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

Gene ID: 143187, updated on 7-Apr-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
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Genomic context

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Location:
10q25.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (112446988..112855368)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (113337655..113746195)
105.20220307 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
  • 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. Genome-wide association study identifies multiple susceptibility loci for glioma. Kinnersley B, et al. Nat Commun, 2015 Oct 1. PMID 26424050, Free PMC Article
  2. A population study of binocular function. Bosten JM, et al. Vision Res, 2015 May. PMID 25771401
  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. 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
  5. Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer. Shanmugam V, et al. BMC Med Genomics, 2014 Jun 18. PMID 24943349, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene variants associated with ischemic stroke: the cardiovascular health study.
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
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 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_2023_10

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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