256 lines
26 KiB
XML
256 lines
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<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4206115/css/4121862/3974050/3917732/251717/4139921/3428953/14534/45193/4062871/4005757/4063811/613474/9685/4140220.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4206115/css/3529741/3348898/3529739.css" media="print" /><script type="text/javascript">
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<strong>Warning:</strong>
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The NCBI web site requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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<div id="dbvar-main-box"><div class="study_information"><div class="dbvar-info"><h3 id="studies">nstd139 (Luo et al. 2019)</h3><dl class="suminfo"><dt>Organism:</dt><dd><a href="/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606" title="Open Human in Taxonomy Browser">Human</a></dd><dt><span class="label">Study Type:</span></dt><dd>Case-Set</dd><dt><span class="label">Submitter:</span></dt><dd><a href="mailto:luotao@ncu.edu.cn" title="Send email to Tao Luo">Tao Luo</a></dd><dt><span class="label">Description:</span></dt><dd>Gene deletion studies in mice have showed that CatSper is crucial for mammalian male fertility. However, the significance of CatSper for human fertilization remains largely unclear. Therefore, a case only containing CatSper deficiency should help reveal the significance of CatSper on human sperm functions. In this study, we identified a CatSper current-deficient man who is an idiopathic infertile patient with normal sperm morphology, count and initial motility. This patient is an ideal case to study the functional significance of CatSper for fertilization success. Thus human whole-genome resequencing was used to identify novel genetic variations responsible for infertility in the patient. See Variant Summary counts for nstd139 in <a title="dbVar Variant Summary" href="/dbvar/content/var_summary/%23nstd139">dbVar Variant Summary</a>.</dd><dt><span class="label">Project:</span></dt><dd><a title="Link to Project ID PRJNA360356" href="/bioproject/?term=PRJNA360356">PRJNA360356</a></dd><dt><span class="label">Publication(s):</span></dt><dd><a href="/sites/entrez?db=pubmed&cmd=search&term=30629171" title="Link to PubMed ID 30629171">Luo et al. 2019</a></dd></dl></div></div></div>
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<ul class="emphasis">
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<a href="https://www.ncbi.nlm.nih.gov/dbvar?dbvartab=variant&term=nstd139">Variants in this study</a>
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</li>
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<li class="">
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<a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606">Open Human in Taxonomy Browser</a>
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<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA360356">BioProjects</a>
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<a class="seemore" href="#">See more...</a>
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<div class="tertiary">Source: NCBI</div>
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<div id="dbvar-main-box2"><div class="study_information"><h3>Detailed Information: <a class="download" href="download/?type=v" target="_blank" title="Preview and Download Variant Regions">Download 1 Variant Region</a>, <a class="download" href="download/?type=i" target="_blank" title="Preview and Download Variant Calls">Download 1 Variant Call</a>, <a class="download" href="download/" target="_blank" title="Preview and Download All Variants">Download Both</a>, <a title="Link to FTP resource" href="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study">FTP</a></h3><div data-jig="ncbitabs" id="studiesDetailsTabmenu"><ul><li><a id="variantTab1" href="#variantTab">Variant Summary</a></li><li><a id="samplesetsTab1" href="#samplesetsTab">Samplesets</a></li><li><a id="experdetailsTab1" href="#experdetailsTab">Experimental
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Details</a></li><li><a id="validationsTab1" href="#validationsTab">Validations</a></li></ul><div id="variantTab"><h2 class="ui-tabs-hide">Variant Summary</h2><h3>Assembly used for analysis:<br /><span class="indentplacement">Remapped: GRCh38.p12 (hg38)</span><style type="text/css">
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}</style></h3><div><h3 id="chromosomes"><label for="submittedvariantdropdown">Variant Summary for: </label><select name="PAFAppLayout.AppController.Page.dbVar_StudyPageNew.dbVar_StudyDisplay_P.submittedvariantdropdown" sid="1" id="submittedvariantdropdown"><option value="1" selected="selected">GRCh38.p12 (hg38)</option><option value="2">GRCh37 (hg19)</option></select></h3><div id="submittedvarianttable1" class=""><div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"><table data-jig="ncbigrid" data-jigconfig="isPageable: true,pageSize:10, isSortable: true, columnTypes: ['str','str', 'numComma', 'numComma', 'str', 'str'], sortFunctions: [strPnumSort,strnumSort,null,null,null,strPnumSort]"><thead><tr><th>Sequence ID</th><th>Chr</th><th>Number of Variant Regions</th><th>Number of Variant Calls</th><th>Placement type</th><th>Link to graphical display</th></tr></thead><tbody><tr><td>NC_000015.10</td><td>Chr15</td><td>1</td><td>1</td><td>Remapped</td><td><a href="/dbvar/browse/org/?taxid=9606&assm=GCF_000001405.39&chr=NC_000015.10&from=43574552&to=43685552&studies=nstd139" title="Link to Genome Browser">NC_000015.10</a></td></tr></tbody></table></div></div></div><div id="submittedvarianttable2" class="hide"><div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"><table data-jig="ncbigrid" data-jigconfig="isPageable: true,pageSize:10, isSortable: true, columnTypes: ['str','str', 'numComma', 'numComma', 'str', 'str'], sortFunctions: [strPnumSort,strnumSort,null,null,null,strPnumSort]"><thead><tr><th>Sequence ID</th><th>Chr</th><th>Number of Variant Regions</th><th>Number of Variant Calls</th><th>Placement type</th><th>Link to graphical display</th></tr></thead><tbody><tr><td>NC_000015.9</td><td>Chr15</td><td>1</td><td>1</td><td>Submitted</td><td><a href="/dbvar/browse/org/?taxid=9606&assm=GCF_000001405.25&chr=NC_000015.9&from=43866750&to=43977750&studies=nstd139" title="Link to Genome Browser">NC_000015.9</a></td></tr></tbody></table></div></div></div><h3 id="remappedchromosomes"><label for="remappedvariantdropdown">Remapping summary: </label><select name="PAFAppLayout.AppController.Page.dbVar_StudyPageNew.dbVar_StudyDisplay_P.remappedvariantdropdown" sid="1" id="remappedvariantdropdown"><option value="1" selected="selected">GRCh37->GRCh38.p12</option></select></h3><div id="remappedvarianttable1" class=""><div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"><table data-jig="ncbigrid" id="remappedchromosomestable" data-jigconfig="isPageable: true,pageSize:10, isSortable: true, sortRowIndex:1,columnTypes: ['str','str','num','num','num','num','num','num','num','num','num','num','num','num'], sortFunctions: [strPnumSort,strnumSort,null,null,null,null,null,null,null,null,null,null,null,null]"><thead><tr><th colspan="3"></th><th class="aa" colspan="5">Variant Region remap status</th><th></th><th class="aa" colspan="5">Variant Call remap status</th></tr><tr><th>Sequence ID</th><th>Chr</th><th>Variant Regions on source</th><th>Perfect</th><th>Good</th><th>Pass</th><th>Fail</th><th>Mult</th><th>Variant Calls on source</th><th>Perfect</th><th>Good</th><th>Pass</th><th>Fail</th><th>Mult</th></tr></thead><tbody><tr><td>NC_000015.9</td><td>Chr15</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td></tr></tbody></table></div></div></div></div></div><div id="samplesetsTab"><h2 class="ui-tabs-hide">Samplesets</h2><h3 id="samplesets">Number of Samplesets: 1</h3><dl class="Samplesetsum"><dt>Name:</dt><dd>LYX-IMI-B</dd><dt>Size:</dt><dd>1</dd><dt>Organisms:</dt><dd><a title="Link to Taxonomy" href="/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606">Homo sapiens</a></dd><dt>Sampleset Phenotype(s):</dt><dd><a title="Link to MeSH" href="https://hpo.jax.org/app/browse/term/HP:0003251">Male infertility</a></dd><dt>Sex:</dt><dd>Male</dd><li><a href="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/csv/samples_for_nstd139_1.csv.gz" title="Download Samples as CSV file">Download Samples as CSV file</a></li><div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"><table data-jig="ncbigrid" id="samplesetshere" data-jigconfig="isPageable: true, pageSize:10, isSortable: true, columnTypes: ['str', 'str','str', 'str','str','str','str'], sortFunctions: [strnumSort2,strnumSort2,strnumSort2,strnumSort,null,null,null], sortColumn:1, sortColumnDir:1"><caption>Samples for sampleset 1</caption><thead><tr><th>Sample ID</th><th>Cell Type</th><th>Subject ID </th><th>Sex</th><th>Ethnicity</th><th>Subject Age</th><th>Subject Phenotype</th></tr></thead><tbody><tr><td><a title="Link to Sample ID" href="/biosample/?term=SAMN06209342">SAMN06209342</a></td><td>whole blood</td><td>6209342</td><td>Male</td><td>Asian</td><td>24 years</td><td>Not reported<br /></td></tr></tbody></table></div></div></dl></div><div id="experdetailsTab"><h2 class="ui-tabs-hide">Experimental Details</h2><div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"><table data-jig="ncbigrid" data-is-sortable="true" data-column-types="["num","str","str","str","numComma"]"><thead><tr><th>Experiment ID</th><th>Type</th><th>Method</th><th>Analysis</th><th>Platforms</th><th>Number of Variant Calls</th></tr></thead><tbody><tr><td>1</td><td>Discovery</td><td>Sequencing</td><td>Paired-end mapping</td><td>Illumina HiSeq X Ten</td><td>1</td></tr></tbody></table></div></div></div><div id="validationsTab"><h2 class="ui-tabs-hide">Validations</h2><h3 id="validations">No validation data were submitted for this study.</h3></div></div></div></div>
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