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VAC14 Gene(Protein Coding)

Vac14, PIKFYVE Complex Component

GCID:
GC16M070688
GIFtS:
55
Genes Participants
UDN Logo

Aliases for VAC14 Gene

Aliases for VAC14 Gene

  • Vac14, PIKFYVE Complex Component 2 3 5
  • TAX1BP2 3 4
  • TRX 3 4
  • Tax1 (Human T-Cell Leukemia Virus Type I) Binding Protein 2 2
  • Tax1 (Human T-Cell Leukemia Virus Type I) Binding Protein 3
  • Vac14 Homolog (S. Cerevisiae) 2
  • Tax1-Binding Protein 2 4
  • Protein VAC14 Homolog 3
  • ArPIKfyve 3

External Ids for VAC14 Gene

Previous HGNC Symbols for VAC14 Gene

  • TAX1BP2

Previous GeneCards Identifiers for VAC14 Gene

  • GC16M069280
  • GC16M070721
  • GC16M056552

Summaries for VAC14 Gene

Entrez Gene Summary for VAC14 Gene

  • This gene encodes a scaffold protein that is a component of the PIKfyve protein kinase complex. This complex is responsible for the synthesis of phosphatidylinositol 3,5-bisphosphate, an important component of cellular membranes, from phosphatidylinositol 3-phosphate. Mice lacking a functional copy of this gene exhibit severe neurodegeneration. Mutations in the human gene have been identified in patients with a childhood onset progressive neurological disorder characterized by impaired movement, dystonia, and striatal abnormalities. [provided by RefSeq, May 2017]

GeneCards Summary for VAC14 Gene

VAC14 (Vac14, PIKFYVE Complex Component) is a Protein Coding gene. Diseases associated with VAC14 include Striatonigral Degeneration, Childhood-Onset and Striatonigral Degeneration. Among its related pathways are HTLV-I infection and PI Metabolism. GO annotations related to this gene include binding and receptor activity.

UniProtKB/Swiss-Prot for VAC14 Gene

  • The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Acts as a positive activator of PIKfyve kinase activity. Also required to maintain normal levels of phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 5-phosphate (PtdIns(5)P). Plays a role in the biogenesis of endosome carrier vesicles (ECV) / multivesicular bodies (MVB) transport intermediates from early endosomes.

Gene Wiki entry for VAC14 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAC14 Gene

Genomics for VAC14 Gene

Products:

  1. Regulatory Element

Regulatory Elements for VAC14 Gene

Enhancers for VAC14 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
GH16G070744 2 FANTOM5 Ensembl ENCODE dbSUPER 15.3 +52.5 52486 7.4 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 FEZF1 ZNF2 LOC400541 PDPR VAC14 LOC100506083 ENSG00000247324 SNORD111 MTSS1L VAC14-AS1 FUK COG4
GH16G070779 1.3 ENCODE dbSUPER 12.5 +21.9 21892 1.4 PKNOX1 ATF1 ARID4B SIN3A FEZF1 ZNF2 ZNF121 ZNF302 FOS DEK LOC100506083 LOC400541 VAC14 VAC14-AS1 PDPR ENSG00000247324 TRG-GCC2-4 PIR32067
GH16G070767 1.3 ENCODE dbSUPER 11.1 +33.0 33011 1.4 HDGF ATF1 CREB3L1 MLX ARID4B SIN3A DMAP1 ZNF48 SLC30A9 ELK1 SF3B3 EXOSC6 PDPR VAC14 COG4 PDXDC2P-NPIPB14P PDXDC2P SNORD111 DDX19B AARS
GH16G070778 0.9 ENCODE dbSUPER 12.5 +22.9 22904 0.0 TBP TFAP4 POLR2A POLR3A SREBF2 SIN3A FOS ZBTB33 VAC14 VAC14-AS1 TRG-GCC3-1 GC16M070784 ENSG00000279122
GH16G070770 1.1 ENCODE dbSUPER 9.9 +30.1 30125 0.8 PKNOX1 RB1 ZNF48 RAD21 YY1 ZNF143 FOS CREM ZNF654 HCFC1 VAC14 AARS DDX19B ENSG00000279122 GC16M070784 TRG-GCC3-1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VAC14 on UCSC Golden Path with GeneCards custom track

Promoters for VAC14 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000087619 266 1401 HDGF MLX CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 KLF13

Transcription factor binding sites by QIAGEN in the VAC14 gene promoter:

Genomic Location for VAC14 Gene

Chromosome:
16
Start:
70,687,439 bp from pter
End:
70,801,166 bp from pter
Size:
113,728 bases
Orientation:
Minus strand

Genomic View for VAC14 Gene

Genes around VAC14 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAC14 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAC14 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VAC14 Gene

Proteins for VAC14 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for VAC14 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q08AM6-VAC14_HUMAN
    Recommended name:
    Protein VAC14 homolog
    Protein Accession:
    Q08AM6
    Secondary Accessions:
    • B3KPJ5
    • B3KSM8
    • Q13174
    • Q6IA12
    • Q7L4Y1
    • Q9BW96
    • Q9H6V6

    Protein attributes for VAC14 Gene

    Size:
    782 amino acids
    Molecular mass:
    87973 Da
    Quaternary structure:
    • Forms homooligomers. Component of the PI(3,5)P2 regulatory complex/PAS complex, at least composed of PIKFYVE, FIG4 and VAC14. VAC14 nucleates the assembly of the complex and serves as a scaffold. Interacts with NOS1. Interacts with HTLV-1 Tax.
    SequenceCaution:
    • Sequence=AAB03813.1; Type=Miscellaneous discrepancy; Note=Unknown C-terminal region.; Evidence={ECO:0000305}; Sequence=BAB15145.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VAC14 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VAC14 Gene

Protein Expression for VAC14 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VAC14 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VAC14 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VAC14 Gene

Domains & Families for VAC14 Gene

Protein Domains for VAC14 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for VAC14 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q08AM6

UniProtKB/Swiss-Prot:

VAC14_HUMAN :
  • The C-terminal domain (residues 523-782) mediates homomeric interactions and is necessary for the formation and maintenance of the PI(3,5)P2 regulatory complex.
  • Belongs to the VAC14 family.
Domain:
  • The C-terminal domain (residues 523-782) mediates homomeric interactions and is necessary for the formation and maintenance of the PI(3,5)P2 regulatory complex.
Family:
  • Belongs to the VAC14 family.
genes like me logo Genes that share domains with VAC14: view

No data available for Gene Families for VAC14 Gene

Function for VAC14 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for VAC14 Gene

UniProtKB/Swiss-Prot Function:
The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Acts as a positive activator of PIKfyve kinase activity. Also required to maintain normal levels of phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 5-phosphate (PtdIns(5)P). Plays a role in the biogenesis of endosome carrier vesicles (ECV) / multivesicular bodies (MVB) transport intermediates from early endosomes.

Gene Ontology (GO) - Molecular Function for VAC14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity NAS 8611628
GO:0005515 protein binding IPI 17161399
genes like me logo Genes that share ontologies with VAC14: view
genes like me logo Genes that share phenotypes with VAC14: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VAC14 Gene

Localization for VAC14 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAC14 Gene

Endosome membrane. Microsome membrane. Note=Mainly associated with membranes of the late endocytic pathway.

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 VAC14 gene
Compartment Confidence
endosome 5
golgi apparatus 4
endoplasmic reticulum 3
cytosol 3
lysosome 2

Gene Ontology (GO) - Cellular Components for VAC14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005768 endosome IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0010008 endosome membrane IEA,IDA 17556371
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with VAC14: view

Pathways & Interactions for VAC14 Gene

genes like me logo Genes that share pathways with VAC14: view

Gene Ontology (GO) - Biological Process for VAC14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0007165 signal transduction NAS 8611628
GO:0016032 viral process IEA --
GO:0043550 regulation of lipid kinase activity IEA --
genes like me logo Genes that share ontologies with VAC14: view

No data available for SIGNOR curated interactions for VAC14 Gene

Drugs & Compounds for VAC14 Gene

Products:

  1. Drug

(1) Drugs for VAC14 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Docetaxel Approved May 1996, Investigational Pharma Microtubulin disassembly inhibitor, Tubulin and VEGF inhibitor, Taxanes, Microtubule stabilizer 1967
genes like me logo Genes that share compounds with VAC14: view

Transcripts for VAC14 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for VAC14 Gene

(9) REFSEQ mRNAs :
(17) Additional mRNA sequences :
(258) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VAC14 Gene

Vac14 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VAC14 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^
SP1:
SP2:
SP3: - -
SP4: - - -
SP5:
SP6: -
SP7: -
SP8:

ExUns: 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for VAC14 Gene

GeneLoc Exon Structure for
VAC14
ECgene alternative splicing isoforms for
VAC14

Expression for VAC14 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VAC14 Gene

mRNA expression in normal human tissues for VAC14 Gene
mRNA expression by BioGPS for VAC14 GenemRNA expression by GTEx for VAC14 Gene

Protein differential expression in normal tissues from HIPED for VAC14 Gene

This gene is overexpressed in Bone (32.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VAC14 Gene



Protein tissue co-expression partners for VAC14 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VAC14 Gene:

VAC14

SOURCE GeneReport for Unigene cluster for VAC14 Gene:

Hs.445061

mRNA Expression by UniProt/SwissProt for VAC14 Gene:

Q08AM6-VAC14_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for VAC14 Gene

  • Nervous system(4.7)
  • Lung(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with VAC14: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VAC14 Gene

Orthologs for VAC14 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VAC14 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia VAC14 34 35
  • 99.49 (n)
dog
(Canis familiaris)
 Mammalia VAC14 34 35
  • 91.6 (n)
cow
(Bos Taurus)
 Mammalia VAC14 34 35
  • 89.86 (n)
mouse
(Mus musculus)
 Mammalia Vac14 34 16 35
  • 89.5 (n)
rat
(Rattus norvegicus)
 Mammalia Vac14 34
  • 89.09 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia VAC14 35
  • 87 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia VAC14 35
  • 86 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves VAC14 34 35
  • 81.81 (n)
lizard
(Anolis carolinensis)
 Reptilia VAC14 35
  • 85 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia vac14 34
  • 73.28 (n)
zebrafish
(Danio rerio)
 Actinopterygii vac14 34 35
  • 72.9 (n)
wufb68e05 34
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP000770 34
  • 59.28 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG5608 34 35
  • 55.84 (n)
worm
(Caenorhabditis elegans)
 Secernentea K04G2.6 34
  • 47.71 (n)
vacl-14 35
  • 38 (a)
 OneToOne
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_AER049W 34
  • 49.03 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes VAC14 34 35 37
  • 47.26 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0E05193g 34
  • 46.7 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT2G01690 34
  • 52.07 (n)
rice
(Oryza sativa)
 Liliopsida Os03g0223700 34
  • 53.5 (n)
Os.11686 34
bread mold
(Neurospora crassa)
 Ascomycetes NCU02409 34
  • 51.04 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.10719 35
  • 50 (a)
 OneToOne
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPBC25H2.03 34
  • 46.94 (n)
Species where no ortholog for VAC14 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 VAC14 Gene

ENSEMBL:
Gene Tree for VAC14 (if available)
TreeFam:
Gene Tree for VAC14 (if available)

Paralogs for VAC14 Gene

(1) SIMAP similar genes for VAC14 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for VAC14 Gene

genes like me logo Genes that share paralogs with VAC14: view

No data available for Paralogs for VAC14 Gene

Variants for VAC14 Gene

Sequence variations from dbSNP and Humsavar for VAC14 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs762388639 Pathogenic, Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054] 70,762,915(+) AGAGC(A/C)ACTTG intron-variant, reference, missense
VAR_077032 Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054]
VAR_077033 Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054]
rs749094914 Pathogenic 70,698,729(+) CGAGG(A/C/T)GAACT reference, missense
rs879255555 Pathogenic 70,744,422(-) CTCTG(A/G)TAAGT splice-donor-variant

Structural Variations from Database of Genomic Variants (DGV) for VAC14 Gene

Variant ID Type Subtype PubMed ID
esv2758653 CNV gain 17122850
esv3892881 CNV gain 25118596
nsv1059226 CNV gain 25217958
nsv471094 CNV loss 18288195
nsv475686 CNV novel sequence insertion 20440878
nsv517391 CNV loss 19592680
nsv572945 CNV gain 21841781
nsv572946 CNV loss 21841781
nsv572947 CNV loss 21841781
nsv572948 CNV loss 21841781
nsv7285 OTHER inversion 18451855

Variation tolerance for VAC14 Gene

Residual Variation Intolerance Score: 6.26% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.21; 39.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VAC14 Gene

Human Gene Mutation Database (HGMD)
VAC14
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VAC14

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAC14 Gene

Disorders for VAC14 Gene

MalaCards: The human disease database

(5) MalaCards diseases for VAC14 Gene - From: ClinVar, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
striatonigral degeneration, childhood-onset
  • lenk-ploski syndrome
striatonigral degeneration
yunis-varon syndrome
  • cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia
charcot-marie-tooth disease, type 4j
  • charcot-marie-tooth disease type 4j
congenital hydrocephalus
- elite association - COSMIC cancer census association via MalaCards
Search VAC14 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VAC14_HUMAN
  • Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054]: An autosomal recessive neurological disorder characterized by sudden childhood onset of developmental regression. Affected children develop impaired movements with dystonia, progressively become non-ambulatory and non-verbal, and exhibit striatal abnormalities on MRI. {ECO:0000269 PubMed:27292112}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VAC14

Genetic Association Database (GAD)
VAC14
Human Genome Epidemiology (HuGE) Navigator
VAC14
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VAC14
genes like me logo Genes that share disorders with VAC14: view

No data available for Genatlas for VAC14 Gene

Publications for VAC14 Gene

  1. A mammalian ortholog of Saccharomyces cerevisiae Vac14 that associates with and up-regulates PIKfyve phosphoinositide 5-kinase activity. (PMID: 15542851) Sbrissa D. … Shisheva A. (Mol. Cell. Biol. 2004) 2 3 4 22 64
  2. Core protein machinery for mammalian phosphatidylinositol 3,5- bisphosphate synthesis and turnover that regulates the progression of endosomal transport. Novel Sac phosphatase joins the ArPIKfyve-PIKfyve complex. (PMID: 17556371) Sbrissa D. … Shisheva A. (J. Biol. Chem. 2007) 3 4 22 64
  3. Binding of Vac14 to neuronal nitric oxide synthase: Characterisation of a new internal PDZ-recognition motif. (PMID: 17161399) Lemaire J.F. … McPherson P.S. (FEBS Lett. 2006) 3 4 22 64
  4. Isolation of a cDNA clone, TRX encoding a human T-cell lymphotrophic virus type-I Tax1 binding protein. (PMID: 8611628) Mireskandari A. … Brady J.N. (Biochim. Biophys. Acta 1996) 3 4 22 64
  5. Biallelic mutations of VAC14 in pediatric-onset neurological disease. (PMID: 27292112) Lenk G.M. … Ploski R. (Am. J. Hum. Genet. 2016) 3 4 64

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