nih-gov/www.ncbi.nlm.nih.gov/omim/400012

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Entry
- *400012 - VARIABLY CHARGED, Y CHROMOSOME; VCY
- OMIM
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<span class="h4">*400012</span>
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<strong>Table of Contents</strong>
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<a href="#description">Description</a>
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<a href="#cloning">Cloning and Expression</a>
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<a href="#geneFamily">Gene Family</a>
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<a href="#geneFunction">Gene Function</a>
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<a href="#geneStructure">Gene Structure</a>
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<a href="#mapping">Mapping</a>
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<a href="#molecularGenetics">Molecular Genetics</a>
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<a href="#references"><strong>References</strong></a>
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<div><a href="https://hprd.org/summary?hprd_id=02453&isoform_id=02453_1&isoform_name=Isoform_1" class="mim-tip-hint" title="The Human Protein Reference Database; manually extracted and visually depicted information on human proteins." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HPRD', 'domain': 'hprd.org'})">HPRD</a></div>
<div><a href="https://www.proteinatlas.org/search/VCY" class="mim-tip-hint" title="The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HumanProteinAtlas', 'domain': 'proteinatlas.org'})">Human Protein Atlas</a></div>
<div><a href="https://www.ncbi.nlm.nih.gov/protein/2580544,4759304,5915799,6094644,68532511" class="mim-tip-hint" title="NCBI protein data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Protein', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Protein</a></div>
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<div><a href="http://biogps.org/#goto=genereport&id=9084" class="mim-tip-hint" title="The Gene Portal Hub; customizable portal of gene and protein function information." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'BioGPS', 'domain': 'biogps.org'})">BioGPS</a></div>
<div><a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000129864;t=ENST00000250825" class="mim-tip-hint" title="Orthologs, paralogs, regulatory regions, and splice variants." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl</a></div>
<div><a href="https://www.genecards.org/cgi-bin/carddisp.pl?gene=VCY" class="mim-tip-hint" title="The Human Genome Compendium; web-based cards integrating automatically mined information on human genes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GeneCards', 'domain': 'genecards.org'})">GeneCards</a></div>
<div><a href="http://amigo.geneontology.org/amigo/search/annotation?q=VCY" class="mim-tip-hint" title="Terms, defined using controlled vocabulary, representing gene product properties (biologic process, cellular component, molecular function) across species." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GeneOntology', 'domain': 'amigo.geneontology.org'})">Gene Ontology</a></div>
<div><a href="https://www.genome.jp/dbget-bin/www_bget?hsa+9084" class="mim-tip-hint" title="Kyoto Encyclopedia of Genes and Genomes; diagrams of signaling pathways." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'KEGG', 'domain': 'genome.jp'})">KEGG</a></div>
<dd><a href="http://v1.marrvel.org/search/gene/VCY" class="mim-tip-hint" title="Model organism Aggregated Resources for Rare Variant ExpLoration." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MARRVEL', 'domain': 'marrvel.org'})">MARRVEL</a></dd>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgGene?db=hg38&hgg_chrom=chrY&hgg_gene=ENST00000250825.5&hgg_start=13985772&hgg_end=13986473&hgg_type=knownGene" class="mim-tip-hint" title="UCSC Genome Bioinformatics; gene-specific structure and function information with links to other databases." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC', 'domain': 'genome.ucsc.edu'})">UCSC</a></div>
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<div><a href="https://www.gwascentral.org/search?q=VCY" class="mim-tip-hint" title="GWAS Central; summary level genotype-to-phenotype information from genetic association studies." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GWAS Central', 'domain': 'gwascentral.org'})">GWAS Central&nbsp;</a></div>
<div><a href="https://evs.gs.washington.edu/EVS/PopStatsServlet?searchBy=Gene+Hugo&target=VCY&upstreamSize=0&downstreamSize=0&x=0&y=0" class="mim-tip-hint" title="National Heart, Lung, and Blood Institute Exome Variant Server." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NHLBI EVS', 'domain': 'evs.gs.washington.edu'})">NHLBI EVS</a></div>
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<div><a href="http://v1.marrvel.org/search/gene/VCY#HomologGenesPanel" class="mim-tip-hint" title="Model organism Aggregated Resources for Rare Variant ExpLoration." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MARRVEL', 'domain': 'marrvel.org'})">MARRVEL</a></div>
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<div><a href="https://www.orthodb.org/?ncbi=9084" class="mim-tip-hint" title="Hierarchical catalogue of orthologs." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'OrthoDB', 'domain': 'orthodb.org'})">OrthoDB</a></div>
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<div><a href="https://reactome.org/content/query?q=VCY&species=Homo+sapiens&types=Reaction&types=Pathway&cluster=true" class="definition" title="Protein-specific information in the context of relevant cellular pathways." target="_blank" onclick="gtag('event', 'mim_outbound', {{'name': 'Reactome', 'domain': 'reactome.org'}})">Reactome</a></div>
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<span class="h3">
<span class="mim-font mim-tip-hint" title="Gene description">
<span class="text-danger"><strong>*</strong></span>
400012
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<a id="preferredTitle" class="mim-anchor"></a>
<h3>
<span class="mim-font">
VARIABLY CHARGED, Y CHROMOSOME; VCY
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<em>Alternative titles; symbols</em>
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VCY1<br />
BASIC PROTEIN, Y CHROMOSOME, 1; BPY1
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<strong><em>HGNC Approved Gene Symbol: <a href="https://www.genenames.org/tools/search/#!/genes?query=VCY" class="mim-tip-hint" title="HUGO Gene Nomenclature Committee." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HGNC', 'domain': 'genenames.org'})">VCY</a></em></strong>
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Cytogenetic location: <a href="/geneMap/Y/28?start=-3&limit=10&highlight=28">Yq11.221</a>
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Genomic coordinates <span class="small">(GRCh38)</span> : <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chrY:13985772-13986473&dgv=pack&knownGene=pack&omimGene=pack" class="mim-tip-hint" title="UCSC Genome Browser; reference sequences and working draft assemblies for a large collection of genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UCSC Genome Browser', 'domain': 'genome.ucsc.edu'})">Y:13,985,772-13,986,473</a> </span>
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<a href="https://www.ncbi.nlm.nih.gov/" target="_blank" class="small"> (from NCBI) </a>
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<strong>TEXT</strong>
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<strong>Description</strong>
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<p>Members of the variably charged X/Y (VCX/Y) gene family, such as VCY, are expressed exclusively in male germ cells and are located on the X and Y chromosomes (<a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page, 2000</a>). <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<strong>Cloning and Expression</strong>
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<p>Ninety-five percent of the length of the human Y chromosome is composed of the nonrecombining portion, or NRY. To identify genes located in the NRY, <a href="#2" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;Functional coherence of the human Y chromosome.&lt;/strong&gt; Science 278: 675-680, 1997.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/9381176/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;9381176&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1126/science.278.5338.675&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="9381176">Lahn and Page (1997)</a> isolated testis cDNAs that hybridized specifically to Y-chromosomal DNA. The authors identified 7 novel genes, BPY1, BPY2 (<a href="/entry/400013">400013</a>), CDY (<a href="/entry/400016">400016</a>), PRY (<a href="/entry/400019">400019</a>), TTY1, TTY2, and XKRY (<a href="/entry/400015">400015</a>), that appeared to exist in multiple copies on the Y chromosome and were expressed specifically in testis. Transcripts from the TTY1 (testis transcript on Y, gene 1) and TTY2 genes did not contain a significant open reading frame. <a href="#2" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;Functional coherence of the human Y chromosome.&lt;/strong&gt; Science 278: 675-680, 1997.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/9381176/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;9381176&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1126/science.278.5338.675&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="9381176">Lahn and Page (1997)</a> speculated that the selective advantage conferred by the NRY's retention and amplification of male fertility factors accounts for the multitude of testis-specific gene families there. The predicted BPY1 (basic protein on Y, gene 1) protein contains 125 amino acids and has a calculated pI of 9.4. Southern blot analysis indicated that a BPY1 homolog exists on the X chromosome; however, these authors did not isolate a cDNA corresponding to the X-linked gene. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p>By screening a human testis cDNA library with a VCY cDNA probe, <a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page (2000)</a> obtained several VCY-homologous sequences. Further analysis revealed 2 identical copies of VCY on the Y chromosome, VCY and VCY1B (<a href="/entry/400050">400050</a>), and multiple related copies on the X chromosome. VCY and VCY1B contain a 30-bp sequence that encodes a 10-amino acid motif rich in glutamic acid that is predicted to be highly negatively charged. Elsewhere in the 125-amino acid predicted VCY/VCY1B protein, an abundance of arg and lys residues creates a positive charge. Both VCY and VCX proteins resemble chromatin-associated proteins and contain putative N-terminal nuclear localization signals. Database analysis identified related sequences in primates, but not other animals. RT-PCR analysis suggested that VCY and VCX expression is restricted to male germ cells. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p>By immunohistochemical analysis of human testis, <a href="#5" class="mim-tip-reference" title="Zou, S. W., Zhang, J. C., Zhang, X. D., Miao, S. Y., Zong, S. D., Sheng, Q., Wang, L. F. &lt;strong&gt;Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis.&lt;/strong&gt; Cell Res. 13: 171-177, 2003.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/12862317/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;12862317&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1038/sj.cr.7290161&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="12862317">Zou et al. (2003)</a> found that VCY localized to nuclei of germ cells of seminiferous epithelium. Fluorescence-tagged VCX8R (VCX3A; <a href="/entry/300533">300533</a>) and VCY colocalized in nucleoli in transfected COS-7 cells. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=12862317" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<p><a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page (2000)</a> stated that approximately 12 X-Y homologous gene pairs were known to be located in the nonrecombining portions of the human sex chromosomes. These X-Y gene pairs fall into 2 categories. In the first category, both X and Y homologs are ubiquitously expressed. In the second category, the X homolog is ubiquitously expressed, whereas the Y homolog is expressed exclusively in the testis. <a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page (2000)</a> described a family of X-Y genes that cannot be assigned to either category. Designated VCX/Y, this gene family has multiple members on both X and Y, and all appear to be 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 is present only once in Y-linked members. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<div>
<a id="geneFunction" class="mim-anchor"></a>
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<strong>Gene Function</strong>
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<p>Using yeast 2-hybrid analysis, <a href="#5" class="mim-tip-reference" title="Zou, S. W., Zhang, J. C., Zhang, X. D., Miao, S. Y., Zong, S. D., Sheng, Q., Wang, L. F. &lt;strong&gt;Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis.&lt;/strong&gt; Cell Res. 13: 171-177, 2003.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/12862317/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;12862317&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1038/sj.cr.7290161&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="12862317">Zou et al. (2003)</a> found that VCY interacted with acidic ribosomal protein P0 (RPLP0; <a href="/entry/180510">180510</a>). <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=12862317" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<div>
<a id="geneStructure" class="mim-anchor"></a>
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<strong>Gene Structure</strong>
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<p><a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page (2000)</a> determined that the VCY gene contains 2 exons. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<div>
<a id="mapping" class="mim-anchor"></a>
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<strong>Mapping</strong>
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<span class="mim-text-font">
<p>By analysis of a panel of partial Y chromosomes, <a href="#2" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;Functional coherence of the human Y chromosome.&lt;/strong&gt; Science 278: 675-680, 1997.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/9381176/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;9381176&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1126/science.278.5338.675&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="9381176">Lahn and Page (1997)</a> mapped the BPY1 gene to region 5G on the long arm of the human Y chromosome. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p>By analysis of BAC clones, <a href="#3" class="mim-tip-reference" title="Lahn, B. T., Page, D. C. &lt;strong&gt;A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.&lt;/strong&gt; Hum. Molec. Genet. 9: 311-319, 2000.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/10607842/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;10607842&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1093/hmg/9.2.311&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="10607842">Lahn and Page (2000)</a> determined that the VCY and VCY1B genes are separated by no more than 140 kb on the Y chromosome. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p><p><a href="#1" class="mim-tip-reference" title="Hartz, P. A. &lt;strong&gt;Personal Communication.&lt;/strong&gt; Baltimore, Md. 8/25/2016."None>Hartz (2016)</a> mapped the VCY gene to chromosome Yq11.22 based on an alignment of the VCY sequence (GenBank <a href="https://www.ncbi.nlm.nih.gov/search/all/?term=AF000979" target="_blank" onclick="gtag(\'event\', \'mim_outbound\', {\'name\': \'GENBANK\', \'domain\': \'ncbi.nlm.nih.gov\'})">AF000979</a>) with the genomic sequence (GRCh38).</p>
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<a id="molecularGenetics" class="mim-anchor"></a>
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<strong>Molecular Genetics</strong>
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<div id="mimMolecularGeneticsFold" class="collapse in mimTextToggleFold">
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<p>Large inverted palindromic repeats that characterize the Y chromosome undergo high rates of structural variation. <a href="#4" class="mim-tip-reference" title="Shi, W., Massaia, A., Louzada, S., Handsaker, J., Chow, W., McCarthy, S., Collins, J., Hallast, P., Howe, K., Church, D. M., Yang, F., Xue, Y., Tyler-Smith, C. &lt;strong&gt;Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.&lt;/strong&gt; Genome Biol. 20: 207, 2019.[PubMed: &lt;a href=&quot;https://pubmed.ncbi.nlm.nih.gov/31610793/&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed&#x27;, &#x27;domain&#x27;: &#x27;pubmed.ncbi.nlm.nih.gov&#x27;})&quot;&gt;31610793&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/?term=31610793[PMID]&amp;report=imagesdocsum&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;name&#x27;: &#x27;PubMed Image&#x27;, &#x27;domain&#x27;: &#x27;ncbi.nlm.nih.gov&#x27;})&quot;&gt;images&lt;/a&gt;] [&lt;a href=&quot;https://doi.org/10.1186/s13059-019-1816-y&quot; target=&quot;_blank&quot; onclick=&quot;gtag(&#x27;event&#x27;, &#x27;mim_outbound&#x27;, {&#x27;destination&#x27;: &#x27;Publisher&#x27;})&quot;&gt;Full Text&lt;/a&gt;]" pmid="31610793">Shi et al. (2019)</a> studied 1 such palindrome containing 2 copies of the VCY gene and found that healthy males can have 1 to 4 copies of VCY due to such complex structural variation. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=31610793" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})"><span class="glyphicon glyphicon-plus-sign mim-tip-hint" title="Click this 'reference-plus' icon to see articles related to this paragraph in PubMed."></span></a></p>
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<a id="references"class="mim-anchor"></a>
<h4 href="#mimReferencesFold" id="mimReferencesToggle" class="mimTriangleToggle" style="cursor: pointer;" data-toggle="collapse">
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<span id="mimReferencesToggleTriangle" class="small mimTextToggleTriangle">&#9660;</span>
<strong>REFERENCES</strong>
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<div id="mimReferencesFold" class="collapse in mimTextToggleFold">
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<a id="1" class="mim-anchor"></a>
<a id="Hartz2016" class="mim-anchor"></a>
<div class="">
<p class="mim-text-font">
Hartz, P. A.
<strong>Personal Communication.</strong>
Baltimore, Md. 8/25/2016.
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<a id="2" class="mim-anchor"></a>
<a id="Lahn1997" class="mim-anchor"></a>
<div class="">
<p class="mim-text-font">
Lahn, B. T., Page, D. C.
<strong>Functional coherence of the human Y chromosome.</strong>
Science 278: 675-680, 1997.
[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/9381176/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">9381176</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=9381176" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
[<a href="https://doi.org/10.1126/science.278.5338.675" target="_blank">Full Text</a>]
</p>
</div>
</li>
<li>
<a id="3" class="mim-anchor"></a>
<a id="Lahn2000" class="mim-anchor"></a>
<div class="">
<p class="mim-text-font">
Lahn, B. T., Page, D. C.
<strong>A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.</strong>
Hum. Molec. Genet. 9: 311-319, 2000.
[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/10607842/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">10607842</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=10607842" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
[<a href="https://doi.org/10.1093/hmg/9.2.311" target="_blank">Full Text</a>]
</p>
</div>
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<li>
<a id="4" class="mim-anchor"></a>
<a id="Shi2019" class="mim-anchor"></a>
<div class="">
<p class="mim-text-font">
Shi, W., Massaia, A., Louzada, S., Handsaker, J., Chow, W., McCarthy, S., Collins, J., Hallast, P., Howe, K., Church, D. M., Yang, F., Xue, Y., Tyler-Smith, C.
<strong>Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.</strong>
Genome Biol. 20: 207, 2019.
[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/31610793/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">31610793</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=31610793[PMID]&report=imagesdocsum" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Image', 'domain': 'ncbi.nlm.nih.gov'})">images</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=31610793" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
[<a href="https://doi.org/10.1186/s13059-019-1816-y" target="_blank">Full Text</a>]
</p>
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<a id="5" class="mim-anchor"></a>
<a id="Zou2003" class="mim-anchor"></a>
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<p class="mim-text-font">
Zou, S. W., Zhang, J. C., Zhang, X. D., Miao, S. Y., Zong, S. D., Sheng, Q., Wang, L. F.
<strong>Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis.</strong>
Cell Res. 13: 171-177, 2003.
[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/12862317/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">12862317</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=12862317" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
[<a href="https://doi.org/10.1038/sj.cr.7290161" target="_blank">Full Text</a>]
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<a id="contributors" class="mim-anchor"></a>
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<a href="#mimCollapseContributors" role="button" data-toggle="collapse"> Contributors: </a>
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
<span class="mim-text-font">
Alan F. Scott - updated : 01/11/2022
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<span class="mim-text-font">
Patricia A. Hartz - updated : 08/25/2016<br>Victor A. McKusick - updated : 2/23/2000
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Creation Date:
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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Rebekah S. Rasooly : 4/27/1999
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<a href="#mimCollapseEditHistory" role="button" data-toggle="collapse"> Edit History: </a>
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<span class="mim-text-font">
mgross : 01/11/2022
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mgross : 08/25/2016<br>mgross : 04/10/2009<br>mgross : 2/24/2003<br>alopez : 2/25/2000<br>alopez : 2/24/2000<br>terry : 2/23/2000<br>alopez : 4/28/1999<br>alopez : 4/27/1999
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<strong>*</strong> 400012
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VARIABLY CHARGED, Y CHROMOSOME; VCY
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<em>Alternative titles; symbols</em>
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VCY1<br />
BASIC PROTEIN, Y CHROMOSOME, 1; BPY1
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<strong><em>HGNC Approved Gene Symbol: VCY</em></strong>
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<strong>
<em>
Cytogenetic location: Yq11.221
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Genomic coordinates <span class="small">(GRCh38)</span> : Y:13,985,772-13,986,473 </span>
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</strong>
<span class="small">(from NCBI)</span>
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<strong>TEXT</strong>
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<strong>Description</strong>
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<p>Members of the variably charged X/Y (VCX/Y) gene family, such as VCY, are expressed exclusively in male germ cells and are located on the X and Y chromosomes (Lahn and Page, 2000). </p>
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<strong>Cloning and Expression</strong>
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<p>Ninety-five percent of the length of the human Y chromosome is composed of the nonrecombining portion, or NRY. To identify genes located in the NRY, Lahn and Page (1997) isolated testis cDNAs that hybridized specifically to Y-chromosomal DNA. The authors identified 7 novel genes, BPY1, BPY2 (400013), CDY (400016), PRY (400019), TTY1, TTY2, and XKRY (400015), that appeared to exist in multiple copies on the Y chromosome and were expressed specifically in testis. Transcripts from the TTY1 (testis transcript on Y, gene 1) and TTY2 genes did not contain a significant open reading frame. Lahn and Page (1997) speculated that the selective advantage conferred by the NRY's retention and amplification of male fertility factors accounts for the multitude of testis-specific gene families there. The predicted BPY1 (basic protein on Y, gene 1) protein contains 125 amino acids and has a calculated pI of 9.4. Southern blot analysis indicated that a BPY1 homolog exists on the X chromosome; however, these authors did not isolate a cDNA corresponding to the X-linked gene. </p><p>By screening a human testis cDNA library with a VCY cDNA probe, Lahn and Page (2000) obtained several VCY-homologous sequences. Further analysis revealed 2 identical copies of VCY on the Y chromosome, VCY and VCY1B (400050), and multiple related copies on the X chromosome. VCY and VCY1B contain a 30-bp sequence that encodes a 10-amino acid motif rich in glutamic acid that is predicted to be highly negatively charged. Elsewhere in the 125-amino acid predicted VCY/VCY1B protein, an abundance of arg and lys residues creates a positive charge. Both VCY and VCX proteins resemble chromatin-associated proteins and contain putative N-terminal nuclear localization signals. Database analysis identified related sequences in primates, but not other animals. RT-PCR analysis suggested that VCY and VCX expression is restricted to male germ cells. </p><p>By immunohistochemical analysis of human testis, Zou et al. (2003) found that VCY localized to nuclei of germ cells of seminiferous epithelium. Fluorescence-tagged VCX8R (VCX3A; 300533) and VCY colocalized in nucleoli in transfected COS-7 cells. </p>
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<strong>Gene Family</strong>
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<p>Lahn and Page (2000) stated that approximately 12 X-Y homologous gene pairs were known to be located in the nonrecombining portions of the human sex chromosomes. These X-Y gene pairs fall into 2 categories. In the first category, both X and Y homologs are ubiquitously expressed. In the second category, the X homolog is ubiquitously expressed, whereas the Y homolog is expressed exclusively in the testis. Lahn and Page (2000) described a family of X-Y genes that cannot be assigned to either category. Designated VCX/Y, this gene family has multiple members on both X and Y, and all appear to be 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 is present only once in Y-linked members. </p>
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<strong>Gene Function</strong>
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<p>Using yeast 2-hybrid analysis, Zou et al. (2003) found that VCY interacted with acidic ribosomal protein P0 (RPLP0; 180510). </p>
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<strong>Gene Structure</strong>
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<p>Lahn and Page (2000) determined that the VCY gene contains 2 exons. </p>
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<strong>Mapping</strong>
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<p>By analysis of a panel of partial Y chromosomes, Lahn and Page (1997) mapped the BPY1 gene to region 5G on the long arm of the human Y chromosome. </p><p>By analysis of BAC clones, Lahn and Page (2000) determined that the VCY and VCY1B genes are separated by no more than 140 kb on the Y chromosome. </p><p>Hartz (2016) mapped the VCY gene to chromosome Yq11.22 based on an alignment of the VCY sequence (GenBank AF000979) with the genomic sequence (GRCh38).</p>
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<strong>Molecular Genetics</strong>
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<p>Large inverted palindromic repeats that characterize the Y chromosome undergo high rates of structural variation. Shi et al. (2019) studied 1 such palindrome containing 2 copies of the VCY gene and found that healthy males can have 1 to 4 copies of VCY due to such complex structural variation. </p>
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<strong>REFERENCES</strong>
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<ol>
<li>
<p class="mim-text-font">
Hartz, P. A.
<strong>Personal Communication.</strong>
Baltimore, Md. 8/25/2016.
</p>
</li>
<li>
<p class="mim-text-font">
Lahn, B. T., Page, D. C.
<strong>Functional coherence of the human Y chromosome.</strong>
Science 278: 675-680, 1997.
[PubMed: 9381176]
[Full Text: https://doi.org/10.1126/science.278.5338.675]
</p>
</li>
<li>
<p class="mim-text-font">
Lahn, B. T., Page, D. C.
<strong>A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.</strong>
Hum. Molec. Genet. 9: 311-319, 2000.
[PubMed: 10607842]
[Full Text: https://doi.org/10.1093/hmg/9.2.311]
</p>
</li>
<li>
<p class="mim-text-font">
Shi, W., Massaia, A., Louzada, S., Handsaker, J., Chow, W., McCarthy, S., Collins, J., Hallast, P., Howe, K., Church, D. M., Yang, F., Xue, Y., Tyler-Smith, C.
<strong>Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.</strong>
Genome Biol. 20: 207, 2019.
[PubMed: 31610793]
[Full Text: https://doi.org/10.1186/s13059-019-1816-y]
</p>
</li>
<li>
<p class="mim-text-font">
Zou, S. W., Zhang, J. C., Zhang, X. D., Miao, S. Y., Zong, S. D., Sheng, Q., Wang, L. F.
<strong>Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis.</strong>
Cell Res. 13: 171-177, 2003.
[PubMed: 12862317]
[Full Text: https://doi.org/10.1038/sj.cr.7290161]
</p>
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Alan F. Scott - updated : 01/11/2022<br>Patricia A. Hartz - updated : 08/25/2016<br>Victor A. McKusick - updated : 2/23/2000
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