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VCX2 Gene(Protein Coding)

Variable Charge, X-Linked 2

GCID:
GC0XM008097
GIFtS:
42
Genes Participants
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Aliases for VCX2 Gene

Aliases for VCX2 Gene

  • Variable Charge, X-Linked 2 2 3 5
  • Variable Charge Protein On X With Two Repeats 3 4
  • Variably Charged Protein X-B 3 4
  • VCX-2r 3 4
  • VCX2R 3 4
  • VCXB 3 4
  • Variably Charged, X Chromosome, With 2 Repeats 3
  • Variable Charge X-Linked Protein 2 3
  • Variably Charged, X Chromosome 2 3
  • Variably Charged, X Chromosome B 3
  • VCX-B 4

External Ids for VCX2 Gene

Previous GeneCards Identifiers for VCX2 Gene

  • GC0XM007550
  • GC0XM007947
  • GC0XM005966

Summaries for VCX2 Gene

Entrez Gene Summary for VCX2 Gene

  • This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes that are expressed exclusively in male germ cells. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. This gene contains two copies of a 30 nt tandem repeat. Deletion of a nearby member of this family was implicated in mental retardation. [provided by RefSeq, Feb 2015]

GeneCards Summary for VCX2 Gene

VCX2 (Variable Charge, X-Linked 2) is a Protein Coding gene. Diseases associated with VCX2 include Ichthyosis, X-Linked and Non-Syndromic X-Linked Intellectual Disability. An important paralog of this gene is VCX3A.

UniProtKB/Swiss-Prot for VCX2 Gene

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

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCX2 Gene

Genomics for VCX2 Gene

Products:

  1. Regulatory Element

Regulatory Elements for VCX2 Gene

Enhancers for VCX2 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
GH0XG008191 0.7 ENCODE 0.4 -19.9 -19898 0.2 MAZ MNT DPF2 FOXA1 MBD2 JUND GATA3 CTBP1 CREB1 FOSL2 MIR651 VCX2 PIR50074
GH0XG008204 0.4 ENCODE 0.3 -33.2 -33168 0.2 GATA3 TCF7L2 VCX3B VCX2 PIR50074
GH0XG008273 0.7 ENCODE 0.1 -102.4 -102428 0.2 JUN USF2 CEBPB EP300 RFX5 GATA3 JUND GATA2 STAT3 RCOR1 VCX2 PIR50074
GH0XG008201 0.2 ENCODE 0.3 -30.7 -30724 1.4 VCX2 PIR50074
GH0XG008342 0.4 ENCODE 0.1 -171.1 -171088 0.2 FOS EGR2 ANOS1 PIR50074 VCX2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VCX2 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the VCX2 gene promoter:

Genomic Location for VCX2 Gene

Chromosome:
X
Start:
8,169,944 bp from pter
End:
8,171,267 bp from pter
Size:
1,324 bases
Orientation:
Minus strand

Genomic View for VCX2 Gene

Genes around VCX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCX2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VCX2 Gene

Proteins for VCX2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for VCX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H322-VCX2_HUMAN
    Recommended name:
    Variable charge X-linked protein 2
    Protein Accession:
    Q9H322
    Secondary Accessions:
    • A3KPB6
    • Q4V9T2
    • Q9P0H5

    Protein attributes for VCX2 Gene

    Size:
    139 amino acids
    Molecular mass:
    14661 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VCX2 Gene

Post-translational modifications for VCX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VCX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VCX2 Gene

Domains & Families for VCX2 Gene

Gene Families for VCX2 Gene

HGNC:

Protein Domains for VCX2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VCX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H322

UniProtKB/Swiss-Prot:

VCX2_HUMAN :
  • Belongs to the VCX/VCY family.
Family:
  • Belongs to the VCX/VCY family.
genes like me logo Genes that share domains with VCX2: view

Function for VCX2 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for VCX2 Gene

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

Gene Ontology (GO) - Molecular Function for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with VCX2: view

Phenotypes for VCX2 Gene

GenomeRNAi human phenotypes for VCX2:
genes like me logo Genes that share phenotypes with VCX2: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VCX2 Gene

Localization for VCX2 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 VCX2 gene
Compartment Confidence
nucleus 3
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with VCX2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for VCX2 Gene

Pathways & Interactions for VCX2 Gene

SuperPathways for VCX2 Gene

PathCards logo More details on SuperPathways for VCX2
No Data Available

Interacting Proteins for VCX2 Gene

Selected Interacting proteins: Q9H322-VCX2_HUMAN for VCX2 Gene via IID

Symbol External ID(s) Details
STS

Gene Ontology (GO) - Biological Process for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IBA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with VCX2: view

No data available for Pathways by source and SIGNOR curated interactions for VCX2 Gene

Drugs & Compounds for VCX2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for VCX2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for VCX2 Gene

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

Unigene Clusters for VCX2 Gene

Variable charge, X-linked 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCX2 Gene

No ASD Table

Relevant External Links for VCX2 Gene

GeneLoc Exon Structure for
VCX2
ECgene alternative splicing isoforms for
VCX2

Expression for VCX2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VCX2 Gene

mRNA expression in normal human tissues for VCX2 Gene
mRNA expression by BioGPS for VCX2 GenemRNA expression by GTEx for VCX2 Gene

mRNA differential expression in normal tissues according to GTEx for VCX2 Gene

This gene is overexpressed in Testis (x52.7).

NURSA nuclear receptor signaling pathways regulating expression of VCX2 Gene:

VCX2

SOURCE GeneReport for Unigene cluster for VCX2 Gene:

Hs.279737

mRNA Expression by UniProt/SwissProt for VCX2 Gene:

Q9H322-VCX2_HUMAN
Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCX2: 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 , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for VCX2 Gene

Orthologs for VCX2 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for VCX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia LOC742075 34
  • 95.66 (n)
VCX2 35
  • 87 (a)
 OneToOne
Species where no ortholog for VCX2 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 VCX2 Gene

ENSEMBL:
Gene Tree for VCX2 (if available)
TreeFam:
Gene Tree for VCX2 (if available)

Paralogs for VCX2 Gene

Paralogs for VCX2 Gene

(5) SIMAP similar genes for VCX2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VCX2: view

Variants for VCX2 Gene

Sequence variations from dbSNP and Humsavar for VCX2 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1008750347 -- 8,171,279(+) TCACA(A/G)TTTTT intron-variant, upstream-variant-2KB
rs1008781271 -- 8,171,688(+) ATAAT(A/G)AGTTA intron-variant, upstream-variant-2KB
rs1013220331 -- 8,172,368(+) AACAA(C/T)CCTAA intron-variant, upstream-variant-2KB
rs1013299039 -- 8,172,553(+) CTACT(A/G)TATTA intron-variant, upstream-variant-2KB
rs1013380752 -- 8,170,866(+) GGGGG(-/T)GGTGA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VCX2 Gene

Variant ID Type Subtype PubMed ID
dgv2214e212 CNV gain 25503493
dgv4208n106 CNV deletion 24896259
dgv499n21 CNV gain 19592680
esv2752335 CNV gain 17911159
esv3576759 CNV gain 25503493
nsv470340 CNV gain 18288195
nsv508752 CNV insertion 20534489
nsv511081 OTHER complex 20534489
nsv524164 CNV gain 19592680
nsv528203 CNV gain 19592680
nsv6788 CNV insertion 18451855

Variation tolerance for VCX2 Gene

Gene Damage Index Score: 5.80; 73.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VCX2 Gene

Human Gene Mutation Database (HGMD)
VCX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VCX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCX2 Gene

Disorders for VCX2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VCX2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ichthyosis, x-linked
  • x-linked ichthyosis
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
- elite association - COSMIC cancer census association via MalaCards
Search VCX2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for VCX2

Genetic Association Database (GAD)
VCX2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VCX2
genes like me logo Genes that share disorders with VCX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VCX2 Gene

Publications for VCX2 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 64
  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 22 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 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. 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) 46 64

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Sources for VCX2 Gene

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