Os02g0265400 33
  • 62.04 (n)
Os.10198 33
barley
(Hordeum vulgare)
Liliopsida Hv.3466 33
corn
(Zea mays)
Liliopsida Zm.8987 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.866 34
  • 76 (a)
OneToOne
Cin.8907 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8907 33
Species where no ortholog for VPS29 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS29 Gene

ENSEMBL:
Gene Tree for VPS29 (if available)
TreeFam:
Gene Tree for VPS29 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS29: view image

Paralogs for VPS29 Gene

(2) SIMAP similar genes for VPS29 Gene using alignment to 4 proteins:

  • VPS29_HUMAN
  • F8VXU5_HUMAN
  • Q05DG7_HUMAN
  • Q8N0S8_HUMAN
genes like me logo Genes that share paralogs with VPS29: view

No data available for Paralogs for VPS29 Gene

Variants for VPS29 Gene

Sequence variations from dbSNP and Humsavar for VPS29 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000044920 -- 110,493,651(-) T/A intron_variant
rs1000077256 -- 110,493,285(-) AAAAAAA/AAAAAA intron_variant
rs1000117245 -- 110,491,038(-) T/A downstream_transcript_variant
rs1000278529 -- 110,497,882(-) C/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000278726 -- 110,497,621(-) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS29 Gene

Variant ID Type Subtype PubMed ID
nsv826512 CNV loss 20364138

Variation tolerance for VPS29 Gene

Residual Variation Intolerance Score: 44% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.19; 4.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS29 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS29

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS29 Gene

Disorders for VPS29 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS29 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spastic paraplegia 36, autosomal dominant
  • spg36
- elite association - COSMIC cancer census association via MalaCards
Search VPS29 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS29

genes like me logo Genes that share disorders with VPS29: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS29 Gene

Publications for VPS29 Gene

  1. Human homologues of yeast vacuolar protein sorting 29 and 35. (PMID: 11062004) Edgar AJ … Polak JM (Biochemical and biophysical research communications 2000) 2 3 4 22 58
  2. VPS29 is not an active metallo-phosphatase but is a rigid scaffold required for retromer interaction with accessory proteins. (PMID: 21629666) Swarbrick JD … Collins BM (PloS one 2011) 2 3 4 58
  3. The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide. (PMID: 16737443) Damen E … van Leeuwen JE (The Biochemical journal 2006) 3 4 22 58
  4. Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites. (PMID: 15788412) Wang D … Liu P (The Journal of biological chemistry 2005) 3 4 22 58
  5. VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface. (PMID: 24856514) Hesketh GG … Owen DJ (Developmental cell 2014) 3 4 58

Products for VPS29 Gene

Sources for VPS29 Gene

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