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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 Protein 3 3
  • 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 Opitz-Kaveggia Syndrome. An important paralog of this gene is VCX.

UniProtKB/Swiss-Prot for VCX3A Gene

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

Additional gene information for VCX3A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCX3A Gene

Genomics for VCX3A Gene

GeneHancer (GH) Regulatory Elements for VCX3A Gene

Top Transcription factor binding sites by QIAGEN in the VCX3A gene promoter:

Genomic Locations for VCX3A Gene

Genomic Locations for VCX3A Gene
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

Post-translational modifications for VCX3A Gene

No Post-translational modifications

Other Protein References for VCX3A Gene

No data available for DME Specific Peptides for VCX3A Gene

Domains & Families for VCX3A Gene

Gene Families for VCX3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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.

Phenotypes for VCX3A Gene

GenomeRNAi human phenotypes for VCX3A:
genes like me logo Genes that share phenotypes with VCX3A: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VCX3A Gene

Localization for VCX3A 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 VCX3A gene
Compartment Confidence
nucleus 5

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

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for VCX3A Gene

Pathways & Interactions for VCX3A Gene

SuperPathways for VCX3A Gene

No Data Available

Interacting Proteins for VCX3A Gene

Selected Interacting proteins: Q9NNX9-VCX3_HUMAN for VCX3A Gene via IID

Symbol External ID(s) Details

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 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 :
(11) 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for VCX3A Gene

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

This gene is overexpressed in Testis (x49.5).

NURSA nuclear receptor signaling pathways regulating expression of VCX3A Gene:


SOURCE GeneReport for Unigene cluster for VCX3A Gene:


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

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 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 Variation AA Info Type
rs143802324 likely-benign, not specified 6,533,845(-) A/G coding_sequence_variant, missense_variant
rs139657007 benign, not specified 6,533,921(-) G/C coding_sequence_variant, intron_variant, missense_variant
rs35874450 benign, not specified 6,533,828(-) C/A/G/T coding_sequence_variant, missense_variant
rs72609545 benign, not specified 6,533,888(-) C/A/G/T coding_sequence_variant, missense_variant
rs1000245377 -- 6,533,274(-) A/C downstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv6783 CNV insertion 18451855
nsv511080 OTHER complex 20534489
nsv508751 CNV insertion 20534489
nsv199 CNV insertion 15895083
nsv1077218 CNV deletion 25765185
esv3576727 CNV gain 25503493
esv2758857 CNV gain 17122850
esv2422493 CNV duplication 17116639
esv2422345 CNV duplication 17116639
dgv265e55 CNV gain 17911159
dgv2202e212 CNV gain 25503493
dgv2201e212 CNV gain 25503493

Variation tolerance for VCX3A Gene

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

Additional Variant Information for VCX3A 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 VCX3A Gene

Disorders for VCX3A Gene

MalaCards: The human disease database

(3) MalaCards diseases for VCX3A Gene - From: HGMD, DISEASES, and Novoseek

Disorder Aliases PubMed IDs
ichthyosis, x-linked
  • xli
opitz-kaveggia syndrome
  • oks
kallmann syndrome
  • familial hypogonadism with anosmia
- elite association - COSMIC cancer census association via MalaCards
Search VCX3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VCX3A

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 BT … Page DC (Human molecular genetics 2000) 2 3 4 58
  2. 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 22 58
  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 SA … González-Huerta LM (The British journal of dermatology 2008) 3 22 58
  4. 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
  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 (European journal of medical genetics 2008) 22 58

Products for VCX3A Gene

Sources for VCX3A Gene

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