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

VMA21 Gene

protein-coding   GIFtS: 45
GCID: GC0XP150564

VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)

(Previous name: myopathy with excessive autophagy )
(Previous symbol: MEAX)
 Explore 6 diseases affiliated with
VMA21 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for VMA21    

Aliases
for VMA21 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
VMA21 Vacuolar H+-ATPase Homolog (S. Cerevisiae)1 2
MEAX1 2 3 5
XMEA1 2 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


Summaries
for VMA21 gene

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

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




Genomic Views
for VMA21 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  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

Proteins
for VMA21 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q3ZAQ7

    • VMA21 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001017980.1  
    ENSEMBL proteins: 
     ENSP00000359386   ENSP00000333255  

    Human Recombinant Protein Products: 
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    Uscn Proteins for VMA21

    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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    Uscn ELISAs and CLIAs for VMA21

    Protein Domains /
    Families
    for VMA21 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    VMA21 for domains           About GeneDecksing

    1 InterPro domain/family:
     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


    Function
    for VMA21 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

    miRNA
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    8/41 QIAGEN miScript miRNA Assays for microRNAs that regulate VMA21 (see all 41):
    hsa-miR-579 hsa-miR-15a hsa-miR-4267 hsa-miR-570 hsa-miR-424 hsa-miR-489 hsa-miR-155 hsa-miR-3148
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    Gene Editing
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    Clone
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    In Situ Assay
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    Pathways & Interactions
    for VMA21 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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



    Drugs & Compounds
    for VMA21 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 

    Transcripts
    for VMA21 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, 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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    8/41 QIAGEN miScript miRNA Assays for microRNAs that regulate VMA21 (see all 41):
    hsa-miR-579 hsa-miR-15a hsa-miR-4267 hsa-miR-570 hsa-miR-424 hsa-miR-489 hsa-miR-155 hsa-miR-3148
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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

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

    7 DOTS entries:

    DT.413693  DT.95159029  DT.95254521  DT.75153488  DT.95248548  DT.97843272  DT.95322184 

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

    BQ640502 AA410488 CD723834 AI422613 AI275886 AL697906 BU629791 CB128290 
    BQ894089 AA976771 AI354919 AI536933 BQ010920 AA327823 AI694134 BU195091 
    AA828340 AA658062 BM817689 CD246074 BF062174 AI970675 AI632057 BE857159 

    GeneLoc Exon Structure


    Expression
    for VMA21 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTTATTGTTT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    VMA21 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    KidneyRenal Collecting Duct SystemIntercalated CellsKidney
    Extraembryonic MesodermExtraembryonic Capillary PlexusExtraembryonic AngioblastsEndothelium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

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

    SOURCE GeneReport for Unigene cluster: Hs.58633
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VMA21

    Orthologs
    for VMA21 gene

    (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 animals.

    Orthologs for VMA21 gene from 5/12 species (see all 12)    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
    		 --
    		 82(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 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG59696
    		 --
    		 28(a)
    		 1 ↔ 1
    		 3L(20466883-20467891)


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

    Paralogs
    for VMA21 gene

    (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


    Genomic Variants
    for VMA21 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/197 NCBI SNPs in VMA21 are shown (see all 197)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr X posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs736210321,2
    		C,--139422895(+) TAGGTC/TGGCTG 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs560703311,2
    		--139423469(+) TTTGAA/GTCCCT 1 -- us2k10--------
    rs1764511,2
    		C,F,A,H,--139423832(+) CTTGCC/GGCCCC 1 -- us2k1 ese310Minor allele frequency- G:0.48MN NS EA NA WA CSA 609
    rs1764521,2
    		C,F,A,--139424062(+) GCGCCT/GGCAAC 1 -- us2k14Minor allele frequency- G:0.33NA WA 6
    rs3699911,2
    		C--139424169(+) TCCGGC/TGCGAA 1 -- ut512Minor allele frequency- T:0.00NA 4
    rs1125149551,2
    		C,--139424736(+) TGAAGA/GAGTAG 1 -- int11Minor allele frequency- G:0.00CSA 1
    rs722691121,2
    		C--139425383(+) TGTTC-/TTGTTGTT 1 -- int10--------
    rs59246311,2
    		C,--139425724(+) TTGCTA/GCAAAA 1 -- int11Minor allele frequency- G:0.00NA 2
    rs112877611,2
    		C--139426754(+) AGAAC-/TTTTTT 1 -- int1 trp31Minor allele frequency- T:0.00CSA 2
    rs604001921,2
    		C--139427321(+) AACAT-/AATGTCTT 1 -- int10--------

    HapMap Linkage Disequilibrium report for VMA21 (150564987 - 150577836 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for VMA21: --
    Human Gene Mutation Database (HGMD): VMA21

    Locus Specific Mutation Databases (LSDB): VMA21

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    Disorders / Diseases
    for VMA21 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    VMA21 for disorders           About GeneDecksing

    OMIM gene information: 310440    OMIM disorders: --

    UniProtKB/Swiss-Prot: VMA21_HUMAN, Q3ZAQ7
  • Defects in VMA21 are the cause of X-linked myopathy with excessive autophagy (MEAX) [MIM:310440]. MEAX is a
    • 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 up-regulates 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

    6 diseases for VMA21:    About MalaCards
    x-linked myopathy with excessive autophagy    myopathy    glycogen storage disease    glycogen storage disease ii
    vacuolar myopathy    danon disease


    Export disorders for VMA21 gene to outside databases

    Publications
    for VMA21 gene

    (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 20):
    (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. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. Retraction notice to: VMA21 Deficiency causes an auto phagic myopathy by compromising V-ATPase activity and lysosomal acidification. (PubMed id 20873370)2 (2010)
    9. Impaired autophagy in sporadic inclusion-body myositis and in endoplasmic reticulum stress-provoked cultured human muscle fibers. (PubMed id 20616343)1 Nogalska A....Askanas V. (2010)
    10. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)

    External Searches for VMA21 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing VMA21 gene

    (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

    Other Databases showing VMA21 gene

    (According to HUGE)
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    Specialized Databases showing VMA21 gene

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

    Intellectual Property
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    IP news from LifeMap Sciences, Inc.)
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