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

Summary

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
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Genomic context

Location:: 12q24.11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (110491083..110502111, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (110468777..110479808, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (110928888..110939916, complement)

Chromosome 12 - NC_000012.12 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
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?

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.
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.
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.
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.
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.
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.
This study demonstrated that Genetic variability of VPS29 in parkinsonism.
Title: Genetic variability of the retromer cargo recognition complex in parkinsonism.
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.
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.
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

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D1S1361 (e-PCR)
- UniSTS:149557

RH47395 (e-PCR)
- UniSTS:12622

GDB:335751 (e-PCR)
- UniSTS:156601

RH80970 (e-PCR)
- UniSTS:86243

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

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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

EC 3.1.3.3

NP_001269080.1

EC 3.1.3.3

NP_057310.1

EC 3.1.3.3

NP_476528.1

EC 3.1.3.3

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.

mRNA and Protein(s)

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
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
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
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

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
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
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
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