U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

VPS29 VPS29 retromer complex component [ Homo sapiens (human) ]

Gene ID: 51699, updated on 3-Nov-2024

Summary

Go to the top of the page Help
Official Symbol
VPS29provided by HGNC
Official Full Name
VPS29 retromer complex componentprovided by HGNC
Primary source
HGNC:HGNC:14340
See related
Ensembl:ENSG00000111237 MIM:606932; AllianceGenome:HGNC:14340
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
DC7; DC15; PEP11
Summary
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]
Expression
Ubiquitous expression in fat (RPKM 31.1), esophagus (RPKM 28.7) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See VPS29 in Genome Data Viewer
Location:
12q24.11
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110491083..110502111, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110468777..110479808, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110928888..110939916, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7005 Neighboring gene uncharacterized LOC124903016 Neighboring gene ribosomal protein L31 pseudogene 49 Neighboring gene GPN-loop GTPase 3 Neighboring gene family with sequence similarity 216 member A Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene Sharpr-MPRA regulatory region 4252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7006 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:110953094-110953337 Neighboring gene RAD9 checkpoint clamp component B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978258-110978758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978759-110979259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7008 Neighboring gene protein phosphatase targeting COQ7 Neighboring gene HNF4 motif-containing MPRA enhancer 250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7013 Neighboring gene tectonic family member 1 Neighboring gene RNA, 7SL, cytoplasmic 387, pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Potential functions and causal associations of VPS29 in hepatocellular carcinoma: a bioinformatic and Mendelian randomization study.
    Title: Potential functions and causal associations of VPS29 in hepatocellular carcinoma: a bioinformatic and Mendelian randomization study.
  2. Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29.
    Title: Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29.
  3. Retromer stabilization results in neuroprotection in a model of Amyotrophic Lateral Sclerosis.
    Title: Retromer stabilization results in neuroprotection in a model of Amyotrophic Lateral Sclerosis.
  4. RidL is critical for binding of the L. pneumophila effector to the Vps29 retromer subunit and displacement of the regulator TBC1D5.
    Title: Structural insights into Legionella RidL-Vps29 retromer subunit interaction reveal displacement of the regulator TBC1D5.
  5. The retromer complex is a highly conserved membrane trafficking assembly composed of three proteins - Vps26, Vps29 and Vps35, which are impaired in neurodegenerative diseases. (Review)
    Title: Retromer's Role in Endosomal Trafficking and Impaired Function in Neurodegenerative Diseases.
  6. Heterotrimer composed of DSCR3, C16orf62 and VPS29 orchestrates endosomal cargo retrieval and recycling.
    Title: Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.
  7. This study demonstrated that Genetic variability of VPS29 in parkinsonism.
    Title: Genetic variability of the retromer cargo recognition complex in parkinsonism.
  8. Data indicate that vesicular transport proteins VPS35 and VPS29 influence the levels of the other subunit of retromer.
    Title: VPS29-VPS35 intermediate of retromer is stable and may be involved in the retromer complex assembly process.
  9. Mutations in the gene composing the retromer cargo recognition subunit are not a common cause of Parkinson's disease.
    Title: Genetic variation of the retromer subunits VPS26A/B-VPS29 in Parkinson's disease.
  10. Conclusion is that VPS29 is a metal ion-independent, rigid scaffolding domain, which is essential but not sufficient for incorporation of retromer into functional endosomal transport assemblies.
    Title: VPS29 is not an active metallo-phosphatase but is a rigid scaffold required for retromer interaction with accessory proteins.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ20492, DKFZp564F0223

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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
  
NOT involved_in regulation of autophagy 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 NAS
Non-traceable Author Statement
more info
 PubMed 
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 early endosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in late endosome 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, 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 

General protein information

Go to the top of the page Help
Preferred Names
vacuolar protein sorting-associated protein 29
Names
PEP11 homolog
epididymis secretory sperm binding protein
hVPS29
retromer protein
vacuolar protein sorting 29 homolog
vacuolar sorting protein VPS29/PEP11
vesicle protein sorting 29
x 007 protein
NP_001269079.1
NP_001269080.1
NP_057310.1
NP_476528.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001282150.2 → NP_001269079.1  vacuolar protein sorting-associated protein 29 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AB578892, AC002350, AL832866, BM806646
    Consensus CDS
    CCDS73525.1
    UniProtKB/TrEMBL
    F8VXU5, Q5JPE4
    Related
    ENSP00000449044.1, ENST00000546588.1
    Conserved Domains (2) summary
    cd07394
    Location:34 → 211
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain
    pfam00149
    Location:35 → 164
    Metallophos; Calcineurin-like phosphoesterase

  2. NM_001282151.2 → NP_001269080.1  vacuolar protein sorting-associated protein 29 isoform 4

    See identical proteins and their annotated locations for NP_001269080.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several alternate exons compared to variant 3. The resulting isoform (4) has shorter and distinct N- and C-termini compared to isoform 3.
    Source sequence(s)
    AB578892, AC002350, AL832866, CB158821
    Conserved Domains (1) summary
    cl13995
    Location:2 → 89
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

  3. NM_016226.5 → NP_057310.1  vacuolar protein sorting-associated protein 29 isoform 1

    See identical proteins and their annotated locations for NP_057310.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks two alternate exons compared to variant 3. The resulting isoform (1) has a shorter and distinct N-terminus compared to isoform 3.
    Source sequence(s)
    AC002350, AL832866, BC095446
    Consensus CDS
    CCDS41832.1
    UniProtKB/Swiss-Prot
    Q502Y5, Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7, Q9UBQ0
    UniProtKB/TrEMBL
    Q5JPE4
    Related
    ENSP00000447058.1, ENST00000549578.6
    Conserved Domains (1) summary
    cd07394
    Location:2 → 179
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

  4. NM_057180.3 → NP_476528.1  vacuolar protein sorting-associated protein 29 isoform 2

    See identical proteins and their annotated locations for NP_476528.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 3. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 3.
    Source sequence(s)
    AB578892, AC002350, AF168716, AL832866
    Consensus CDS
    CCDS53832.1
    UniProtKB/TrEMBL
    A0A384MR19, Q5JPE4
    Related
    ENSP00000353786.7, ENST00000360579.11
    Conserved Domains (1) summary
    cd07394
    Location:6 → 183
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

RNA

  1. NR_104099.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate exon and contains another alternate exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AC002350, AL832866, BU568689

  2. NR_104100.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks two alternate exons and contains another alternate exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AC002350, AL832866, BC015095

  3. NR_104101.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon and uses an alternate splice junction at the 3' end of an exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB578892, AC002350, AL832866, BC095446, BF030144

  4. NR_104102.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks two alternate exons and uses an alternate splice junction at the 5' end of an exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA148059, AB578892, AC002350, AL832866

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110491083..110502111 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110468777..110479808 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UBQ0.1 GenPept UniProtKB/Swiss-Prot:Q9UBQ0

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous