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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 Yunis-Varon Syndrome. Among its related pathways are PI Metabolism and Metabolism. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for VAC14 Gene

Promoters and enhancers for VAC14 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I070800 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 555.6 +0.2 176 1.8 HDGF SMAD1 MLX ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 ZNF207 VAC14 ENSG00000262890 PDPR PDXDC2P-NPIPB14P DDX19A SF3B3 PDXDC2P NPIPB14P ZNF19 LOC400541
GH16I070744 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 15.3 +52.5 52485 7.4 HDGF CLOCK FOXA2 MLX ARID4B SIN3A DMAP1 YY1 ZNF766 CBX5 ENSG00000260156 VAC14 SNORD111 MTSS1L VAC14-AS1 FUK COG4 ZNF23
GH16I070779 Enhancer 1.2 ENCODE dbSUPER 12.5 +21.9 21892 1.4 PKNOX1 ARID4B SIN3A FEZF1 ZNF2 ETS1 ZNF121 ZNF213 ZNF302 FOS GC16M070786 TRG-GCC2-4 TRG-GCC3-1 ENSG00000279123 ZNF23 LOC400541 PDPR ENSG00000247324 ZNF19 LOC100506083
GH16I070680 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.2 +106.5 106464 29.2 HDGF PKNOX1 CLOCK SMAD1 FOXA2 ZFP64 ARID4B NEUROD1 SIN3A DMAP1 MTSS1L VAC14-AS1 CLEC18A NPIPB14P NOB1 VAC14 EXOSC6 NQO1 SMG1P7 MARVELD3
GH16I070986 Enhancer 1.2 Ensembl ENCODE 9.9 -186.3 -186296 1.1 PKNOX1 ZNF2 FOS KLF13 SP3 REST SMARCA4 GLIS1 NR2C1 NBN SF3B3 PDPR PDXDC2P-NPIPB14P DDX19A LOC400541 EXOSC6 HYDIN DDX19B NPIPB14P PDXDC2P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VAC14 on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for VAC14 Gene

Genomic Locations for VAC14 Gene
chr16:70,687,439-70,801,166
(GRCh38/hg38)
Size:
113,728 bases
Orientation:
Minus strand
chr16:70,721,342-70,835,064
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for VAC14 Gene

Proteins for VAC14 Gene

  • 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

Post-translational modifications for VAC14 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VAC14 Gene

Domains & Families for VAC14 Gene

Gene Families for VAC14 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for VAC14 Gene

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

Function for VAC14 Gene

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.

Phenotypes From GWAS Catalog for VAC14 Gene

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

Human Phenotype Ontology for VAC14 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

  • Addgene plasmids for VAC14

No data available for Enzyme Numbers (IUBMB) , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Vesicles (2)
See all subcellular structures

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

(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 2040
genes like me logo Genes that share compounds with VAC14: view

Transcripts for VAC14 Gene

Unigene Clusters for VAC14 Gene

Vac14 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

  • Addgene plasmids for VAC14

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

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

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 33 34
  • 99.49 (n)
dog
(Canis familiaris)
Mammalia VAC14 33 34
  • 91.6 (n)
cow
(Bos Taurus)
Mammalia VAC14 33 34
  • 89.86 (n)
mouse
(Mus musculus)
Mammalia Vac14 33 16 34
  • 89.5 (n)
rat
(Rattus norvegicus)
Mammalia Vac14 33
  • 89.09 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VAC14 34
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VAC14 34
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves VAC14 33 34
  • 81.81 (n)
lizard
(Anolis carolinensis)
Reptilia VAC14 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vac14 33
  • 73.28 (n)
zebrafish
(Danio rerio)
Actinopterygii vac14 33 34
  • 72.9 (n)
wufb68e05 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000770 33
  • 59.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5608 33 34
  • 55.84 (n)
worm
(Caenorhabditis elegans)
Secernentea K04G2.6 33
  • 47.71 (n)
vacl-14 34
  • 38 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER049W 33
  • 49.03 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAC14 33 34 36
  • 47.26 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E05193g 33
  • 46.7 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G01690 33
  • 52.07 (n)
rice
(Oryza sativa)
Liliopsida Os03g0223700 33
  • 53.5 (n)
Os.11686 33
bread mold
(Neurospora crassa)
Ascomycetes NCU02409 33
  • 51.04 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10719 34
  • 50 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC25H2.03 33
  • 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 Variation AA Info Type
rs1060499667 uncertain-significance, Yunis Varon syndrome 70,697,199(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs749094914 pathogenic, Striatonigral degeneration, childhood-onset, Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054] 70,698,729(-) C/A/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs762388639 pathogenic, Striatonigral degeneration, childhood-onset, Striatonigral degeneration, childhood-onset (SNDC) [MIM:617054] 70,762,915(-) C/A coding_sequence_variant, missense_variant
rs769608639 uncertain-significance, Yunis Varon syndrome 70,781,892(-) A/T coding_sequence_variant, stop_gained
rs879255555 pathogenic, Striatonigral degeneration, childhood-onset 70,744,422(-) C/T splice_donor_variant

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

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

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)

Additional Variant Information 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

(6) MalaCards diseases for VAC14 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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.

Additional Disease Information for VAC14

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Molecular and cellular biology 2004) 2 3 4 22 58
  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 (The Journal of biological chemistry 2007) 3 4 22 58
  3. Binding of Vac14 to neuronal nitric oxide synthase: Characterisation of a new internal PDZ-recognition motif. (PMID: 17161399) Lemaire JF … McPherson PS (FEBS letters 2006) 3 4 22 58
  4. Isolation of a cDNA clone, TRX encoding a human T-cell lymphotrophic virus type-I Tax1 binding protein. (PMID: 8611628) Mireskandari A … Brady JN (Biochimica et biophysica acta 1996) 3 4 22 58
  5. Biallelic Mutations of VAC14 in Pediatric-Onset Neurological Disease. (PMID: 27292112) Lenk GM … Ploski R (American journal of human genetics 2016) 3 4 58

Products for VAC14 Gene

Sources for VAC14 Gene

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