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VCX3A Gene

protein-coding   GIFtS: 43
GCID: GC0XM006461

Variable Charge, X-Linked 3A

(Previous names: variable charge, X-linked 3)
(Previous symbol: VCX3)
  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)
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Aliases
Variable Charge, X-Linked 3A1 2     VCX-8r2 3
VCX31 2 3     VCX-A2 3
VCX8R2 3 5     Variable Charge, X-Linked 31
VCXA2 3 5     Variable Charge X-Linked Protein 32
Variable Charge Protein On X With Eight Repeats2 3     Variably Charged X-A2
Variably Charged Protein X-A2 3     

External Ids:    HGNC: 181591   Entrez Gene: 514812   Ensembl: ENSG000001690597   OMIM: 3005335   UniProtKB: Q9NNX93   

Export aliases for VCX3A gene to outside databases

Previous GC identifers: GC0XP007622 GC0XP007623


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for VCX3A Gene:
This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are
expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked
members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high
degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but
occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different
individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of
unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members
are nuclear proteins. This gene contains 8 repeats of the 30-bp unit. (provided by RefSeq, Jul 2008)

GeneCards Summary for VCX3A Gene:
VCX3A (variable charge, X-linked 3A) is a protein-coding gene. Diseases associated with VCX3A include x-linked ichthyosis, and ocular albinism. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NT_167197.2  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VCX3A gene promoter:
         POU2F2 (Oct-2.1)   POU2F2   POU2F2C   POU2F1   POU2F1a   FOXO1a   NF-Y   POU2F2B   CBF(2)   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVCX3A promoter sequence
   Search Chromatin IP Primers for VCX3A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCX3A


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

Entrez Gene cytogenetic band: Xp22   Ensembl cytogenetic band:  Xp22.31   HGNC cytogenetic band: Xp22.31

VCX3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VCX3A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM006461:  view genomic region     (about GC identifiers)

Start:
6,451,659 bp from pter      End:
6,453,159 bp from pter
Size:
1,501 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9 (See protein sequence)
Recommended Name: Variable charge X-linked protein 3  
Size: 186 amino acids; 20020 Da
Secondary accessions: Q9P0H4

Explore the universe of human proteins at neXtProt for VCX3A: NX_Q9NNX9

Explore proteomics data for VCX3A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VCX3A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057463.2  
    ENSEMBL proteins: 
     ENSP00000370479   ENSP00000381713  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR026653 VCX/VCY1

    Graphical View of Domain Structure for InterPro Entry Q9NNX9

    ProtoNet protein and cluster: Q9NNX9

    UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
    Similarity: Belongs to the VCX/VCY family


    VCX3A 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VCX3_HUMAN, Q9NNX9
    Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

    Animal Models:

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--
    GO:0005730nucleolus ISS--

    VCX3A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VCX3A
    Interactions:

        Search GeneGlobe Interaction Network for VCX3A

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007420brain development IMP10903929

    VCX3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for VCX3A (VCX3)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for VCX3A gene: 
    NM_016379.3  

    Unigene Clusters for VCX3A:

    Variable charge, X-linked 3A
    Hs.170076  [show with all ESTs], Hs.278906  [show with all ESTs]
    Unigene Representative Sequences: BU595028, AF167078
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381089(uc022bsg.1 uc004crs.3 uc010ndk.2) ENST00000398729

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      QuantiFast Probe-based Assays in human, mouse, rat VCX3A

    Additional mRNA sequence: 

    AF159128.1 AF167078.1 BC039722.1 BC098149.1 BC126902.1 

    5 DOTS entries:

    DT.120654203  DT.443460  DT.91679712  DT.121292751  DT.313846 

    10 AceView cDNA sequences:

    BQ212742 NM_016379 BV184444 CB160710 AF167078 BC039722 BV206645 AF159128 
    AA994122 AA897187 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VCX3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGGATTTT
    VCX3A Expression
    About this image

    VCX3A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VCX3A Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.170076 Hs.278906

    UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
    Tissue specificity: Expressed exclusively in testis

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCX3A

    (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)
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      --

    ENSEMBL Gene Tree for VCX3A (if available)
    TreeFam Gene Tree for VCX3A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VCX3A gene
    VCX1 2  VCX3B2  VCY2  VCX22  VCY1B2  ENSG000002680802  
    5 SIMAP similar genes for VCX3A using alignment to 5 protein entries:     VCX3_HUMAN (see all proteins):
    VCX    VCX3B    VCY    VCX2    VCY1B

    VCX3A for paralogs           About GeneDecksing



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VCX3A (see all 163)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1871683021,2
    --6451368(+) CCTCCC/TCACAC 1 -- ds50010--------
    rs1912726031,2
    --6451610(+) CTTCCC/TCCCTC 1 -- ds50010--------
    rs2000710141,2
    C--6451752(+) TTAGTC/TGCTGC 1 -- ut310--------
    rs1836323281,2
    --6451762(+) CTCTCA/GGAGAT 1 -- ut310--------
    rs774135901,2
    C--6451777(+) GAGTAC/GCTGGC 1 -- ut311Minor allele frequency- G:0.00NA 2
    rs10582441,2
    C--6451778(-) GGCCAA/G/TCTACT 2 -- ut312MN NA 186
    rs1493650611,2
    C,F--6451784(+) TGGCCG/ATCTAC 1 -- ut311Minor allele frequency- A:0.01NA 4502
    rs743939381,2
    C--6451791(+) CTACAC/TACTCG 2 M V mis10--------
    rs59895111,2
    C,H--6451799(-) AGAACC/TACCGA 2 P L mis1 ese30--------
    rs1487486801,2
    F--6451804(+) AGTTCT/CTCCAT 2 /E syn11Minor allele frequency- C:0.00NA 4544

    HapMap Linkage Disequilibrium report for VCX3A (6451659 - 6453159 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for VCX3A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422345CNV Duplication17116639
    esv2422493CNV Duplication17116639
    nsv199CNV Insertion15895083
    nsv6783CNV Insertion18451855
    nsv508751CNV Insertion20534489
    dgv265e55CNV Gain17911159
    dgv2434e1CNV Complex17122850
    nsv511080CNV Complex20534489

    Human Gene Mutation Database (HGMD): VCX3A
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing VCX3A
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300533    OMIM disorders: --

    7 diseases for VCX3A:    
    About MalaCards
    x-linked ichthyosis    ocular albinism    intellectual disability    kallmann syndrome
    albinism    mental retardation, x-linked    mental retardation

    2 diseases from the University of Copenhagen DISEASES database for VCX3A:
    X-linked ichthyosis     Kallmann syndrome

    VCX3A for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for VCX3A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ichthyosis x-linked 91 4 15888481 (1), 18076704 (1)
    mental retardation 69.4 9 10903929 (2), 15888481 (2), 16470742 (1), 18076704 (1)


    Export disorders for VCX3A 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)
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    PubMed articles for VCX3A gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with VCX3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PubMed id 10607842)1, 2, 3 Lahn B.T. and Page D.C. (Hum. Mol. Genet. 2000)
    2. A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)1, 2, 9 Fukami M.... Rappold G.A. (Am. J. Hum. Genet. 2000)
    3. Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis. (PubMed id 18076704)1, 9 Cuevas-Covarrubias S.A. and GonzA!lez-Huerta L.M. (Br. J. Dermatol. 2008)
    4. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. (PubMed id 19812318)1 Jiao X....Kiledjian M. (J. Neurosci. 2009)
    5. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
    6. Identification of an mRNA-decapping regulator implicated in X-linked mental retardation. (PubMed id 17157254)1 Jiao X....Kiledjian M. (Mol. Cell 2006)
    7. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    9. DNA cloning using in vitro site-specific recombination. (PubMed id 11076863)1 Hartley J.L....Brasch M.A. (Genome Res. 2000)
    10. Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome. (PubMed id 1549475)1 Li X.M....Shapiro L.J. (Nucleic Acids Res. 1992)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (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)
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    Entrez Gene: 51481 HGNC: 18159 AceView: VCX3 Ensembl:ENSG00000169059 euGenes: HUgn51481
    ECgene: VCX3A H-InvDB: VCX3A

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VCX3A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VCX3A gene:
    Search GeneIP for patents involving VCX3A

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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