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VCX2 Gene

protein-coding   GIFtS: 42
GCID: GC0XM008097

Variable Charge, X-Linked 2
  See related diseases
at
MalaCards
 

Aliases
for VCX2 gene

(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 21 2     VCX-2r2 3
VCX2R2 3 5     VCX-B2 3
VCXB2 3 5     Variable Charge X-Linked Protein 22
Variable Charge Protein On X With Two Repeats2 3     Variably Charged X-B2
Variably Charged Protein X-B2 3     

External Ids:    HGNC: 181581   Entrez Gene: 514802   Ensembl: ENSG000001775047   OMIM: 3005325   UniProtKB: Q9H3223   

Export aliases for VCX2 gene to outside databases

Previous GC identifers: GC0XM007550 GC0XM007947 GC0XM005966


Summaries
for VCX2 gene

(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 VCX2 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 2 repeats of the 30-bp unit. (provided by RefSeq, Jul 2008)

GeneCards Summary for VCX2 Gene:
VCX2 (variable charge, X-linked 2) is a protein-coding gene. Diseases associated with VCX2 include x-linked ichthyosis, and ocular albinism. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322
Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion




Genomic Views
for VCX2 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_167197.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VCX2 gene promoter:
         FOXF2   FOXO1a   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): VCX2 promoter sequence
   Search Chromatin IP Primers for VCX2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCX2


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

Entrez Gene cytogenetic band: Xp22.32   Ensembl cytogenetic band:  Xp22.31   HGNC cytogenetic band: Xp22.32

VCX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VCX2 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM008097:  view genomic region     (about GC identifiers)

Start:
 8,137,985 bp from pter      End:
 8,139,308 bp from pter
Size:
 1,324 bases      Orientation:
 minus strand

Proteins
for VCX2 gene

(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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322 (See protein sequence)
Recommended Name: Variable charge X-linked protein 2  
Size: 139 amino acids; 14661 Da
Secondary accessions: A3KPB6 Q4V9T2 Q9P0H5

Explore the universe of human proteins at neXtProt for VCX2: NX_Q9H322

Explore proteomics data for VCX2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

    • See VCX2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057462.2  
    ENSEMBL proteins: 
     ENSP00000321309  

    VCX2 Human Recombinant Protein Products:

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    VCX2 Assay Products:

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    Domains /
    Families
    for VCX2 gene

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

    Graphical View of Domain Structure for InterPro Entry Q9H322

    ProtoNet protein and cluster: Q9H322

    UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322
    Similarity: Belongs to the VCX/VCY family


    VCX2 for domains           About GeneDecksing


    Function
    for VCX2 gene

    (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: VCX2_HUMAN, Q9H322
    Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    VCX2 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for VCX2
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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VCX2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCX2

    Cell Line
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    In Situ Assay
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    Localization
    for VCX2 gene

    (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
    nucleus3
    cytoskeleton1
    cytosol1
    extracellular1
    mitochondrion1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    VCX2 for ontologies           About GeneDecksing


    Pathways & Interactions
    for VCX2 gene

    (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 VCX2
    Interactions:

        Search GeneGlobe Interaction Network for VCX2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    VCX2 for ontologies           About GeneDecksing



    Drugs & Compounds
    for VCX2 gene

    (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 VCX2



    Transcripts
    for VCX2 gene

    (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,
    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 VCX2 gene: 
    NM_016378.2  

    Unigene Cluster for VCX2:

    Variable charge, X-linked 2
    Hs.279737  [show with all ESTs]
    Unigene Representative Sequence: AF167079
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000317103(uc004csb.3)
    miRNA
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    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat VCX2
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    GenScript: all cDNA clones in your preferred vector: VCX2 (NM_016378)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCX2
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat VCX2
      QuantiTect SYBR Green Assays in human, mouse, rat VCX2
      QuantiFast Probe-based Assays in human, mouse, rat VCX2

    Additional mRNA sequence: 

    AF159127.1 AF167079.1 BC096715.1 BC098101.1 BC098113.1 BC098163.1 BC104153.2 BC104167.1 
    BC104168.1 BC134350.1 

    2 DOTS entries:

    DT.313845  DT.313846 

    11 AceView cDNA sequences:

    AF167081 AA565702 AF159129 NM_013452 BE504628 AA206042 BF885187 AU099954 
    BV184446 AI824821 AA897187 

    GeneLoc Exon Structure


    Expression
    for VCX2 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™, 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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    VCX2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    VCX2 Expression
    About this image

    VCX2 Protein expression data from MOPED1, PaxDb2 and MaxQB3:     About this image

    VCX2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.279737

    UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322
    Tissue specificity: Expressed exclusively in testis

        Custom PCR Arrays for VCX2
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCX2

    Orthologs
    for VCX2 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)
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    This gene was present in the common ancestor of human and chimp.

    Orthologs for VCX2 gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chimpanzee
    (Pan troglodytes)    		 Mammalia LOC7420751 variable charge X-linked protein 3B-like 95.66(n)
    91.87(a)    		   742075  XM_003318999.2  XP_003319047.2 


    ENSEMBL Gene Tree for VCX2 (if available)
    TreeFam Gene Tree for VCX2 (if available)

    Paralogs
    for VCX2 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VCX2 gene
    VCY1 2  VCY1B1 2  VCX3B2  VCX2  VCX3A2  ENSG000002680802  
    5 SIMAP similar genes for VCX2 using alignment to 4 protein entries:     VCX2_HUMAN (see all proteins):
    VCY    VCY1B    VCX3A    VCX    VCX3B

    VCX2 for paralogs           About GeneDecksing



    Genomic Variants
    for VCX2 gene

    (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 VCX2 (see all 127)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr X posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1861236651,2
    		C--8137917(+) CCCTCA/CCCACA 1 -- ds50010--------
    rs773985351,2
    		C--8137936(+) CTTCCT/CCCCTC 1 -- ds50011Minor allele frequency- C:0.00NA 2
    rs1905423221,2
    		C--8137972(+) AACACA/GGAGTC 1 -- ds50010--------
    rs1827247061,2
    		C--8138030(+) AAGCAC/TCCCGC 1 -- ut310--------
    rs2015686371,2
    		C--8138039(+) GCTGGC/TGAGAT 1 -- ut310--------
    rs2009357951,2
    		C--8138058(+) TCTGGA/CGGCTG 1 -- ut310--------
    rs1457086561,2
    		C,F--8138078(+) TTAGTC/TGGTGC 2 N D mis11Minor allele frequency- T:0.00NA 4540
    rs10582391,2,,4
    		C,F,H--8138080(-) GAGCAG/CCGACT 2 /T /S mis1 ese311Minor allele frequency- C:0.14MN NS EA NA WA CSA 5139
    rs777807681,2
    		C,F--8138088(-) GTCTCC/G/TGAGAG 3 S syn12CSA NA 4543
    rs1481145401,2
    		C--8138093(+) GGAGAC/TAGGGG 2 I V mis11Minor allele frequency- T:0.00NA 4542

    HapMap Linkage Disequilibrium report for VCX2 (8137985 - 8139308 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for VCX2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6788CNV Insertion18451855
    nsv508752CNV Insertion20534489
    esv2752335CNV Gain17911159
    nsv528203CNV Gain19592680
    nsv524164CNV Gain19592680
    nsv470340CNV Gain18288195
    dgv499n21CNV Gain19592680
    nsv511081CNV Complex20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VCX2
    DNA2.0 Custom Variant and Variant Library Synthesis for VCX2

    Disorders / Diseases
    for VCX2 gene

    (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.)
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    OMIM gene information: 300532    OMIM disorders: --

    6 diseases for VCX2:    
    About MalaCards
    x-linked ichthyosis    ocular albinism    kallmann syndrome    albinism
    mental retardation, x-linked    mental retardation

    2 diseases from the University of Copenhagen DISEASES database for VCX2:
    X-linked ichthyosis     Kallmann syndrome

    VCX2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): VCX2

    Export disorders for VCX2 gene to outside databases

    Publications
    for VCX2 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)
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    PubMed articles for VCX2 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with VCX2)    		    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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. 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 Fukami M.... Rappold G.A. (Am. J. Hum. Genet. 2000)
    4. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PubMed id 19734545)4 Need A.C....Goldstein D.B. (Hum. Mol. Genet. 2009)
    5. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)
    6. 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)
    7. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. (PubMed id 11337467)1 Suzuki Y....Sugano S. (Genome Res. 2001)
    8. 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)9 Cuevas-Covarrubias S.A. and GonzA!lez-Huerta L.M. (Br. J. Dermatol. 2008)
    9. Sushi repeat protein X-linked 2, a novel mediator of angiogenesis. (PubMed id 19667118)9 Miljkovic-Licina M....Imhof B.A. (FASEB J. 2009)
    10. Deletion of VCX-A due to NAHR plays a major role in the occurrence of mental retardation in patients with X-linked ichthyosis. (PubMed id 15888481)9 Van Esch H....Froyen G. (Hum. Mol. Genet. 2005)

    External Searches for VCX2 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing VCX2 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51480 HGNC: 18158 AceView: VCX Ensembl:ENSG00000177504 euGenes: HUgn51480
    ECgene: VCX2 H-InvDB: VCX2

    Other Databases showing VCX2 gene

    (According to HUGE)
    About This Section

    TryGeneCards Plus    		   --

    Specialized Databases showing VCX2 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for VCX2 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for VCX2 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

    TryGeneCards Plus    		Patent Information for VCX2 gene:
    Search GeneIP for patents involving VCX2

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



    Products
    for VCX2 gene

    (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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     OriGene MassSpec something-or-other for VCX2   OriGene clones in human, mouse for VCX2  
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     Block miRNA regulation of human, mouse, rat VCX2 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing VCX2
     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCX2 Predesigned siRNA for gene silencing in human, mouse, rat VCX2
     QuantiFast Probe-based Assays in human, mouse, rat VCX2 QuantiTect SYBR Green Assays in human, mouse, rat VCX2
     Custom PCR Arrays for VCX2 Search Chromatin IP Primers for VCX2
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     Regulatory tfbs in VCX2 promoter
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     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCX2
     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for VCX2
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