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Aliases for VCY Gene

Aliases for VCY Gene

  • Variable Charge, Y-Linked 2 3 5
  • Variable Charge, Y Chromosome 2 3
  • Variably Charged Protein Y 3 4
  • Basic Charge, Y-Linked 1 3 4
  • VCY1A 3 4
  • BPY1 3 4
  • Testis-Specific Basic Protein On Y, 1 3
  • Testis-Specific Basic Protein Y 1 3
  • Basic Protein On Y Chromosome, 1 3
  • VCY VCY1B 4
  • BPY1B 4
  • VCY1 3

External Ids for VCY Gene

Previous GeneCards Identifiers for VCY Gene

  • GC0YP015485
  • GC0YM015407
  • GC0YM015106
  • GC0YP014607
  • GC0YP014678
  • GC0YP016169
  • GC0YM010741
  • GC0YM016098

Summaries for VCY Gene

Entrez Gene Summary for VCY Gene

  • The protein encoded by this gene is a member of a family of human VCX/Y genes. This gene family has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. Members of the VCX/Y family 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. VCX/Y genes encode small and highly charged proteins of unknown function. This gene encodes a small, positively charged protein. The presence of a putative bipartite nuclear localization signal suggests that this gene encodes a nuclear protein. The genome has two identical copies of this gene within a palindromic region; this record represents the more centromeric copy. [provided by RefSeq, Jul 2008]

GeneCards Summary for VCY Gene

VCY (Variable Charge, Y-Linked) is a Protein Coding gene. Diseases associated with VCY include Spermatogenic Failure, Y-Linked, 2 and Chronic Laryngitis. An important paralog of this gene is VCY1B.

UniProtKB/Swiss-Prot for VCY Gene

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

Additional gene information for VCY Gene

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

Genomics for VCY Gene

GeneHancer (GH) Regulatory Elements for VCY Gene

Promoters and enhancers for VCY Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0YI013986 Promoter 0.5 EPDnew 550.8 +0.0 20 0.1 VCY GC0YP013878
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VCY on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for VCY Gene

Genomic Locations for VCY Gene
742 bases
Minus strand

Genomic View for VCY Gene

Genes around VCY on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for VCY Gene

Proteins for VCY Gene

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

    Protein Symbol:
    Recommended name:
    Testis-specific basic protein Y 1
    Protein Accession:

    Protein attributes for VCY Gene

    125 amino acids
    Molecular mass:
    12917 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VCY Gene

Post-translational modifications for VCY Gene

No Post-translational modifications

Other Protein References for VCY Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VCY Gene

Domains & Families for VCY Gene

Gene Families for VCY Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCY Gene


Suggested Antigen Peptide Sequences for VCY Gene

GenScript: Design optimal peptide antigens:

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 VCY: view

Function for VCY Gene

Molecular function for VCY Gene

GENATLAS Biochemistry:
variable charge X/Y,basic protein on chromosome Y,1,testis specific,in a AZF deleted region
UniProtKB/Swiss-Prot Function:
May mediate a process in spermatogenesis or may play a role in sex ratio distortion.

Phenotypes for VCY Gene

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

Human Phenotype Ontology for VCY Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Localization for VCY Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for VCY Gene

Pathways & Interactions for VCY Gene

No Data Available

Interacting Proteins for VCY Gene

Selected Interacting proteins: O14598-VCY1_HUMAN for VCY Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for VCY Gene

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

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

Drugs & Compounds for VCY Gene

No Compound Related Data Available

Transcripts for VCY Gene

mRNA/cDNA for VCY Gene

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

Unigene Clusters for VCY Gene

Variable charge, Y-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for VCY Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCY Gene

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

Protein differential expression in normal tissues from HIPED for VCY Gene

This gene is overexpressed in Ovary (38.6) and Testis (30.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VCY Gene

Protein tissue co-expression partners for VCY Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VCY Gene:


SOURCE GeneReport for Unigene cluster for VCY Gene:


mRNA Expression by UniProt/SwissProt for VCY Gene:

Tissue specificity: Expressed exclusively in testis.
genes like me logo Genes that share expression patterns with VCY: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for VCY Gene

Orthologs for VCY Gene

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

Orthologs for VCY Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC742075 33
  • 95.69 (n)
Species where no ortholog for VCY 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 VCY Gene

Gene Tree for VCY (if available)
Gene Tree for VCY (if available)

Paralogs for VCY Gene

Paralogs for VCY Gene

(5) SIMAP similar genes for VCY Gene using alignment to 2 proteins:

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

Variants for VCY Gene

Sequence variations from dbSNP and Humsavar for VCY Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs111715503 -- 13,985,622(-) C/T downstream_transcript_variant
rs112070685 -- 13,985,519(-) G/T downstream_transcript_variant
rs113518653 -- 13,988,144(-) A/G upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv2552e212 CNV gain 25503493
nsv469834 CNV gain 16826518

Additional Variant Information for VCY Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for VCY Gene

Disorders for VCY Gene

MalaCards: The human disease database

(2) MalaCards diseases for VCY Gene - From: GTR and DISEASES

Disorder Aliases PubMed IDs
spermatogenic failure, y-linked, 2
  • spgfy2
chronic laryngitis
- elite association - COSMIC cancer census association via MalaCards
Search VCY in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with VCY: view

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

Publications for VCY Gene

  1. Functional coherence of the human Y chromosome. (PMID: 9381176) Lahn BT … Page DC (Science (New York, N.Y.) 1997) 2 3 4 58
  2. 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 58
  3. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PMID: 12815422) Skaletsky H … Page DC (Nature 2003) 3 4 58
  4. A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets. (PMID: 24970476) Taguchi A … Hanash SM (Cancer research 2014) 3 58
  5. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. (PMID: 21244100) Virok DP … Fülöp L (Journal of proteome research 2011) 3 58

Products for VCY Gene

Sources for VCY Gene

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