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

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 Kallmann Syndrome. Gene Ontology (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

Additional gene information for VCX Gene

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

Genomics for VCX Gene

GeneHancer (GH) Regulatory Elements for VCX Gene

Promoters and enhancers for VCX Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ007843 Promoter 0.5 EPDnew 600.7 +0.9 890 0.1 VCX ENSG00000274923
GH0XJ007925 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 1.4 +85.3 85268 3.1 SP1 ZFX CTCF NKRF POLR2A GTF2F1 CSDE1 ZNF687 MAFK ELF1 PNPLA4 VCX ENSG00000274923
GH0XJ007890 Enhancer 0.2 Ensembl 11.5 +48.6 48639 1 VCX ENSG00000274923
GH0XJ007815 Enhancer 0.2 Ensembl 0.3 -27.2 -27161 0.2 VCX GC0XP007774
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VCX on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VCX gene promoter:
  • CBF(2)
  • NF-Y
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for VCX Gene

Genomic Locations for VCX Gene
1,882 bases
Plus strand
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

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCX Gene


Suggested Antigen Peptide Sequences for VCX Gene

GenScript: Design optimal peptide antigens:
  • Variable charge, X-linked (A0JNS5_HUMAN)
  • VCX protein (Q4V774_HUMAN)
  • Variably charged protein X-B1 (VCX1_HUMAN)

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

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

Phenotypes From GWAS Catalog for VCX Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VCX

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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VCX gene
Compartment Confidence
nucleus 5

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 and Subcellular locations from the Human Protein Atlas (HPA) for VCX Gene

Pathways & Interactions for VCX Gene

PathCards logo

SuperPathways for VCX Gene

No Data Available

Interacting Proteins for VCX Gene

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 21873635
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

Drugs & Compounds for VCX Gene

No Compound Related Data Available

Transcripts for VCX Gene

mRNA/cDNA for VCX Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Unigene Clusters for VCX Gene

Variable charge, X-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VCX

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 CGAP 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 , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 Variation AA Info Type
rs1006706523 -- 7,840,746(+) C/G upstream_transcript_variant
rs1018161806 -- 7,840,436(+) G/C upstream_transcript_variant
rs1018554642 -- 7,840,762(+) G/A/C upstream_transcript_variant
rs1020216756 -- 7,840,825(+) G/A upstream_transcript_variant
rs1026771676 -- 7,840,373(+) G/A upstream_transcript_variant

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)

Additional Variant Information for VCX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards
Search VCX in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VCX

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 BT … Page DC (Human molecular genetics 2000) 2 3 4 58
  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 GA (American journal of human genetics 2000) 2 3 4 58
  3. Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis. (PMID: 27705943) Ji J … Lu C (Oncotarget 2016) 3 58
  4. 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 SM (Cancer research 2014) 3 58
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 58

Products for VCX Gene

Sources for VCX Gene

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