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 excepti... See more...

Aliases for VCX3A Gene

Aliases for VCX3A Gene

  • Variable Charge X-Linked 3A 2 3 5
  • VCX-8r 2 3 4
  • VCX-A 2 3 4
  • Variable Charge Protein On X With Eight Repeats 3 4
  • Variable Charge X-Linked Protein 3 3 4
  • Variably Charged Protein X-A 3 4
  • VCX8R 3 4
  • VCX3 3 4
  • VCXA 3 4
  • Variable Charge, X-Linked 3 2
  • Variably Charged X-A 3
  • VCX-8R 2
  • VCX3A 5

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 Combined Oxidative Phosphorylation Deficiency 6. An important paralog of this gene is VCX.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for VCX3A Gene

Genomics for VCX3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VCX3A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ006382 Enhancer 0.6 Ensembl ENCODE 5.2 +151.1 151148 2.9 NR2F2 HNF4A RXRA SP1 MIR4770 VCX3A RPS5P8 NLGN4X
GH0XJ006462 Enhancer 0.2 Ensembl 4.2 +72.3 72317 0.4 HSALNG0136506 VCX3A HSALNG0136501 NLGN4X
GH0XJ006737 Enhancer 1.1 Ensembl ENCODE dbSUPER 0.1 -203.8 -203828 1.9 SP1 BACH1 LARP7 ZNF143 TCF12 IKZF2 TRIM22 PKNOX1 EED ARID3A lnc-VCX3A-2 piR-31937-259 VCX3A PUDP STS
GH0XJ006505 Enhancer 0.2 Ensembl 0.3 +29.1 29117 0.4 piR-50443-397 piR-33863-187 VCX3A NLGN4X
GH0XJ006692 Enhancer 0.4 Ensembl ENCODE 0.1 -159.3 -159281 3.3 NANOG NLGN4X piR-33735-107 piR-48325-153 lnc-VCX3A-1 lnc-VCX3A-2 VCX3A PUDP STS
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VCX3A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VCX3A

Top Transcription factor binding sites by QIAGEN in the VCX3A gene promoter:
  • CBF(2)
  • FOXO1
  • FOXO1a
  • NF-Y
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for VCX3A Gene

Genomic Locations for VCX3A Gene
chrX:6,533,618-6,535,118
(GRCh38/hg38)
Size:
1,501 bases
Orientation:
Minus strand
chrX:6,451,659-6,453,159
(GRCh37/hg19)
Size:
1,501 bases
Orientation:
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:
    Q9NNX9-VCX3_HUMAN
    Recommended name:
    Variable charge X-linked protein 3
    Protein Accession:
    Q9NNX9
    Secondary Accessions:
    • Q9P0H4

    Protein attributes for VCX3A Gene

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

neXtProt entry for VCX3A Gene

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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCX3A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VCX3A Gene

GenScript: Design optimal peptide antigens:
  • VCX3A protein (A0JNS4_HUMAN)
  • VCX3A protein (Q3SXR8_HUMAN)
  • Variable charge, X-linked 3A (Q4V756_HUMAN)
  • Variably charged protein X-A (VCX3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NNX9

UniProtKB/Swiss-Prot:

VCX3_HUMAN :
  • Belongs to the VCX/VCY family.
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 From GWAS Catalog for VCX3A Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VCX3A

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 VCX3A Gene

Localization for VCX3A Gene

Subcellular locations from

COMPARTMENTS
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
endosome 1
cytosol 1

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

PathCards logo

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 IBA,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

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VCX3A

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

No ASD Table

Relevant External Links for VCX3A Gene

GeneLoc Exon Structure for
VCX3A

Expression for VCX3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VCX3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

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

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VCX3A

SOURCE GeneReport for Unigene cluster for VCX3A Gene:

Hs.170076

mRNA Expression by UniProt/SwissProt for VCX3A Gene:

Q9NNX9-VCX3_HUMAN
Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCX3A: view

Primer Products

No data available for 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

ENSEMBL:
Gene Tree for VCX3A (if available)
TreeFam:
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:

  • VCX3_HUMAN
  • A0JNS4_HUMAN
  • E7ESE9_HUMAN
  • Q3SXR8_HUMAN
  • Q4V756_HUMAN
genes like me logo Genes that share paralogs with VCX3A: view

Variants for VCX3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VCX3A Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs139657007 Benign: not specified 6,533,921(-) G/C MISSENSE_VARIANT
rs143802324 Likely Benign: not specified 6,533,845(-) A/G MISSENSE_VARIANT
rs35874450 Benign: not specified 6,533,828(-) C/T MISSENSE_VARIANT
rs72609545 Benign: not specified 6,533,888(-) C/T MISSENSE_VARIANT
rs779109893 Uncertain Significance: not provided 6,533,889(-) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for VCX3A Gene

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

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

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)
VCX3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VCX3A

SNP Genotyping and Copy Number Assay Products

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

Disorders for VCX3A Gene

MalaCards: The human disease database

(7) MalaCards diseases for VCX3A Gene - From: DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search VCX3A in MalaCards View complete list of genes associated with diseases
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 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 23
  2. 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
  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 23
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  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

Products for VCX3A Gene

Sources for VCX3A Gene