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Aliases for VCX3B Gene

Aliases for VCX3B Gene

  • Variable Charge, X-Linked 3B 2 3 5
  • Variably Charged Protein X-C 3 4
  • VCX-C 3 4
  • VCXC 3 4
  • Variable Charge X-Linked Protein 3B 3

External Ids for VCX3B Gene

Previous GeneCards Identifiers for VCX3B Gene

  • GC0XU900564
  • GC0XP008393

Summaries for VCX3B Gene

Entrez Gene Summary for VCX3B 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 the Y-linked members are two identical copies of the gene within a palindromic region on chromosome Yq11. The family members share a high degree of sequence identity, with the exception that a 30-nt 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. This family member, as represented by the reference genome allele, contains 14 copies of the 30-nt repeat unit. VCX/Y genes encode small and highly charged proteins containing putative bipartite nuclear localization signals. Although the exact function of this family member has yet to be determined, a role in mRNA stability regulation can be inferred from the ability of the highly similar family member, VCX-A, to inhibit mRNA decapping. A possible role in the regulation of ribosome assembly during spermatogenesis has also been suggested. [provided by RefSeq, Aug 2010]

GeneCards Summary for VCX3B Gene

VCX3B (Variable Charge, X-Linked 3B) is a Protein Coding gene. An important paralog of this gene is VCX.

UniProtKB/Swiss-Prot for VCX3B Gene

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

Additional gene information for VCX3B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCX3B Gene

Genomics for VCX3B Gene

GeneHancer (GH) Regulatory Elements for VCX3B Gene

Promoters and enhancers for VCX3B 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
GH0XI008465 Promoter 0.5 EPDnew 550.8 +0.6 569 0.1 PIR46429 VCX3B
GH0XI008204 Enhancer 0.4 ENCODE 4.6 -260.4 -260395 0.2 GATA3 TCF7L2 VCX3B VCX2 PIR50074
GH0XI008404 Enhancer 0.2 ENCODE 0.2 -60.2 -60205 0.2 PIR50074 VCX3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VCX3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VCX3B gene promoter:

Genomic Locations for VCX3B Gene

Genomic Locations for VCX3B Gene
1,681 bases
Plus strand

Genomic View for VCX3B Gene

Genes around VCX3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCX3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCX3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VCX3B Gene

Proteins for VCX3B Gene

  • Protein details for VCX3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Variable charge X-linked protein 3B
    Protein Accession:
    Secondary Accessions:
    • C9JS46
    • Q4KN12

    Protein attributes for VCX3B Gene

    246 amino acids
    Molecular mass:
    26878 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for VCX3B Gene


neXtProt entry for VCX3B Gene

Post-translational modifications for VCX3B Gene

No Post-translational modifications

Other Protein References for VCX3B Gene

No data available for DME Specific Peptides for VCX3B Gene

Domains & Families for VCX3B Gene

Gene Families for VCX3B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCX3B Gene


Suggested Antigen Peptide Sequences for VCX3B Gene

GenScript: Design optimal peptide antigens:

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 VCX3B: view

Function for VCX3B Gene

Molecular function for VCX3B Gene

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

Phenotypes From GWAS Catalog for VCX3B Gene

Phenotypes for VCX3B Gene

genes like me logo Genes that share phenotypes with VCX3B: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VCX3B Gene

Localization for VCX3B 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 VCX3B gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for VCX3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005730 nucleolus ISS --
genes like me logo Genes that share ontologies with VCX3B: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for VCX3B Gene

Pathways & Interactions for VCX3B Gene

SuperPathways for VCX3B Gene

No Data Available

Interacting Proteins for VCX3B Gene

Gene Ontology (GO) - Biological Process for VCX3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IBA --
genes like me logo Genes that share ontologies with VCX3B: view

No data available for Pathways by source and SIGNOR curated interactions for VCX3B Gene

Drugs & Compounds for VCX3B Gene

No Compound Related Data Available

Transcripts for VCX3B Gene

mRNA/cDNA for VCX3B Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VCX3B Gene

Variable charge, X-linked 3B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCX3B Gene

No ASD Table

Relevant External Links for VCX3B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCX3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VCX3B Gene

mRNA differential expression in normal tissues according to GTEx for VCX3B Gene

This gene is overexpressed in Testis (x44.4).

NURSA nuclear receptor signaling pathways regulating expression of VCX3B Gene:


SOURCE GeneReport for Unigene cluster for VCX3B Gene:


mRNA Expression by UniProt/SwissProt for VCX3B Gene:

Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCX3B: 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 VCX3B Gene

Orthologs for VCX3B Gene

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

Orthologs for VCX3B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC751066 33
  • 91.29 (n)
-- 34
  • 90 (a)
-- 34
  • 89 (a)
-- 34
  • 89 (a)
Species where no ortholog for VCX3B 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 VCX3B Gene

Gene Tree for VCX3B (if available)
Gene Tree for VCX3B (if available)

Paralogs for VCX3B Gene

Paralogs for VCX3B Gene

(5) SIMAP similar genes for VCX3B Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with VCX3B: view

Variants for VCX3B Gene

Sequence variations from dbSNP and Humsavar for VCX3B Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1003055612 -- 8,464,536(+) A/G upstream_transcript_variant
rs1006713455 -- 8,464,651(+) A/C/G upstream_transcript_variant
rs1010434601 -- 8,463,365(+) T/C upstream_transcript_variant
rs1010490710 -- 8,464,026(+) T/C upstream_transcript_variant
rs1016659249 -- 8,464,294(+) TGTGTGT/TGTGT upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VCX3B Gene

Variant ID Type Subtype PubMed ID
nsv953401 CNV deletion 24416366
nsv524164 CNV gain 19592680
nsv1144314 CNV deletion 24896259
nsv1137688 CNV deletion 24896259
nsv1077219 CNV deletion 25765185
esv2752339 CNV gain 17911159
esv2752335 CNV gain 17911159

Variation tolerance for VCX3B Gene

Gene Damage Index Score: 10.55; 91.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VCX3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCX3B Gene

Disorders for VCX3B Gene

Additional Disease Information for VCX3B

No disorders were found for VCX3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VCX3B Gene

Publications for VCX3B Gene

  1. 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) 3 44 58
  2. Molecular cytogenetic analysis of a familial interstitial deletion Xp22.2-22.3 with a highly variable phenotype in female carriers. (PMID: 16470742) Chocholska S … Kehrer-Sawatzki H (American journal of medical genetics. Part A 2006) 3 22 58
  3. Deletion of VCX-A due to NAHR plays a major role in the occurrence of mental retardation in patients with X-linked ichthyosis. (PMID: 15888481) Van Esch H … Froyen G (Human molecular genetics 2005) 3 22 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. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. (PMID: 19812318) Jiao X … Kiledjian M (The Journal of neuroscience : the official journal of the Society for Neuroscience 2009) 3 58

Products for VCX3B Gene

Sources for VCX3B Gene

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