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    VTI1A vesicle transport through interaction with t-SNAREs 1A [ Homo sapiens (human) ]

    Gene ID: 143187, updated on 29-Oct-2024

    Summary

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    Official Symbol
    VTI1Aprovided by HGNC
    Official Full Name
    vesicle transport through interaction with t-SNAREs 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:17792
    See related
    Ensembl:ENSG00000151532 MIM:614316; AllianceGenome:HGNC:17792
    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
    MMDS3; MVti1; VTI1RP2; Vti1-rp2
    Summary
    The protein encoded by this gene is a member of the family of soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptors (SNAREs) that function in intracellular trafficking. This family member is involved in vesicular transport between endosomes and the trans-Golgi network. It is a vesicle-associated SNARE (v-SNARE) that interacts with target membrane SNAREs (t-SNAREs). Polymorphisms in this gene have been associated with binocular function, and also with susceptibility to colorectal and lung cancers. A recurrent rearrangement has been found between this gene and the transcription factor 7-like 2 (TCF7L2) gene in colorectal cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in brain (RPKM 1.6), bone marrow (RPKM 1.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VTI1A in Genome Data Viewer
    Location:
    10q25.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (112446988..112855368)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (113337655..113746195)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (114206746..114615127)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2832 Neighboring gene guanylate cyclase 2G, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:114135606-114136106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:114136107-114136607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2833 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4066 Neighboring gene acyl-CoA synthetase long chain family member 5 Neighboring gene Sharpr-MPRA regulatory region 13267 Neighboring gene zinc finger DHHC-type palmitoyltransferase 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4067 Neighboring gene uncharacterized LOC124902503 Neighboring gene microRNA 4295 Neighboring gene Sharpr-MPRA regulatory region 921 Neighboring gene Sharpr-MPRA regulatory region 3692 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:114492107-114492608 Neighboring gene Sharpr-MPRA regulatory region 7283 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:114563987-114564486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:114570610-114571310 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:114571311-114572009 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:114572010-114572709 Neighboring gene uncharacterized LOC103344931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4068 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:114658623-114659435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:114661023-114661523 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:114672820-114673320 Neighboring gene MPRA-validated peak1093 silencer Neighboring gene long intergenic non-protein coding RNA 2935 Neighboring gene uncharacterized LOC124902502 Neighboring gene transcription factor 7 like 2

    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 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. Monocytes and macrophages as biomarkers for the diagnosis of megalencephalic leukoencephalopathy with subcortical cysts. Petrini S, et al. Mol Cell Neurosci, 2013 Sep. PMID 23851226
    2. Trans-ethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A. Wang H, et al. Nat Commun, 2014 Aug 8. PMID 25105248, Free PMC Article
    3. Single nucleotide polymorphisms in VTI1A gene contribute to the susceptibility of Chinese population to non-small cell lung cancer. Su WM, et al. Int J Biol Markers, 2015 Jul 22. PMID 25744365
    4. A population study of binocular function. Bosten JM, et al. Vision Res, 2015 May. PMID 25771401
    5. Genome-wide association study identifies multiple susceptibility loci for glioma. Kinnersley B, et al. Nat Commun, 2015 Oct 1. PMID 26424050, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57.
      Title: Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57.
    2. Transfection of LS174T cells showed that the VTI1A promoter is highly active compared to the TCF7L2 promoter, and that CDX2 activates transcription of VTI1A.
      Title: The VTI1A-TCF4 colon cancer fusion protein is a dominant negative regulator of Wnt signaling and is transcriptionally regulated by intestinal homeodomain factor CDX2.
    3. Novel variants of VTI1A-TCF7L2 fusion transcripts, including a novel fusion partner gene, RP11-57H14.3, was identified and demonstrated detectable levels in a large fraction of colorectal cancer samples.[RP11-57H14.3]
      Title: High frequency of fusion transcripts involving TCF7L2 in colorectal cancer: novel fusion partner and splice variants.
    4. our results indicate that genetic variants in VTI1A may modify individual susceptibility to non-GBM of glioma in the Han Chinese population and support the role of the VTI1A genes in the occurrence of glioma.
      Title: Additional evidence supports association of common genetic variants in VTI1A and ETFA with increased risk of glioma susceptibility.
    5. The AA genotype of VTI1A (rs7086803) polymorphism had an increased risk of developing NSCLC compared with the GG genotype. Smoking lung cancer patients with the AA genotype of VTI1A gene (rs7086803) had a poor survival rate.
      Title: Single nucleotide polymorphisms in VTI1A gene contribute to the susceptibility of Chinese population to non-small cell lung cancer.
    6. analysis of a new susceptibility locus for colorectal cancer in VTI1A [meta-analysis]
      Title: Trans-ethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A.
    7. Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure.
      Title: VAMP4 is required to maintain the ribbon structure of the Golgi apparatus.
    8. We found a colorectal carcinoma cell line harboring the fusion gene to be dependent on VTI1A-TCF7L2 for anchorage-independent growth using RNA interference-mediated knockdown.
      Title: Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. The present results suggest that a SNARE complex containing VAMP7 and Vti1a defines a novel traffic pathway to the cell surface in both neuronal and non-neuronal cells.
      Title: A VAMP7/Vti1a SNARE complex distinguishes a non-conventional traffic route to the cell surface used by KChIP1 and Kv4 potassium channels.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    A genome-wide association study of brain lesion distribution in multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia.
    EBI GWAS Catalog
    Trans-ethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with vesicle transport through interaction with t-SNAREs homolog 1A (VTI1A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Potential readthrough

    Included gene: TCF7L2

    Homology

    Clone Names

    • FLJ23106, FLJ23891, FLJ44519, MGC138209

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNAP receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNAP receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intra-Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in macroautophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic vesicle to endosome fusion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle fusion with Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle fusion with Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in voluntary musculoskeletal movement IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in ER to Golgi transport vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SNARE complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of SNARE complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in clathrin-coated vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuron projection terminus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synaptic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    vesicle transport through interaction with t-SNAREs homolog 1A
    Names
    SNARE Vti1a-beta protein
    vesicle transport v-SNARE protein Vti1-like 2

    NCBI Reference Sequences (RefSeq)

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    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_001318203.2 → NP_001305132.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AI693064, AK095476, AL158212, BC017052, BQ447044
      Consensus CDS
      CCDS91346.1
      UniProtKB/TrEMBL
      A0A994J5N6
      Related
      ENSP00000516199.1, ENST00000705995.1
      Conserved Domains (2) summary
      cd15891
      Location:129 → 190
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 90
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    2. NM_001318205.2 → NP_001305134.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, and uses an alternate splice site that results in an early stop codon and a difference in the 3' UTR, compared to variant 1. The encoded isoform (c) is shorter at the C-terminus, compared to isoform a.
      Source sequence(s)
      AK095476, AK303646, AL158212, BC017052, BI010424, BQ447044
      UniProtKB/Swiss-Prot
      Q96AJ9
      Conserved Domains (2) summary
      cd15891
      Location:122 → 183
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 89
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    3. NM_001365710.2 → NP_001352639.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform d

      Status: REVIEWED

      Source sequence(s)
      AL139120, BC017052, BG492365
      Consensus CDS
      CCDS91347.1
      Related
      ENSP00000395017.1, ENST00000432306.5
      Conserved Domains (2) summary
      cd15891
      Location:122 → 183
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 90
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    4. NM_001365711.1 → NP_001352640.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform e

      Status: REVIEWED

      Source sequence(s)
      AC022018, AL139120, AL158212
      Conserved Domains (2) summary
      cd15891
      Location:129 → 190
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 89
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    5. NM_001365712.1 → NP_001352641.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform f

      Status: REVIEWED

      Source sequence(s)
      AC022018, AL139120, AL158212
      Conserved Domains (2) summary
      cd15891
      Location:129 → 190
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 89
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    6. NM_001365713.1 → NP_001352642.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform f

      Status: REVIEWED

      Source sequence(s)
      AC022018, AL139120, AL158212
      Conserved Domains (2) summary
      cd15891
      Location:129 → 190
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 89
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    7. NM_001365714.1 → NP_001352643.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform g

      Status: REVIEWED

      Source sequence(s)
      AC022018, AL133323, AL139120
      Conserved Domains (2) summary
      cd15891
      Location:122 → 183
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 89
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    8. NM_145206.4 → NP_660207.2  vesicle transport through interaction with t-SNAREs homolog 1A isoform b

      See identical proteins and their annotated locations for NP_660207.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AK095476, AK303646, AL158212, BC017052, BQ447044
      Consensus CDS
      CCDS7575.2
      UniProtKB/Swiss-Prot
      A2A307, B4E137, Q5W0D7, Q96AJ9
      Related
      ENSP00000376792.2, ENST00000393077.3
      Conserved Domains (2) summary
      cd15891
      Location:122 → 183
      SNARE_Vti1a; SNARE motif of Vti1b-like
      pfam05008
      Location:12 → 90
      V-SNARE; Vesicle transport v-SNARE protein N-terminus

    RNA

    1. NR_134521.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) shares the 5' terminal exon but lacks the remaining exons found in variant 1, and instead contains alternate 3' exon structure. 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)
      AC022018, AK095476, BC064614

    2. NR_134522.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) shares the 5' terminal exon but lacks the remaining exons found in variant 1, and instead contains alternate 3' exon structure. 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)
      AC022018, AK095476, BC064614, DB105695
      Related
      ENST00000483122.1

    3. NR_134523.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022018, AK095476, BC064614, DA324398, DA349859

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      112446988..112855368
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      113337655..113746195
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_015409.1: Suppressed sequence

      Description
      NR_015409.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96AJ9.2 GenPept UniProtKB/Swiss-Prot:Q96AJ9

    Gene LinkOut

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