Human Gene VAC14 (uc002ezm.3)
  Description: Homo sapiens Vac14 homolog (S. cerevisiae) (VAC14), mRNA.
RefSeq Summary (NM_018052): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:70,721,342-70,835,061 Size: 113,720 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr16:70,721,831-70,834,803 Size: 112,973 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:70,721,342-70,835,061)mRNA (may differ from genome)Protein (782 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VAC14_HUMAN
DESCRIPTION: RecName: Full=Protein VAC14 homolog; AltName: Full=Tax1-binding protein 2;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Endosome membrane. Microsome membrane (By similarity). Note=Mainly associated with membranes of the late endocytic pathway.
TISSUE SPECIFICITY: Ubiquitously expressed.
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.
SIMILARITY: Belongs to the VAC14 family.
SIMILARITY: Contains 6 HEAT repeats.
SEQUENCE CAUTION: Sequence=AAB03813.1; Type=Miscellaneous discrepancy; Note=Unknown C-terminal region; Sequence=BAB15145.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VAC14
CDC HuGE Published Literature: VAC14
Positive Disease Associations: Body Height
Related Studies:
  1. Body Height
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: VAC14
Diseases sorted by gene-association score: striatonigral degeneration, childhood-onset* (1230), striatonigral degeneration (17), yunis-varon syndrome (13), charcot-marie-tooth disease, type 4j (12), congenital hydrocephalus (7), dystonia (6), neuropathy, congenital hypomyelinating (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.58 RPKM in Spleen
Total median expression: 307.54 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -143.30258-0.555 Picture PostScript Text
3' UTR -190.51489-0.390 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR026825 - VAC14
IPR021841 - VAC14_Fig4p_bd

Pfam Domains:
PF11916 - Vacuolar protein 14 C-terminal Fig4p binding
PF12755 - Vacuolar 14 Fab1-binding region

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q08AM6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0006661 phosphatidylinositol biosynthetic process
GO:0007165 signal transduction
GO:0016032 viral process

Cellular Component:
GO:0000139 Golgi membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0031090 organelle membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0070772 PAS complex


-  Descriptions from all associated GenBank mRNAs
  BC000536 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3162364), partial cds.
AK025479 - Homo sapiens cDNA: FLJ21826 fis, clone HEP01350.
BC007214 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:2819370), partial cds.
BC110852 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:6501756).
AK001167 - Homo sapiens cDNA FLJ10305 fis, clone NT2RM2000239.
AK307766 - Homo sapiens cDNA, FLJ97714.
AK056433 - Homo sapiens cDNA FLJ31871 fis, clone NT2RP7002243, highly similar to Homo sapiens Vac14 homolog (VAC14), mRNA.
BC125108 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone MGC:149815 IMAGE:40118772), complete cds.
BC125109 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone MGC:149816 IMAGE:40118777), complete cds.
AK297564 - Homo sapiens cDNA FLJ53136 complete cds, highly similar to Homo sapiens Vac14 homolog (VAC14), mRNA.
KJ902860 - Synthetic construct Homo sapiens clone ccsbBroadEn_12254 VAC14 gene, encodes complete protein.
KJ894238 - Synthetic construct Homo sapiens clone ccsbBroadEn_03632 VAC14 gene, encodes complete protein.
CR457343 - Homo sapiens full open reading frame cDNA clone RZPDo834A0521D for gene FLJ10305, hypothetical protein FLJ10305; complete cds, incl. stopcodon.
BC110072 - Homo sapiens Vac14 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:40015379).
AL137396 - Homo sapiens mRNA; cDNA DKFZp434J032 (from clone DKFZp434J032).
AK090627 - Homo sapiens cDNA FLJ33308 fis, clone BNGH42004291.
AX746543 - Sequence 68 from Patent EP1308459.
AK128439 - Homo sapiens cDNA FLJ46582 fis, clone THYMU3043327.
AK093941 - Homo sapiens cDNA FLJ36622 fis, clone TRACH2016690, highly similar to Homo sapiens Vac14 homolog (VAC14), mRNA.
JD248194 - Sequence 229218 from Patent EP1572962.
JD414108 - Sequence 395132 from Patent EP1572962.
JD328999 - Sequence 310023 from Patent EP1572962.
JD260865 - Sequence 241889 from Patent EP1572962.
JD156726 - Sequence 137750 from Patent EP1572962.
JD138735 - Sequence 119759 from Patent EP1572962.
AK310466 - Homo sapiens cDNA, FLJ17508.
U25801 - Human Tax1 binding protein mRNA, partial cds.
JD305720 - Sequence 286744 from Patent EP1572962.
JD369395 - Sequence 350419 from Patent EP1572962.
JD355111 - Sequence 336135 from Patent EP1572962.
JD158381 - Sequence 139405 from Patent EP1572962.
JD408972 - Sequence 389996 from Patent EP1572962.
JD486086 - Sequence 467110 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q08AM6 (Reactome details) participates in the following event(s):

R-HSA-1676174 PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the early endosome membrane
R-HSA-1676168 PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the early endosome membrane
R-NUL-1675886 PI3P is phosphorylated to PI(3,5)P2 by Pikfyve at the early endosome membrane
R-NUL-1675925 PI3P is phosphorylated to PI(3,5)P2 by Pikfyve at the late endosome membrane
R-NUL-1676051 PI is phosphorylated to PI5P by Pikfyve at the late endosome membrane
R-HSA-1675866 PI is phosphorylated to PI5P by PIKFYVE at the late endosome membrane
R-HSA-1676020 PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the late endosome membrane
R-HSA-1675910 PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the late endosome membrane
R-NUL-1675982 PI3P is phosphorylated to PI(3,5)P2 by Pikfyve at the Golgi membrane
R-HSA-1676005 PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the Golgi membrane
R-HSA-1675921 PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the Golgi membrane
R-HSA-1660516 Synthesis of PIPs at the early endosome membrane
R-HSA-1660517 Synthesis of PIPs at the late endosome membrane
R-HSA-1660514 Synthesis of PIPs at the Golgi membrane
R-HSA-1483255 PI Metabolism
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B3KPJ5, NM_018052, NP_060522, Q08AM6, Q13174, Q6IA12, Q7L4Y1, Q9BW96, Q9H6V6, TAX1BP2, TRX, VAC14_HUMAN
UCSC ID: uc002ezm.3
RefSeq Accession: NM_018052
Protein: Q08AM6 (aka VAC14_HUMAN)
CCDS: CCDS10896.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018052.3
exon count: 19CDS single in 3' UTR: no RNA size: 3107
ORF size: 2349CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4842.50frame shift in genome: no % Coverage: 99.65
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.