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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VMA21 Gene

protein-coding   GIFtS: 44
GCID: GC0XP150564

VMA21 Vacuolar H+-ATPase Homolog (S. Cerevisiae)

(Previous name: myopathy with excessive autophagy)
(Previous symbol: MEAX)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
VMA21 Vacuolar H+-ATPase Homolog (S. Cerevisiae)1 2
MEAX1 2 3 5
XMEA2 3 5
Myopathy With Excessive Autophagy Protein2 3
Myopathy With Excessive Autophagy1
Vacuolar ATPase Assembly Integral Membrane Protein VMA212

External Ids:    HGNC: 220821   Entrez Gene: 2035472   Ensembl: ENSG000001601317   OMIM: 3104405   UniProtKB: Q3ZAQ73   

Export aliases for VMA21 gene to outside databases

Previous GC identifers: GC0XP150315 GC0XP139424


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for VMA21 Gene:
This gene encodes a chaperone for assembly of lysosomal vacuolar ATPase.(provided by RefSeq, Jul 2012)

GeneCards Summary for VMA21 Gene: 
VMA21 (VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)) is a protein-coding gene. Diseases associated with VMA21 include x-linked myopathy with excessive autophagy, and vacuolar myopathy.

UniProtKB/Swiss-Prot: VMA21_HUMAN, Q3ZAQ7
Function: Required for the assembly of the V0 complex of the vacuolar ATPase (V-ATPase) in the endoplasmic
reticulum




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_167198.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VMA21 gene promoter:
         RFX1   Sox5   Tal-1   AML1a   HNF-3beta   Tal-1beta   E47   TGIF   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for VMA21

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VMA21


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq28   Ensembl cytogenetic band:  Xq28   HGNC cytogenetic band: Xq28

VMA21 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VMA21 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP150564:  view genomic region     (about GC identifiers)

Start:
150,564,987 bp from pter      End:
150,577,836 bp from pter
Size:
12,850 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VMA21_HUMAN, Q3ZAQ7 (See protein sequence)
Recommended Name: Vacuolar ATPase assembly integral membrane protein VMA21  
Size: 101 amino acids; 11354 Da
Subunit: Associates with the V0 complex of the vacuolar ATPase (V-ATPase)
Subcellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein. Endoplasmic reticulum-Golgi
intermediate compartment membrane; Multi-pass membrane protein. Cytoplasmic vesicle, COPII-coated vesicle
membrane; Multi-pass membrane protein
Caution: Protein characterization data are from PubMed:19379691. Due to a number of errors in the figure panels,
the article has been retracted but the authors stand by the validity of the main results and conclusions
(PubMed:20873370)
Secondary accessions: A6NKV7 B3KUA9
Alternative splicing: 2 isoforms:  Q3ZAQ7-1   Q3ZAQ7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VMA21: NX_Q3ZAQ7

Explore proteomics data for VMA21 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q3ZAQ7

  • VMA21 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    VMA21 Protein Expression
    REFSEQ proteins: NP_001017980.1  
    ENSEMBL proteins: 
     ENSP00000359386   ENSP00000333255  

    Human Recombinant Protein Products for VMA21: 
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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005764NOT lysosome IDA--
    GO:0005789endoplasmic reticulum membrane IDA--
    GO:0016021integral to membrane IEA--
    GO:0030127COPII vesicle coat IDA--
    GO:0033116endoplasmic reticulum-Golgi intermediate compartment membrane IEA--

    VMA21 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR019013 VMA21-like_domain

    Graphical View of Domain Structure for InterPro Entry Q3ZAQ7

    ProtoNet protein and cluster: Q3ZAQ7

    UniProtKB/Swiss-Prot: VMA21_HUMAN, Q3ZAQ7
    Similarity: Belongs to the VMA21 family


    VMA21 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VMA21_HUMAN, Q3ZAQ7
    Function: Required for the assembly of the V0 complex of the vacuolar ATPase (V-ATPase) in the endoplasmic
    reticulum

    Animal Models:

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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VMA21

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/46 Interacting proteins for VMA21 (Q3ZAQ73 ENSP000003332554) via UniProtKB, MINT, STRING, and/or I2D (see all 46)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATP6V1C2Q8NEY43I2D: score=1 
    HLA-BP304803I2D: score=1 
    IKBKEQ141643I2D: score=1 
    PRKAB1Q9Y4783I2D: score=1 
    VHLP403373I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0070072vacuolar proton-transporting V-type ATPase complex assembly IDA--

    VMA21 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VMA21

    Search CenterWatch for drugs/clinical trials and news about VMA21

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for VMA21 gene: 
    NM_001017980.3  

    Unigene Cluster for VMA21:

    VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)
    Hs.58633  [show with all ESTs]
    Unigene Representative Sequence: NM_001017980
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000477649 ENST00000370361 ENST00000330374(uc004feu.3)
    miRNA
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    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Additional mRNA sequence: 

    AF086459.1 AK025798.1 AK091301.1 AK096835.1 AL833596.1 BC103701.1 BC103702.1 BC105693.1 
    BC105694.1 BC110800.1 

    6 DOTS entries:

    DT.413693  DT.95254521  DT.75153488  DT.95248548  DT.97843272  DT.95322184 

    24/199 AceView cDNA sequences (see all 199):

    CD246074 BU192523 AA327823 BU629791 BG163331 AI354919 AF086459 BF060705 
    AW027246 AI536933 AI693110 AA283799 AI471645 BQ894089 CB122601 CB105326 
    AL697906 AA410488 BE467194 AI694134 CF529001 AA761068 AW071626 BQ010920 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VMA21 expression in normal human tissues (normalized intensities)      VMA21 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTATTGTTT
    VMA21 Expression
    About this image


    VMA21 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Kidney (Urinary System)
             Intercalated Cells Renal Collecting Duct System

    See VMA21 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VMA21

    SOURCE GeneReport for Unigene cluster: Hs.58633
        SABiosciences Custom PCR Arrays for VMA21
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VMA21

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for VMA21 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vma211 , 5 VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)1, 5 86.8(n)1
    96.04(a)1
      X (37.07 cM)5
    670481  NM_001081356.21  NP_001074825.11 
     718159245 
    chicken
    (Gallus gallus)
    Aves VMA211 VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) 75.58(n)
    82.18(a)
      422385  NM_001031127.1  NP_001026298.1 
    lizard
    (Anolis carolinensis)
    Reptilia VMA216
    Uncharacterized protein
    81(a)
    1 ↔ 1
    GL343310.1(586715-592908)
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch73-26o5.11 si:ch73-26o5.1 71.26(n)
    80.46(a)
      100307085  NM_001202424.1  NP_001189353.1 


    ENSEMBL Gene Tree for VMA21 (if available)
    TreeFam Gene Tree for VMA21 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VMA21 gene

    VMA21 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for VMA21
    PGOHUM00000233208


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/242 SNPs in VMA21 are shown (see all 242)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs112877611,2
    C--139426754(+) AGAAC-/TTTTTT 1 -- int1 trp31Minor allele frequency- T:0.00CSA 2
    rs1380371071,2
    C--139432243(+) AAAAG-/TTAAA 
            
    GTTAG
    1 -- ut310--------
    rs2020686391,2
    --139432245(+) AAGTT-/AAGTTA 1 -- ut310--------
    rs574123331,2
    C--139432246(+) AGTTA-/AATTA 
            
    GTTAC
    1 -- ut310--------
    rs1410821401,2
    --150430286(+) AGTCAC/GAATTC 1 -- us2k10--------
    rs1997192561,2
    --150430380(+) AACAG-/TCTTT 
            
    TCTTA
    1 -- us2k10--------
    rs1852241901,2
    --150430416(+) ATCATC/GATATA 1 -- us2k10--------
    rs736210321,2
    C,F--150430898(+) TAGGTC/TGGCTG 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs1764501,2
    C,F,H--150430926(+) CAGAGC/GTAGAT 1 -- us2k18Minor allele frequency- G:0.00WA NA CSA 17
    rs1811508381,2
    --150430942(+) TTGTAC/TCCCAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for VMA21 (150564987 - 150577836 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for VMA21: --

    Human Gene Mutation Database (HGMD): VMA21

    Locus Specific Mutation Databases (LSDB): VMA21
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 310440    OMIM disorders: --

    UniProtKB/Swiss-Prot: VMA21_HUMAN, Q3ZAQ7
  • X-linked myopathy with excessive autophagy (MEAX) [MIM:310440]: Childhood-onset disease characterized by
    progressive vacuolation and atrophy of skeletal muscle. It is inherited in recessive fashion, affecting boys and
    sparing carrier females. Onset is in childhood, and patients exhibit weakness of the proximal muscles of the
    lower extremities, progressing slowly to involve other skeletal muscle groups over time. Other organs including
    the heart and brain are clinically unaffected. Phenotype is due to an increase of lysosomal pH from 4.7 to 5.2,
    which reduces lysosomal degradative ability and blocks autophagy. This reduces cellular free amino acids, which
    upregulates the mTOR pathway and mTOR-dependent macroautophagy, resulting in proliferation of large and
    ineffective autolysosomes that engulf sections of cytoplasm, merge together, and vacuolate the cell. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 8 diseases for VMA21:    About MalaCards
    x-linked myopathy with excessive autophagy    vacuolar myopathy    glycogen storage disease ii    myopathy
    danon disease    glycogen storage disease    inclusion body myositis    myositis


    VMA21 for disorders           About GeneDecksing


    Export disorders for VMA21 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for VMA21 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with VMA21)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. VMA21 deficiency causes an autophagic myopathy by compromising V- ATPase activity and lysosomal acidification. (PubMed id 19379691)2, 3 Ramachandran N.... Minassian B.A. (2009)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Linkage of X-linked myopathy with excessive autophagy (XMEA) to Xq28. (PubMed id 10757644)1, 3 Villard L....Fontes M. (2000)
    4. Linkage studies in a new X-linked myopathy, suggesting exclusion of DMD locus and tentative assignment to distal Xq. (PubMed id 2892402)1, 3 Saviranta P....de la Chapelle A. (1988)
    5. VMA21 deficiency prevents vacuolar ATPase assembly and causes autophagic vacuolar myopathy. (PubMed id 23315026)1 Ramachandran N....Minassian B.A. (2013)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. Viral immune modulators perturb the human molecular ne twork by common and unique strategies. (PubMed id 22810585)1 Pichlmair A....Superti-Furga G. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Retraction notice to: VMA21 Deficiency causes an auto phagic myopathy by compromising V-ATPase activity and lysosomal acidification. (PubMed id 20873370)2 (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 203547 HGNC: 22082 AceView: LOC203547 Ensembl:ENSG00000160131 euGenes: HUgn203547
    ECgene: VMA21 H-InvDB: VMA21

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VMA21 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for VMA21 gene:
    Search GeneIP for patents involving VMA21

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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