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VTA1 vesicle trafficking 1 [ Homo sapiens (human) ]

Gene ID: 51534, updated on 7-Apr-2024

Summary

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Official Symbol
VTA1provided by HGNC
Official Full Name
vesicle trafficking 1provided by HGNC
Primary source
HGNC:HGNC:20954
See related
Ensembl:ENSG00000009844 MIM:610902; AllianceGenome:HGNC:20954
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DRG1; LIP5; SBP1; DRG-1; My012; 6orf55; C6orf55; HSPC228
Summary
C6ORF55 encodes a protein involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes (Ward et al., 2005 [PubMed 15644320]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in brain (RPKM 16.7), colon (RPKM 13.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
6q24.1-q24.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (142147263..142224685)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (143339355..143416853)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (142468400..142545822)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986654 Neighboring gene MPRA-validated peak6171 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409105-142409658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409659-142410210 Neighboring gene neuromedin B receptor Neighboring gene Sharpr-MPRA regulatory region 1984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:142468581-142469101 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142476776-142477403 Neighboring gene gap junction protein epsilon 1 Neighboring gene Sharpr-MPRA regulatory region 15423 Neighboring gene long intergenic non-protein coding RNA 2919 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:142596514-142597713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17614 Neighboring gene Sharpr-MPRA regulatory region 14737 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142695388-142695989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:142695947-142697146 Neighboring gene Sharpr-MPRA regulatory regions 3748 and 6738

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Structural Insights into AQP2 Targeting to Multivesicular Bodies. Roche JV, et al. Int J Mol Sci, 2019 Oct 28. PMID 31661793, Free PMC Article
  2. Phosphorylation of human aquaporin 2 (AQP2) allosterically controls its interaction with the lysosomal trafficking protein LIP5. Roche JV, et al. J Biol Chem, 2017 Sep 1. PMID 28710278, Free PMC Article
  3. Characterization of human dopamine responsive protein DRG-1 that binds to p75NTR-associated cell death executor NADE. Yu Y, et al. Brain Res, 2006 Jul 19. PMID 16777077
  4. Distinct mechanisms of recognizing endosomal sorting complex required for transport III (ESCRT-III) protein IST1 by different microtubule interacting and trafficking (MIT) domains. Guo EZ, et al. J Biol Chem, 2015 Mar 27. PMID 25657007, Free PMC Article
  5. A novel mechanism of regulating the ATPase VPS4 by its cofactor LIP5 and the endosomal sorting complex required for transport (ESCRT)-III protein CHMP5. Vild CJ, et al. J Biol Chem, 2015 Mar 13. PMID 25637630, Free PMC Article

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. High expression of VTA1 is an adverse prognostic factor in lung adenocarcinoma.
    Title: High expression of VTA1 is an adverse prognostic factor in lung adenocarcinoma.
  2. A structural model of the AQP2-LIP5 complex, giving the very first structural insight into how membrane proteins are recruited to multivesicular bodies inner vesicles.
    Title: Structural Insights into AQP2 Targeting to Multivesicular Bodies.
  3. Data suggest that AQP2 binds LIP5 in a AQP2-phosphorylation-dependent manner; phospho-mimicking mutations and phosphorylation reduce thermal stability of AQP2; AQP2 phosphorylation allosterically controls its interaction with LIP5. [AQP2 = aquaporin 2; LIP5 = LYST-interacting protein 5; LYST = lysosomal trafficking regulator protein]
    Title: Phosphorylation of human aquaporin 2 (AQP2) allosterically controls its interaction with the lysosomal trafficking protein LIP5.
  4. Crystal structures of three molecular complexes reveal that IST1 binds to the MIT domains of VPS4 and LIP5.
    Title: Distinct mechanisms of recognizing endosomal sorting complex required for transport III (ESCRT-III) protein IST1 by different microtubule interacting and trafficking (MIT) domains.
  5. ESCRT-III protein CHMP5 inhibits LIP5-mediated VPS4 activation by inducing a moderate conformational change within LIP5.
    Title: A novel mechanism of regulating the ATPase VPS4 by its cofactor LIP5 and the endosomal sorting complex required for transport (ESCRT)-III protein CHMP5.
  6. Vps4 stimulatory element of the cofactor Vta1 contacts the ATPase Vps4 alpha7 and alpha9 subunits to stimulate ATP hydrolysis.
    Title: Vps4 stimulatory element of the cofactor Vta1 contacts the ATPase Vps4 α7 and α9 to stimulate ATP hydrolysis.
  7. the tandem MIT domain of LIP5 binds different types of ESCRT-III proteins, promoting assembly of active VPS4 enzymes on the polymeric ESCRT-III substrate.
    Title: Interactions of the human LIP5 regulatory protein with endosomal sorting complexes required for transport.
  8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
  9. LIP5 protein expression in a mouse tissue panel and various rodent and human tissues were studied.
    Title: The lysosomal trafficking regulator interacting protein-5 localizes mainly in epithelial cells.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
EBI GWAS Catalog
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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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

Homology

Clone Names

  • FLJ27228

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ESCRT III complex disassembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in late endosome to vacuole transport via multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in multivesicular body assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in multivesicular body sorting pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport 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 endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in multivesicular body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein VTA1 homolog
Names
LYST-interacting protein 5
SKD1-binding protein 1
Vps20-associated 1 homolog
dopamine-responsive gene 1 protein
homolog of mouse SKD1-binding protein 1
vesicle (multivesicular body) trafficking 1

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)

  1. NM_001286371.2 → NP_001273300.1  vacuolar protein sorting-associated protein VTA1 homolog isoform b

    See identical proteins and their annotated locations for NP_001273300.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF271994, AL033522, BM806661, DA299959
    Consensus CDS
    CCDS75531.1
    UniProtKB/TrEMBL
    A0A087WY55
    Related
    ENSP00000481525.1, ENST00000620996.4
    Conserved Domains (1) summary
    pfam04652
    Location:22 → 152
    Vta1; Vta1 like

  2. NM_001286372.2 → NP_001273301.1  vacuolar protein sorting-associated protein VTA1 homolog isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region that results in the use of an alternate translational start codon, and it lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AF271994, AK301376, AL033522
    Consensus CDS
    CCDS69214.1
    UniProtKB/TrEMBL
    Q5TGM0
    Related
    ENSP00000395767.2, ENST00000452973.6
    Conserved Domains (2) summary
    pfam04652
    Location:8 → 94
    Vta1; Vta1 like
    cl26000
    Location:177 → 215
    YciM; Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain [Cell wall/membrane/envelope biogenesis]

  3. NM_016485.5 → NP_057569.2  vacuolar protein sorting-associated protein VTA1 homolog isoform a

    See identical proteins and their annotated locations for NP_057569.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF271994, AL033522, BC022536
    Consensus CDS
    CCDS5197.1
    UniProtKB/Swiss-Prot
    B4DW55, E1P594, E7ETQ7, Q5TGM1, Q6IAE8, Q9H0R2, Q9H3K9, Q9NP79, Q9P0Q0
    Related
    ENSP00000356602.3, ENST00000367630.9
    Conserved Domains (1) summary
    pfam04652
    Location:22 → 152
    Vta1; Vta1 like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    142147263..142224685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    143339355..143416853
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NP79.1 GenPept UniProtKB/Swiss-Prot:Q9NP79

Gene LinkOut

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