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    VAC14 VAC14 component of PIKFYVE complex [ Homo sapiens (human) ]

    Gene ID: 55697, updated on 6-Jun-2024

    Summary

    Official Symbol
    VAC14provided by HGNC
    Official Full Name
    VAC14 component of PIKFYVE complexprovided by HGNC
    Primary source
    HGNC:HGNC:25507
    See related
    Ensembl:ENSG00000103043 MIM:604632; AllianceGenome:HGNC:25507
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TRX; TAX1BP2; ArPIKfyve
    Summary
    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]
    Expression
    Ubiquitous expression in lymph node (RPKM 2.8), thyroid (RPKM 2.5) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See VAC14 in Genome Data Viewer
    Location:
    16q22.1-q22.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (70687439..70801158, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (76498610..76612330, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70721342..70835061, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70613305-70613810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70613811-70614316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70655383-70655930 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:70655931-70656478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70683694-70684194 Neighboring gene interleukin 34 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70721484-70721990 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70726089-70726916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70726917-70727742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70727743-70728568 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70728569-70729394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70729395-70730221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70731048-70731874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70731875-70732699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70736831-70737596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70737597-70738364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70738365-70739130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70739131-70739896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70748263-70748982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70750423-70751140 Neighboring gene Sharpr-MPRA regulatory region 12359 Neighboring gene MTSS I-BAR domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70771856-70772386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70774210-70775017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70779970-70780470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70780471-70780971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70781216-70781850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70784627-70785306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70788515-70789155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70789156-70789796 Neighboring gene VAC14 antisense RNA 1 Neighboring gene tRNA-Gly (anticodon GCC) 3-1 Neighboring gene tRNA-Gly (anticodon GCC) 2-4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70834747-70835369 Neighboring gene tRNA-Gly (anticodon GCC) 2-5 Neighboring gene RNA, U6atac small nuclear 25, pseudogene Neighboring gene Sharpr-MPRA regulatory region 4373 Neighboring gene HYDIN axonemal central pair apparatus protein Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:71020999-71022198 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:71042849-71044048 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:71061796-71062512 Neighboring gene Sharpr-MPRA regulatory region 1178 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:71113179-71114378 Neighboring gene Sharpr-MPRA regulatory region 1449 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:71195224-71195424 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:71289688-71289924 Neighboring gene uncharacterized LOC102723786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7676 Neighboring gene cap methyltransferase 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10305, FLJ36622, FLJ46582, MGC149815, MGC149816

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in phosphatidylinositol biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of postsynaptic neurotransmitter receptor internalization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    part_of PAS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in early endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in presynaptic endosome IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    protein VAC14 homolog
    Names
    Vac14, PIKFYVE complex component

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_054902.1 RefSeqGene

      Range
      5012..118731
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001351157.2NP_001338086.1  protein VAC14 homolog isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC020763, AC027281, AK307766, AL137396
      Conserved Domains (1) summary
      pfam11916
      Location:308483
      Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
    2. NM_018052.5NP_060522.3  protein VAC14 homolog isoform 1

      See identical proteins and their annotated locations for NP_060522.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK056433, AL137396
      Consensus CDS
      CCDS10896.1
      UniProtKB/Swiss-Prot
      B3KPJ5, B3KSM8, Q08AM6, Q13174, Q6IA12, Q7L4Y1, Q9BW96, Q9H6V6
      UniProtKB/TrEMBL
      B4DMP4
      Related
      ENSP00000261776.5, ENST00000261776.10
      Conserved Domains (3) summary
      sd00044
      Location:94122
      HEAT; HEAT repeat [structural motif]
      pfam11916
      Location:542717
      Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
      pfam12755
      Location:67163
      Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      70687439..70801158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005256038.5XP_005256095.1  protein VAC14 homolog isoform X1

      UniProtKB/TrEMBL
      B4DMP4
      Conserved Domains (3) summary
      pfam11916
      Location:543717
      Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
      pfam12755
      Location:67163
      Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
      sd00044
      Location:94122
      HEAT; HEAT repeat [structural motif]
    2. XM_011523225.4XP_011521527.1  protein VAC14 homolog isoform X2

      Conserved Domains (2) summary
      pfam12755
      Location:67163
      Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
      sd00044
      Location:5378
      HEAT; HEAT repeat [structural motif]
    3. XM_047434360.1XP_047290316.1  protein VAC14 homolog isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      76498610..76612330 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313459.1XP_054169434.1  protein VAC14 homolog isoform X1

      UniProtKB/TrEMBL
      B4DMP4
    2. XM_054313460.1XP_054169435.1  protein VAC14 homolog isoform X2

    3. XM_054313461.1XP_054169436.1  protein VAC14 homolog isoform X3