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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. Diseases associated with VCX3B include Non-Syndromic X-Linked Intellectual Disability. 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.

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

Genomics for VCX3B Gene

Regulatory Elements for VCX3B Gene

Enhancers for VCX3B 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
GH0XF008204 0.4 ENCODE 4.6 -260.4 -260396 0.2 GATA3 TCF7L2 VCX3B VCX2 PIR50074
GH0XF008404 0.5 Ensembl ENCODE 0.2 -60.1 -60138 0.6 PIR50074 VCX3B
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around VCX3B on UCSC Golden Path with GeneCards custom track

Genomic Location for VCX3B Gene

8,464,830 bp from pter
8,466,510 bp from pter
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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

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 for VCX3B Gene

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

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

Jensen Localization Image for VCX3B Gene 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,IBA --
genes like me logo Genes that share ontologies with VCX3B: view

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

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:

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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 and Protein tissue co-expression partners 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 34
  • 91.29 (n)
-- 35
  • 90 (a)
-- 35
  • 89 (a)
-- 35
  • 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 Sequence Context AA Info Type
rs1092635 -- 8,466,732(-) ccctc(C/G)ctccc downstream-variant-500B
rs111384512 -- 8,466,456(+) ATCTC(A/G)CCAGC utr-variant-3-prime
rs111479735 -- 8,463,505(+) AACTA(A/G)ACATT upstream-variant-2KB
rs112103242 -- 8,466,407(+) ATCTC(C/T)GAGAG utr-variant-3-prime
rs112774168 -- 8,466,481(+) TCTGA(A/T)GATAA utr-variant-3-prime

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

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

Variation tolerance for VCX3B Gene

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

Relevant External Links 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

MalaCards: The human disease database

(1) MalaCards diseases for VCX3B Gene - From: DISEASES

Disorder Aliases PubMed IDs
non-syndromic x-linked intellectual disability
  • mrx
- elite association - COSMIC cancer census association via MalaCards
Search VCX3B in MalaCards View complete list of genes associated with diseases

Relevant External Links for VCX3B

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VCX3B: view

No data available for 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 A.C. … Goldstein D.B. (Hum. Mol. Genet. 2009) 3 46 64
  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. (Am. J. Med. Genet. A 2006) 3 22 64
  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. (Hum. Mol. Genet. 2005) 3 22 64
  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 G.A. (Am. J. Hum. Genet. 2000) 3 4 64
  5. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. (PMID: 19812318) Jiao X. … Kiledjian M. (J. Neurosci. 2009) 3 64

Products for VCX3B Gene

Sources for VCX3B Gene

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