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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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    See VTA1 in Genome Data Viewer
    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

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

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