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Aliases for VMP1 Gene

Aliases for VMP1 Gene

  • Vacuole Membrane Protein 1 2 3 5
  • Transmembrane Protein 49 2 3 4
  • TMEM49 3 4
  • Ectopic P-Granules Autophagy Protein 3 Homolog (C. Elegans) 2
  • Transport And Golgi Organization 5 Homolog (Drosophila) 2
  • Ectopic P-Granules Autophagy Protein 3 Homolog 3
  • Transport And Golgi Organization 5 Homolog 3
  • TANGO5 3
  • EPG3 3
  • TDC1 4

External Ids for VMP1 Gene

Previous HGNC Symbols for VMP1 Gene

  • TMEM49

Previous GeneCards Identifiers for VMP1 Gene

  • GC17P057536
  • GC17P060234
  • GC17P058126
  • GC17P058259
  • GC17P055139
  • GC17P057785

Summaries for VMP1 Gene

Entrez Gene Summary for VMP1 Gene

  • This gene encodes a transmembrane protein that plays a key regulatory role in the process of autophagy. The ectopic overexpression of the encoded protein in cultured cells triggers autophagy even under nutrient-rich conditions. This gene is overexpressed in pancreatitis affected acinar cells where the encoded protein mediates sequestration and degradation of potentially deleterious activated zymogen granules in a process termed, zymophagy. [provided by RefSeq, Jul 2016]

GeneCards Summary for VMP1 Gene

VMP1 (Vacuole Membrane Protein 1) is a Protein Coding gene. Diseases associated with VMP1 include Pancreatitis and Acute Pancreatitis. Among its related pathways are Autophagy Pathway and Autophagy - animal.

UniProtKB/Swiss-Prot for VMP1 Gene

  • Stress-induced protein that, when overexpressed, promotes formation of intracellular vacuoles followed by cell death. May be involved in the cytoplasmic vacuolization of acinar cells during the early stage of acute pancreatitis. Plays a role in the initial stages of the autophagic process through its interaction with BECN1 (By similarity). Involved in cell-cell adhesion. Plays an essential role in formation of cell junctions.

Gene Wiki entry for VMP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VMP1 Gene

Genomics for VMP1 Gene

Regulatory Elements for VMP1 Gene

Enhancers for VMP1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G060161 1.5 FANTOM5 Ensembl ENCODE 31.4 +455.4 455415 2.5 HDGF PKNOX1 ARNT ZNF493 ZSCAN4 KLF17 BMI1 NFXL1 RAD21 GLIS2 VMP1 USP32 CA4 LOC100996660 RPL32P32 HEATR6 PPM1D GC17M060146
GH17G060149 1.1 FANTOM5 Ensembl 35.8 +443.4 443394 2.3 CTCF SUZ12 MAX NFXL1 RBBP5 ETV6 HES1 EZH2 ZNF202 SP3 VMP1 USP32 CA4 RPL32P32 ENSG00000265415 PPM1D GC17M060146
GH17G059824 2.4 VISTA FANTOM5 Ensembl ENCODE dbSUPER 12.4 +135.7 135694 36.2 CREB3L1 MLX AGO1 ZFP64 DMAP1 YBX1 FEZF1 YY1 SLC30A9 ZNF143 RPS6KB1 NDUFB8P2 LOC101927755 PPM1D TUBD1 VMP1 PTRH2 APPBP2 SMG8 RNFT1
GH17G059781 2.3 VISTA FANTOM5 Ensembl ENCODE dbSUPER 7.4 +80.5 80483 11.9 CREB3L1 MLX ZFP64 YBX1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 LOC101927755 DHX40 SKA2 RPS6KB1 LOC100996660 MIR21 RNU6-450P PPM1D TRIM37 VMP1
GH17G059667 1.3 Ensembl ENCODE dbSUPER 11.8 -37.9 -37946 3.6 NFRKB SIN3A FEZF1 RAD21 SCRT2 ZNF143 RCOR1 FOS DEK ZNF263 VMP1 PTRH2 TUBD1 RPS6KB1 HEATR6 PRR11 GC17M059649 ENSG00000273702
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VMP1 on UCSC Golden Path with GeneCards custom track

Promoters for VMP1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000096402 98 2801 MLX CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC GLIS1

Genomic Location for VMP1 Gene

Chromosome:
17
Start:
59,707,192 bp from pter
End:
59,842,255 bp from pter
Size:
135,064 bases
Orientation:
Plus strand

Genomic View for VMP1 Gene

Genes around VMP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VMP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VMP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VMP1 Gene

Proteins for VMP1 Gene

  • Protein details for VMP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96GC9-VMP1_HUMAN
    Recommended name:
    Vacuole membrane protein 1
    Protein Accession:
    Q96GC9
    Secondary Accessions:
    • B4DVV9
    • Q9H0P4
    • Q9P089

    Protein attributes for VMP1 Gene

    Size:
    406 amino acids
    Molecular mass:
    46238 Da
    Quaternary structure:
    • Interacts with BECN1. Interacts with TJP1. Interacts with TP53INP2.

    Alternative splice isoforms for VMP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VMP1 Gene

Post-translational modifications for VMP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VMP1 Gene

Domains & Families for VMP1 Gene

Protein Domains for VMP1 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q96GC9

UniProtKB/Swiss-Prot:

VMP1_HUMAN :
  • Belongs to the VMP1 family.
Family:
  • Belongs to the VMP1 family.
genes like me logo Genes that share domains with VMP1: view

No data available for Gene Families for VMP1 Gene

Function for VMP1 Gene

Molecular function for VMP1 Gene

UniProtKB/Swiss-Prot Function:
Stress-induced protein that, when overexpressed, promotes formation of intracellular vacuoles followed by cell death. May be involved in the cytoplasmic vacuolization of acinar cells during the early stage of acute pancreatitis. Plays a role in the initial stages of the autophagic process through its interaction with BECN1 (By similarity). Involved in cell-cell adhesion. Plays an essential role in formation of cell junctions.

Gene Ontology (GO) - Molecular Function for VMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17724469
genes like me logo Genes that share ontologies with VMP1: view
genes like me logo Genes that share phenotypes with VMP1: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VMP1 Gene

Localization for VMP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VMP1 Gene

Endoplasmic reticulum-Golgi intermediate compartment membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein. Vacuole membrane; Multi-pass membrane protein. Endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VMP1 gene
Compartment Confidence
plasma membrane 5
nucleus 5
endoplasmic reticulum 5
extracellular 1

Gene Ontology (GO) - Cellular Components for VMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000407 pre-autophagosomal structure IBA --
GO:0000421 autophagosome membrane ISS,IEA --
GO:0005730 nucleolus IDA --
GO:0005773 vacuole IEA --
GO:0005774 vacuolar membrane IEA --
genes like me logo Genes that share ontologies with VMP1: view

Pathways & Interactions for VMP1 Gene

genes like me logo Genes that share pathways with VMP1: view

Pathways by source for VMP1 Gene

1 KEGG pathway for VMP1 Gene
2 R&D Systems pathways for VMP1 Gene

Gene Ontology (GO) - Biological Process for VMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IBA --
GO:0006914 autophagy IEA --
GO:0007029 endoplasmic reticulum organization IBA --
GO:0007030 Golgi organization IBA --
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with VMP1: view

No data available for SIGNOR curated interactions for VMP1 Gene

Drugs & Compounds for VMP1 Gene

No Compound Related Data Available

Transcripts for VMP1 Gene

Unigene Clusters for VMP1 Gene

Vacuole membrane protein 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VMP1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c
SP1: - - - -
SP2:
SP3: -
SP4:
SP5: -
SP6: -
SP7:

Relevant External Links for VMP1 Gene

GeneLoc Exon Structure for
VMP1
ECgene alternative splicing isoforms for
VMP1

Expression for VMP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VMP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VMP1 Gene

This gene is overexpressed in Whole Blood (x9.7).

Protein differential expression in normal tissues from HIPED for VMP1 Gene

This gene is overexpressed in Breast (12.5), Ovary (11.2), and Testis (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VMP1 Gene



Protein tissue co-expression partners for VMP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of VMP1 Gene:

VMP1

SOURCE GeneReport for Unigene cluster for VMP1 Gene:

Hs.444569

Evidence on tissue expression from TISSUES for VMP1 Gene

  • Blood(4.8)
  • Nervous system(4.7)
  • Kidney(4.6)
  • Spleen(4.4)
  • Liver(4)
  • Intestine(3.5)
  • Lung(2.9)
  • Heart(2.5)
  • Muscle(2.4)
  • Pancreas(2.4)
  • Lymph node(2.3)
  • Stomach(2.3)
  • Gall bladder(2.1)
genes like me logo Genes that share expression patterns with VMP1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VMP1 Gene

Orthologs for VMP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VMP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VMP1 34 35
  • 99.84 (n)
dog
(Canis familiaris)
Mammalia VMP1 34 35
  • 94.91 (n)
cow
(Bos Taurus)
Mammalia VMP1 34 35
  • 94.5 (n)
mouse
(Mus musculus)
Mammalia Vmp1 34 16 35
  • 91.05 (n)
rat
(Rattus norvegicus)
Mammalia Vmp1 34
  • 90.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 76 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 89 (a)
OneToMany
-- 35
  • 67 (a)
OneToMany
chicken
(Gallus gallus)
Aves VMP1 34 35
  • 80.54 (n)
lizard
(Anolis carolinensis)
Reptilia VMP1 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vmp1 34
  • 76.85 (n)
Str.11181 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.13697 34
zebrafish
(Danio rerio)
Actinopterygii vmp1 34 35
  • 69.88 (n)
Dr.982 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010304 34
  • 57.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta Tango5 35 34
  • 56.27 (n)
OneToMany
CG32087 35
  • 43 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea epg-3 35 34
  • 54.79 (n)
OneToOne
Y37D8A.22 36
  • 51 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G05360 34
  • 50.64 (n)
rice
(Oryza sativa)
Liliopsida Os01g0778700 34
  • 51.13 (n)
Os.14351 34
corn
(Zea mays)
Liliopsida Zm.17241 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6481 35
  • 58 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10369 34
Species where no ortholog for VMP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VMP1 Gene

ENSEMBL:
Gene Tree for VMP1 (if available)
TreeFam:
Gene Tree for VMP1 (if available)

Paralogs for VMP1 Gene

Pseudogenes.org Pseudogenes for VMP1 Gene

genes like me logo Genes that share paralogs with VMP1: view

No data available for Paralogs for VMP1 Gene

Variants for VMP1 Gene

Sequence variations from dbSNP and Humsavar for VMP1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs869025245 Uncertain significance 59,738,864(+) AGTTT(-/CT)TTTGT intron-variant, reference, frameshift-variant, utr-variant-5-prime
rs1000046922 -- 59,761,639(+) GTTGA(C/T)CACAA intron-variant
rs1000082737 -- 59,765,758(+) GAGGT(A/G)GAGGA intron-variant
rs1000098222 -- 59,718,321(+) CTCCC(-/A)AAGTA intron-variant
rs1000132367 -- 59,832,746(+) CCACC(A/C)CCGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VMP1 Gene

Variant ID Type Subtype PubMed ID
dgv1491n106 CNV deletion 24896259
dgv959e212 CNV loss 25503493
esv2483856 CNV deletion 19546169
esv2662935 CNV deletion 23128226
esv2716083 CNV deletion 23290073
esv3554612 CNV deletion 23714750
esv3640910 CNV loss 21293372
esv3640911 CNV loss 21293372
esv3640912 CNV loss 21293372
esv998658 CNV gain 20482838
nsv1109095 CNV deletion 24896259
nsv512497 CNV loss 21212237
nsv821151 CNV deletion 20802225
nsv828072 CNV gain+loss 20364138
nsv833501 CNV loss 17160897

Variation tolerance for VMP1 Gene

Residual Variation Intolerance Score: 20.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.74; 15.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VMP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VMP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VMP1 Gene

Disorders for VMP1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VMP1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pancreatitis
acute pancreatitis
  • acute necrotizing pancreatitis
- elite association - COSMIC cancer census association via MalaCards
Search VMP1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for VMP1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VMP1
genes like me logo Genes that share disorders with VMP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VMP1 Gene

Publications for VMP1 Gene

  1. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S. … Poustka A. (Genome Res. 2001) 2 3 4 64
  2. The TP53INP2 protein is required for autophagy in mammalian cells. (PMID: 19056683) Nowak J. … Iovanna J.L. (Mol. Biol. Cell 2009) 3 4 64
  3. Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells. (PMID: 17724469) Sauermann M. … Arlt D. (Oncogene 2008) 3 4 64
  4. Cloning and expression of the rat vacuole membrane protein 1 (VMP1), a new gene activated in pancreas with acute pancreatitis, which promotes vacuole formation. (PMID: 11785947) Dusetti N.J. … Iovanna J.L. (Biochem. Biophys. Res. Commun. 2002) 2 3 64
  5. TMEM49-related apoptosis and metastasis in ovarian cancer and regulated cell death. (PMID: 27023910) Zheng L. … Chen J. (Mol. Cell. Biochem. 2016) 3 64

Products for VMP1 Gene

Sources for VMP1 Gene

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