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

Summary

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

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_000010.11 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?

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S1269 (e-PCR), detects polymorphism
- UniSTS:36608

D10S1207 (e-PCR)
- UniSTS:34566

RH103741 (e-PCR)
- UniSTS:98066

WI-14968 (e-PCR)
- UniSTS:63264

SHGC-107221 (e-PCR)
- UniSTS:170289

RH123356 (e-PCR)
- UniSTS:135732

STS-T91988 (e-PCR)
- UniSTS:26946

D11S4048E (e-PCR)
- UniSTS:153927

G33022 (e-PCR)
- UniSTS:117599

RH121236 (e-PCR)
- UniSTS:138347

RH104345 (e-PCR)
- UniSTS:98670

VTI1A__5078 (e-PCR)
- UniSTS:466554

G29168 (e-PCR)
- UniSTS:62348

CHLC.GGAT3D06 (e-PCR)
- UniSTS:60571

SHGC-107210 (e-PCR)
- UniSTS:182176

L18447 (e-PCR)
- UniSTS:15536

SHGC-141998 (e-PCR)
- UniSTS:171184

SHGC-132763 (e-PCR)
- UniSTS:182194

RH1567 (e-PCR)
- UniSTS:51920

STS-H51777 (e-PCR)
- UniSTS:10723

D10S1445 (e-PCR)
- UniSTS:68068

SHGC-152845 (e-PCR)
- UniSTS:182249

RH65359 (e-PCR)
- UniSTS:60396

A009Z29 (e-PCR)
- UniSTS:37628

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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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_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
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
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
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
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
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
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
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

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
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
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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

112446988..112855368

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NR_015409.1: Suppressed sequence

Description

NR_015409.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.