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 im... See more...

Aliases for VCX2 Gene

Aliases for VCX2 Gene

  • Variable Charge X-Linked 2 2 3 5
  • VCX-2r 2 3 4
  • Variable Charge Protein On X With Two Repeats 3 4
  • Variable Charge X-Linked Protein 2 3 4
  • Variably Charged Protein X-B 3 4
  • VCX2R 3 4
  • VCXB 3 4
  • Variably Charged, X Chromosome, With 2 Repeats 3
  • Variably Charged, X Chromosome 2 3
  • Variably Charged, X Chromosome B 3
  • VCX-2R 2
  • VCX-B 4
  • VCX2 5

External Ids for VCX2 Gene

Previous GeneCards Identifiers for VCX2 Gene

  • GC0XM007550
  • GC0XM007947
  • GC0XM008097
  • 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 cognitive disability. [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 Ichthyosis. An important paralog of this gene is VCX.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for VCX2 Gene

Genomics for VCX2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VCX2 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
GH0XJ008170 Promoter 0.3 EPDnew 600.7 +0.6 571 0.1 LOC107985676 VCX2 piR-52430-003 ENSG00000285679 LOC107985675 PNPLA4
GH0XJ008067 Enhancer 0.8 Ensembl ENCODE 7.3 +103.4 103366 0.6 JUND PKNOX1 TCF7L2 CEBPB FOS JUN FOSL1 EP300 FOXA1 ZHX1 VCX2 lnc-VCX2-1 piR-58484 LOC107985675 PNPLA4 ENSG00000285679
GH0XJ008082 Enhancer 0.4 Ensembl ENCODE 8.1 +87.6 87566 2.2 RCOR1 lnc-VCX2-1 VCX2 piR-39098-285 ENSG00000285679 LOC107985675 PNPLA4
GH0XJ008404 Enhancer 0.4 Ensembl ENCODE 5.4 -233.4 -233379 1.5 NFIB VCX2 piR-56075 HSALNG0136556 VCX3B ENSG00000285679 LOC107985675
GH0XJ008191 Enhancer 0.7 Ensembl ENCODE 0.4 -19.9 -19934 0.8 CREB1 FOXA1 CTBP1 MBD2 GATA3 DPF2 JUND FOSL2 MAZ FOS MIR651 VCX2 LOC107985676 piR-47211-684 ENSG00000285679 LOC107985675 VCX3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VCX2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VCX2

Top Transcription factor binding sites by QIAGEN in the VCX2 gene promoter:
  • FOXF2
  • FOXO1
  • FOXO1a

Genomic Locations for VCX2 Gene

Genomic Locations for VCX2 Gene
chrX:8,169,944-8,171,267
(GRCh38/hg38)
Size:
1,324 bases
Orientation:
Minus strand
chrX:8,137,985-8,139,308
(GRCh37/hg19)
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 StructureGene Density

RefSeq DNA sequence for VCX2 Gene

Proteins for VCX2 Gene

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

Protein Domains for VCX2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VCX2 Gene

GenScript: Design optimal peptide antigens:
  • VCX2 protein (Q3SXQ9_HUMAN)
  • VCX2 protein (Q3SXR9_HUMAN)
  • VCX2 protein (Q4V780_HUMAN)
  • Variably charged protein X-B (VCX2_HUMAN)

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

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VCX2

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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 0
cytoskeleton 0
mitochondrion 0
cytosol 0

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 and Subcellular locations from the Human Protein Atlas (HPA) for VCX2 Gene

Pathways & Interactions for VCX2 Gene

PathCards logo

SuperPathways for VCX2 Gene

No Data Available

Interacting Proteins for VCX2 Gene

Gene Ontology (GO) - Biological Process for VCX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IBA 21873635
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

No Compound Related Data Available

Transcripts for VCX2 Gene

mRNA/cDNA for VCX2 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
1 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 VCX2

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

No ASD Table

Relevant External Links for VCX2 Gene

GeneLoc Exon Structure for
VCX2

Expression for VCX2 Gene

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

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

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 30
  • 95.66 (n)
VCX2 31
  • 87 (a)
OneToOne
Species where no ortholog for VCX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for VCX2: view image

Paralogs for VCX2 Gene

Paralogs for VCX2 Gene

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

  • VCX2_HUMAN
  • Q3SXQ9_HUMAN
  • Q3SXR9_HUMAN
  • Q4V780_HUMAN
genes like me logo Genes that share paralogs with VCX2: view

Variants for VCX2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VCX2 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
769171 Likely Benign: not provided 8,170,119(-) T/C SYNONYMOUS_VARIANT
769172 Benign: not provided 8,170,129(-) C/G MISSENSE_VARIANT
rs1058237 - p.Val110Leu
rs1058239 - p.Thr138Ser
rs41305169 - p.Leu104Pro

Additional dbSNP identifiers (rs#s) for VCX2 Gene

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)

Additional Variant Information for VCX2 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for VCX2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
ichthyosis, x-linked
  • xli
ichthyosis
  • ichthyoses
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards
Search VCX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 BT … Page DC (Human molecular genetics 2000) 2 3 4
  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 SA … González-Huerta LM (The British journal of dermatology 2008) 3 23
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  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 GA (American journal of human genetics 2000) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for VCX2 Gene

Sources for VCX2 Gene