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Aliases for VCX3A Gene

Aliases for VCX3A Gene

  • Variable Charge, X-Linked 3A 2 3 5
  • 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
  • VCX8R 3 4
  • VCX3 3 4
  • VCXA 3 4
  • Variable Charge, X-Linked 3 2
  • Variably Charged X-A 3

External Ids for VCX3A Gene

Previous HGNC Symbols for VCX3A Gene

  • VCX3

Previous GeneCards Identifiers for VCX3A Gene

  • GC0XP007622
  • GC0XP007623
  • GC0XM006461

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. Diseases associated with VCX3A include Ichthyosis, X-Linked and Non-Syndromic X-Linked Intellectual Disability. 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

Regulatory Elements for VCX3A Gene

Enhancers for VCX3A Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VCX3A on UCSC Golden Path with GeneCards custom track

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

Genes around VCX3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCX3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCX3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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 & Families for VCX3A Gene

Gene Families for VCX3A Gene

Protein Domains for VCX3A Gene


Suggested Antigen Peptide Sequences for VCX3A 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 VCX3A: view

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.

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets 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 5
vacuole 1

Gene Ontology (GO) - Cellular Components for VCX3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus ISS --
genes like me logo Genes that share ontologies with VCX3A: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for VCX3A Gene

Pathways & Interactions for VCX3A Gene

SuperPathways for VCX3A Gene

No Data Available

Interacting Proteins for VCX3A Gene

Gene Ontology (GO) - Biological Process for VCX3A Gene


No data available for Pathways by source and SIGNOR curated interactions for VCX3A Gene

Drugs & Compounds for VCX3A Gene

No Compound Related Data Available

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 (x49.5).

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 expression patterns with VCX3A: 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 and Protein tissue co-expression partners for VCX3A Gene

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

(5) 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
rs748046471 -- 6,533,836(+) CGCTC(G/T)CCTGA reference, missense
rs748321234 -- 6,533,307(+) ACACC(A/T)CCTCT downstream-variant-500B
rs748324488 -- 6,533,645(+) TATTA(C/T)CTTCA utr-variant-3-prime
rs748353866 -- 6,533,666(+) CACCC(C/G/T)GCTGG utr-variant-3-prime
rs748520492 -- 6,533,996(+) ACTCA(G/T)GGGGT reference, missense

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

Variation tolerance for VCX3A Gene

Gene Damage Index Score: 4.20; 61.94% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VCX3A Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCX3A Gene

Disorders for VCX3A Gene

MalaCards: The human disease database

(2) MalaCards diseases for VCX3A Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
ichthyosis, x-linked
  • x-linked ichthyosis
non-syndromic x-linked intellectual disability
  • mrx
- elite association - COSMIC cancer census association via MalaCards
Search VCX3A in MalaCards View complete list of genes associated with diseases

Relevant External Links for VCX3A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VCX3A: view

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

Publications for VCX3A Gene

  1. 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 67
  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 S.A. … GonzA!lez-Huerta L.M. (Br. J. Dermatol. 2008) 3 23
  3. 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 23
  4. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. (PMID: 19812318) Jiao X. … Kiledjian M. (J. Neurosci. 2009) 3
  5. 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

Products for VCX3A Gene

Sources for VCX3A Gene