Free for academic non-profit institutions. Other users need a Commercial license

Aliases for VCX2 Gene

Aliases for VCX2 Gene

  • Variable Charge, X-Linked 2 2 3 5
  • Variable Charge Protein On X With Two Repeats 3 4
  • Variably Charged Protein X-B 3 4
  • VCX-2r 3 4
  • VCX2R 3 4
  • VCXB 3 4
  • Variably Charged, X Chromosome, With 2 Repeats 3
  • Variable Charge X-Linked Protein 2 3
  • Variably Charged, X Chromosome 2 3
  • Variably Charged, X Chromosome B 3
  • VCX-B 4

External Ids for VCX2 Gene

Previous GeneCards Identifiers for VCX2 Gene

  • GC0XM007550
  • GC0XM007947
  • GC0XM005966

Summaries for VCX2 Gene

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 that are expressed exclusively in male germ cells. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. This gene contains two copies of a 30 nt tandem repeat. Deletion of a nearby member of this family was implicated in cognitive disability. [provided by RefSeq, Feb 2015]

GeneCards Summary for VCX2 Gene

VCX2 (Variable Charge, X-Linked 2) is a Protein Coding gene. Diseases associated with VCX2 include Ichthyosis, X-Linked. An important paralog of this gene is VCX.

UniProtKB/Swiss-Prot for VCX2 Gene

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

Additional gene information for VCX2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCX2 Gene

Genomics for VCX2 Gene

GeneHancer (GH) Regulatory Elements for VCX2 Gene

Promoters and enhancers for VCX2 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
GH0XI008170 Promoter 0.5 EPDnew 550.8 +0.6 571 0.1 VCX2 GC0XP008127
GH0XI008191 Enhancer 0.6 ENCODE 0.4 -19.9 -19898 0.2 SMARCE1 MAZ DPF2 MNT FOXA1 CTBP1 GATA3 JUND CREB1 FOS MIR651 VCX2 PIR50074
GH0XI008204 Enhancer 0.4 ENCODE 0.3 -33.2 -33168 0.2 GATA3 TCF7L2 VCX3B VCX2 PIR50074
GH0XI008201 Enhancer 0.2 ENCODE 0.3 -30.7 -30724 1.4 VCX2 PIR50074
GH0XI008273 Enhancer 0.6 ENCODE 0.1 -102.4 -102428 0.2 JUN USF2 CEBPB EP300 RFX5 GATA3 JUND STAT3 RCOR1 FOS VCX2 PIR50074
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VCX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VCX2 gene promoter:

Genomic Locations for VCX2 Gene

Genomic Locations for VCX2 Gene
1,324 bases
Minus strand

Genomic View for VCX2 Gene

Genes around VCX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VCX2 Gene

Proteins for VCX2 Gene

  • Protein details for VCX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Variable charge X-linked protein 2
    Protein Accession:
    Secondary Accessions:
    • A3KPB6
    • Q4V9T2
    • Q9P0H5

    Protein attributes for VCX2 Gene

    139 amino acids
    Molecular mass:
    14661 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VCX2 Gene

Post-translational modifications for VCX2 Gene

No Post-translational modifications

Other Protein References for VCX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VCX2 Gene

Domains & Families for VCX2 Gene

Gene Families for VCX2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCX2 Gene


Suggested Antigen Peptide Sequences for VCX2 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 VCX2: view

Function for VCX2 Gene

Molecular function for VCX2 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 VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with VCX2: view

Phenotypes for VCX2 Gene

GenomeRNAi human phenotypes for VCX2:
genes like me logo Genes that share phenotypes with VCX2: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VCX2 Gene

Localization for VCX2 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 VCX2 gene
Compartment Confidence
nucleus 3
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with VCX2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for VCX2 Gene

Pathways & Interactions for VCX2 Gene

No Data Available

Interacting Proteins for VCX2 Gene

Selected Interacting proteins: Q9H322-VCX2_HUMAN for VCX2 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IBA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with VCX2: view

No data available for Pathways by source and SIGNOR curated interactions for VCX2 Gene

Drugs & Compounds for VCX2 Gene

No Compound Related Data Available

Transcripts for VCX2 Gene

mRNA/cDNA for VCX2 Gene

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

Unigene Clusters for VCX2 Gene

Variable charge, X-linked 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCX2 Gene

No ASD Table

Relevant External Links for VCX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VCX2 Gene

mRNA differential expression in normal tissues according to GTEx for VCX2 Gene

This gene is overexpressed in Testis (x52.7).

NURSA nuclear receptor signaling pathways regulating expression of VCX2 Gene:


SOURCE GeneReport for Unigene cluster for VCX2 Gene:


mRNA Expression by UniProt/SwissProt for VCX2 Gene:

Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCX2: view

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 VCX2 Gene

Orthologs for VCX2 Gene

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

Orthologs for VCX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC742075 33
  • 95.66 (n)
VCX2 34
  • 87 (a)
Species where no ortholog for VCX2 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 VCX2 Gene

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

Paralogs for VCX2 Gene

Paralogs for VCX2 Gene

(5) SIMAP similar genes for VCX2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VCX2: view

Variants for VCX2 Gene

Sequence variations from dbSNP and Humsavar for VCX2 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1008750347 -- 8,171,279(-) A/G upstream_transcript_variant
rs1008781271 -- 8,171,688(-) G/A upstream_transcript_variant
rs1013220331 -- 8,172,368(-) T/C upstream_transcript_variant
rs1013299039 -- 8,172,553(-) A/G upstream_transcript_variant
rs1013380752 -- 8,170,867(-) /C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VCX2 Gene

Variant ID Type Subtype PubMed ID
dgv2214e212 CNV gain 25503493
dgv4208n106 CNV deletion 24896259
dgv499n21 CNV gain 19592680
esv2752335 CNV gain 17911159
esv3576759 CNV gain 25503493
nsv470340 CNV gain 18288195
nsv508752 CNV insertion 20534489
nsv511081 OTHER complex 20534489
nsv524164 CNV gain 19592680
nsv528203 CNV gain 19592680
nsv6788 CNV insertion 18451855

Variation tolerance for VCX2 Gene

Gene Damage Index Score: 5.80; 73.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VCX2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCX2 Gene

Disorders for VCX2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VCX2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
ichthyosis, x-linked
  • xli
- elite association - COSMIC cancer census association via MalaCards
Search VCX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VCX2

genes like me logo Genes that share disorders with VCX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VCX2 Gene

Publications for VCX2 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. 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. (PMID: 18076704) Cuevas-Covarrubias SA … González-Huerta LM (The British journal of dermatology 2008) 3 22 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. 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) 3 4 58
  5. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PMID: 19734545) Need AC … Goldstein DB (Human molecular genetics 2009) 44 58

Products for VCX2 Gene

Sources for VCX2 Gene

Loading form....