Human Gene VAC14 (uc002ezl.3) Description and Page Index
  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 chr16:70,721,342-70,765,462 Size: 44,121 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr16:70,721,831-70,732,671 Size: 10,841 Coding Exon Count: 5 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:70,721,342-70,765,462)mRNA (may differ from genome)Protein (214 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCETreefamUniProtKBWikipedia

-  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 -26.6081-0.328 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
IPR026825 - VAC14
IPR021841 - VAC14_Fig4p_bd

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

ModBase Predicted Comparative 3D Structure on B3KSM8
FrontTopSide
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KSM8, B3KSM8_HUMAN, BC110072, NM_018052, NP_060522
UCSC ID: uc002ezl.3
RefSeq Accession: NM_018052
Protein: B3KSM8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC110072.1
exon count: 6CDS single in 3' UTR: no RNA size: 689
ORF size: 645CDS single in intron: no Alignment % ID: 99.85
txCdsPredict score: 1478.50frame shift in genome: no % Coverage: 94.05
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.