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Aliases for VCX Gene

Aliases for VCX Gene

  • Variable Charge, X-Linked 2 3 5
  • Variable Charge Protein On X With Ten Repeats 3 4
  • Variable Charge, X Chromosome 2 3
  • Variably Charged Protein X-B1 3 4
  • VCX-10r 3 4
  • VCX-B1 3 4
  • VCX10R 3 4
  • VCXB1 3 4
  • VCX1 3 4
  • Variable Charge X-Linked Protein 1 3

External Ids for VCX Gene

Previous GeneCards Identifiers for VCX Gene

  • GC0XP006659
  • GC0XP007169
  • GC0XP007221
  • GC0XP007620
  • GC0XP007770
  • GC0XP005618

Summaries for VCX Gene

Entrez Gene Summary for VCX 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 10 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]

GeneCards Summary for VCX Gene

VCX (Variable Charge, X-Linked) is a Protein Coding gene. Diseases associated with VCX include Non-Syndromic X-Linked Intellectual Disability. GO annotations related to this gene include chromatin binding. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot for VCX Gene

  • May mediate a process in spermatogenesis or may play a role in sex ratio distortion.

Gene Wiki entry for VCX Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCX Gene

Genomics for VCX Gene

Regulatory Elements for VCX Gene

Enhancers for VCX Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF007928 0.4 FANTOM5 1.4 +86.7 86660 0.4 VCX PNPLA4 GC0XM007955
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around VCX on UCSC Golden Path with GeneCards custom track

Genomic Location for VCX Gene

7,842,262 bp from pter
7,844,143 bp from pter
1,882 bases
Plus strand

Genomic View for VCX Gene

Genes around VCX on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCX Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VCX Gene

Proteins for VCX Gene

  • Protein details for VCX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Variable charge X-linked protein 1
    Protein Accession:
    Secondary Accessions:
    • A0JNS5
    • Q4V774
    • Q9P0H3

    Protein attributes for VCX Gene

    206 amino acids
    Molecular mass:
    22289 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VCX Gene

Post-translational modifications for VCX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VCX Gene

No data available for DME Specific Peptides for VCX Gene

Domains & Families for VCX Gene

Gene Families for VCX Gene

Protein Domains for VCX Gene


Suggested Antigen Peptide Sequences for VCX Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the VCX/VCY family.
  • Belongs to the VCX/VCY family.
genes like me logo Genes that share domains with VCX: view

Function for VCX Gene

Molecular function for VCX Gene

GENATLAS Biochemistry:
basic protein variable charge X/Y on chromosome X,testis specific,most likely present in germ cells,included in the CRI-S232 sequence flanking the STS gene
UniProtKB/Swiss-Prot Function:
May mediate a process in spermatogenesis or may play a role in sex ratio distortion.

Gene Ontology (GO) - Molecular Function for VCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding TAS 12862317
genes like me logo Genes that share ontologies with VCX: view
genes like me logo Genes that share phenotypes with VCX: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VCX Gene

Localization for VCX Gene

Subcellular locations from

Jensen Localization Image for VCX Gene COMPARTMENTS Subcellular localization image for VCX gene
Compartment Confidence
nucleus 5
vacuole 2

Gene Ontology (GO) - Cellular Components for VCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 12862317
GO:0005730 nucleolus IDA 12862317
genes like me logo Genes that share ontologies with VCX: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for VCX Gene

Pathways & Interactions for VCX Gene

SuperPathways for VCX Gene

No Data Available

Interacting Proteins for VCX Gene

Selected Interacting proteins: Q9H320-VCX1_HUMAN for VCX Gene via IID

Gene Ontology (GO) - Biological Process for VCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS 12862317
GO:0007283 spermatogenesis TAS 10607842
GO:0007420 brain development IBA --
GO:0042255 ribosome assembly NAS 12862317
genes like me logo Genes that share ontologies with VCX: view

No data available for Pathways by source and SIGNOR curated interactions for VCX Gene

Transcripts for VCX Gene

mRNA/cDNA for VCX Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VCX Gene

Variable charge, X-linked:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCX Gene

No ASD Table

Relevant External Links for VCX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCX Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VCX Gene

mRNA differential expression in normal tissues according to GTEx for VCX Gene

This gene is overexpressed in Testis (x45.2).

NURSA nuclear receptor signaling pathways regulating expression of VCX Gene:


SOURCE GeneReport for Unigene cluster for VCX Gene:


mRNA Expression by UniProt/SwissProt for VCX Gene:

Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCX: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for VCX Gene

Orthologs for VCX Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for VCX Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia -- 35
  • 89 (a)
-- 35
  • 89 (a)
Species where no ortholog for VCX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for VCX Gene

Gene Tree for VCX (if available)
Gene Tree for VCX (if available)

Paralogs for VCX Gene

Paralogs for VCX Gene

(5) SIMAP similar genes for VCX Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with VCX: view

Variants for VCX Gene

Sequence variations from dbSNP and Humsavar for VCX Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1103931 -- 7,844,478(-) cctct(C/T)cctcc downstream-variant-500B
rs111462905 -- 7,842,611(+) AAACT(A/G)CCGAC intron-variant, upstream-variant-2KB
rs112068586 -- 7,844,583(+) GTGGT(A/G)TGTGG downstream-variant-500B
rs112105768 -- 7,844,306(+) TGTGG(G/T)GAGGG downstream-variant-500B
rs112517702 -- 7,844,305(+) GTGTG(G/T)GGAGG downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for VCX Gene

Variant ID Type Subtype PubMed ID
dgv1n30 CNV gain 18288195
dgv499n21 CNV gain 19592680
esv2422194 CNV duplication 17116639
esv33658 CNV loss 17666407
esv3576758 CNV gain 25503493
esv3576759 CNV gain 25503493

Variation tolerance for VCX Gene

Gene Damage Index Score: 0.36; 7.90% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VCX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCX Gene

Disorders for VCX Gene

MalaCards: The human disease database

(1) MalaCards diseases for VCX Gene - From: DISEASES

Disorder Aliases PubMed IDs
non-syndromic x-linked intellectual disability
  • mrx
- elite association - COSMIC cancer census association via MalaCards
Search VCX in MalaCards View complete list of genes associated with diseases

Relevant External Links for VCX

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VCX: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VCX Gene

Publications for VCX Gene

  1. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PMID: 10607842) Lahn B.T. … Page D.C. (Hum. Mol. Genet. 2000) 2 3 4 64
  2. A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PMID: 10903929) Fukami M. … Rappold G.A. (Am. J. Hum. Genet. 2000) 2 3 4 64
  3. A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets. (PMID: 24970476) Taguchi A. … Hanash S.M. (Cancer Res. 2014) 3 64
  4. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. (PMID: 17342728) Hansen M.A. … Leffers H. (Mol. Reprod. Dev. 2008) 3 64
  5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PMID: 17903299) Kathiresan S. … Cupples L.A. (BMC Med. Genet. 2007) 46 64

Products for VCX Gene

Sources for VCX Gene

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