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Aliases for VCX3A Gene

Aliases for VCX3A Gene

  • Variable Charge, X-Linked 3A 2 3
  • VCX8R 3 4 6
  • VCXA 3 4 6
  • Variable Charge Protein On X With Eight Repeats 3 4
  • Variably Charged Protein X-A 3 4
  • VCX-8r 3 4
  • VCX-A 3 4
  • VCX3 3 4
  • Variable Charge X-Linked Protein 3 3
  • Variable Charge, X-Linked 3 2
  • Variably Charged X-A 3

External Ids for VCX3A Gene

Previous Symbols for VCX3A Gene

  • VCX3

Summaries for VCX3A Gene

Entrez Gene Summary for VCX3A 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 8 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]

GeneCards Summary for VCX3A Gene

VCX3A (Variable Charge, X-Linked 3A) is a Protein Coding gene. An important paralog of this gene is VCY1B.

UniProtKB/Swiss-Prot for VCX3A 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 VCX3A Gene

Genomics for VCX3A Gene

Genomic Location for VCX3A Gene

6,533,618 bp from pter
6,535,118 bp from pter
1,501 bases
Minus strand

Genomic View for VCX3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VCX3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VCX3A Gene

Regulatory Elements for VCX3A Gene

Proteins for VCX3A Gene

  • Protein details for VCX3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Variable charge X-linked protein 3
    Protein Accession:
    Secondary Accessions:
    • Q9P0H4

    Protein attributes for VCX3A Gene

    186 amino acids
    Molecular mass:
    20020 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VCX3A Gene

Proteomics data for VCX3A Gene at MOPED

Post-translational modifications for VCX3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VCX3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VCX3A Gene

Domains for VCX3A Gene

Protein Domains for VCX3A Gene



  • Belongs to the VCX/VCY family.:
    • Q9NNX9
genes like me logo Genes that share domains with VCX3A: view

No data available for Gene Families for VCX3A Gene

Function for VCX3A Gene

Molecular function for VCX3A Gene

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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for VCX3A Gene

Localization for VCX3A Gene

Subcellular locations from

Jensen Localization Image for VCX3A Gene COMPARTMENTS Subcellular localization image for VCX3A gene
Compartment Confidence
nucleus 4

Gene Ontology (GO) - Cellular Components for VCX3A 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 VCX3A: view

Pathways for VCX3A Gene

SuperPathways for VCX3A Gene

No Data Available

Interacting Proteins for VCX3A Gene

Gene Ontology (GO) - Biological Process for VCX3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IMP 10903929
genes like me logo Genes that share ontologies with VCX3A: view

No data available for Pathways by source for VCX3A Gene

Transcripts for VCX3A Gene

mRNA/cDNA for VCX3A Gene

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

Unigene Clusters for VCX3A Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for VCX3A Gene

No ASD Table

Relevant External Links for VCX3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCX3A Gene

mRNA expression in normal human tissues for VCX3A Gene

mRNA differential expression in normal tissues according to GTEx for VCX3A Gene

This gene is overexpressed in Testis (49.5).

SOURCE GeneReport for Unigene cluster for VCX3A Gene Hs.170076

mRNA Expression by UniProt/SwissProt for VCX3A Gene

Tissue specificity: Expressed exclusively in testis
genes like me logo Genes that share expressions with VCX3A: view

Orthologs for VCX3A Gene

Evolution for VCX3A Gene

Gene Tree for VCX3A (if available)
Gene Tree for VCX3A (if available)

No data available for Orthologs for VCX3A Gene

Paralogs for VCX3A Gene

Paralogs for VCX3A Gene

Selected SIMAP similar genes for VCX3A Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with VCX3A: view

Variants for VCX3A Gene

Sequence variations from dbSNP and Humsavar for VCX3A Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs1058244 -- 6,533,737(-) GGCCA(A/G/T)CTACT utr-variant-3-prime
rs1058245 -- 6,533,720(-) TCTCC(C/G)AGAGC utr-variant-3-prime
rs1728760 -- 6,533,984(+) CTCGC(C/T)CTCCT reference, missense
rs3198862 -- 6,533,702(-) AAGTT(C/T)AGGCC utr-variant-3-prime
rs5934292 -- 6,533,995(-) CCCCC(C/T)GAGTC missense, reference

Structural Variations from Database of Genomic Variants (DGV) for VCX3A Gene

Variant ID Type Subtype PubMed ID
esv2422345 CNV Duplication 17116639
esv2422493 CNV Duplication 17116639
dgv265e55 CNV Gain 17911159
dgv2434e1 CNV Complex 17122850
nsv511080 CNV Complex 20534489
nsv508751 CNV Insertion 20534489
nsv6783 CNV Insertion 18451855
nsv199 CNV Insertion 15895083

Relevant External Links for VCX3A Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

Disorders for VCX3A Gene

(2) University of Copenhagen DISEASES for VCX3A Gene

(2) Novoseek inferred disease relationships for VCX3A Gene

Disease -log(P) Hits PubMed IDs
ichthyosis x-linked 91 2
mental retardation 69.4 6
genes like me logo Genes that share disorders with VCX3A: view

No data available for UniProtKB/Swiss-Prot for VCX3A Gene

Publications for VCX3A Gene

  1. 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 23
  2. 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
  3. 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 S.A. … GonzA!lez-Huerta L.M. (Br. J. Dermatol. 2008) 3 23
  4. Normal intelligence and social interactions in a male patient despite the deletion of NLGN4X and the VCX genes. (PMID: 18194880) Mochel F. … Moncla A. (Eur J Med Genet 2008) 23
  5. Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome. (PMID: 1549475) Li X.M. … Shapiro L.J. (Nucleic Acids Res. 1992) 3

Products for VCX3A Gene

  • QIAGEN qRT-PCR Assays for microRNAs that regulate VCX3A
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for VCX3A
    • Block miRNA regulation of VCX3A using miScript Target Protectors

    Sources for VCX3A Gene

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