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Entry
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- *142955 - HOMEOBOX A1; HOXA1
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- OMIM
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<p>
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<span class="h4">*142955</span>
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<br />
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<strong>Table of Contents</strong>
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</p>
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<a href="#title"><strong>Title</strong></a>
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<a href="#geneMap"><strong>Gene-Phenotype Relationships</strong></a>
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<li role="presentation">
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<a href="#text"><strong>Text</strong></a>
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<li role="presentation" style="margin-left: 1em">
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<a href="#cloning">Cloning and Expression</a>
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<li role="presentation" style="margin-left: 1em">
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<a href="#geneFunction">Gene Function</a>
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<a href="#mapping">Mapping</a>
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<li role="presentation" style="margin-left: 1em">
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<a href="#molecularGenetics">Molecular Genetics</a>
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<a href="#animalModel">Animal Model</a>
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<a href="#allelicVariants"><strong>Allelic Variants</strong></a>
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<li role="presentation" style="margin-left: 1em">
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<a href="/allelicVariants/142955">Table View</a>
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<li role="presentation">
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<a href="#references"><strong>References</strong></a>
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<li role="presentation">
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<a href="#contributors"><strong>Contributors</strong></a>
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<li role="presentation">
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<a href="#creationDate"><strong>Creation Date</strong></a>
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<li role="presentation">
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<a href="#editHistory"><strong>Edit History</strong></a>
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</ul>
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<div class="col-lg-2 col-lg-push-8 col-md-2 col-md-push-8 col-sm-2 col-sm-push-8 col-xs-12">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimExternalLinks">
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<h4 class="panel-title">
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<a href="#mimExternalLinksFold" id="mimExternalLinksToggle" class="mimTriangleToggle" role="button" data-toggle="collapse">
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<div style="display: table-row">
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<div id="mimExternalLinksToggleTriangle" class="small" style="color: white; display: table-cell;">▼</div>
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<div style="display: table-cell;">External Links</div>
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</div>
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</a>
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</h4>
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</div>
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</div>
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<div class="panel-group" id="mimExternalLinksAccordion" role="tablist" aria-multiselectable="true">
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimGenome">
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<span class="panel-title">
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<span class="small">
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<a href="#mimGenomeLinksFold" id="mimGenomeLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimGenomeLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> Genome
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</a>
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</span>
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</span>
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</div>
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<div id="mimGenomeLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel" aria-labelledby="genome">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000105991;t=ENST00000643460" class="mim-tip-hint" title="Genome databases for vertebrates and other eukaryotic species." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/gene/?id=3198" class="mim-tip-hint" title="Detailed views of the complete genomes of selected organisms from vertebrates to protozoa." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Genome Viewer', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Genome Viewer</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgFind=omimGeneAcc&position=142955" 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'})">UCSC Genome Browser</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimDna">
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<span class="panel-title">
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<span class="small">
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<a href="#mimDnaLinksFold" id="mimDnaLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimDnaLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> DNA
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</a>
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</span>
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</span>
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<div id="mimDnaLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000105991;t=ENST00000643460" class="mim-tip-hint" title="Transcript-based views for coding and noncoding DNA." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Ensembl', 'domain': 'ensembl.org'})">Ensembl (MANE Select)</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/nuccore/NM_005522,NM_153620" class="mim-tip-hint" title="A collection of genome, gene, and transcript sequence data from several sources, including GenBank, RefSeq." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI RefSeq', 'domain': 'ncbi.nlm.nih'})">NCBI RefSeq</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/nuccore/NM_005522" class="mim-tip-hint" title="A collection of genome, gene, and transcript sequence data from several sources, including GenBank, RefSeq." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI RefSeq (MANE)', 'domain': 'ncbi.nlm.nih'})">NCBI RefSeq (MANE Select)</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgFind=omimGeneAcc&position=142955" 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'})">UCSC Genome Browser</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimProtein">
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<span class="panel-title">
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<span class="small">
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<a href="#mimProteinLinksFold" id="mimProteinLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimProteinLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">►</span> Protein
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</a>
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</span>
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</span>
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</div>
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<div id="mimProteinLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://hprd.org/summary?hprd_id=00843&isoform_id=00843_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>
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<div><a href="https://www.proteinatlas.org/search/HOXA1" 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>
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<div><a href="https://www.ncbi.nlm.nih.gov/protein/500757,1051227,1051228,1051229,1195540,8176740,8176754,21595839,41350071,51094984,51094985,119614267,119614268,189069262,209985365,209985367,1677502188,1746322656,2813266255" 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="https://www.uniprot.org/uniprotkb/P49639" class="mim-tip-hint" title="Comprehensive protein sequence and functional information, including supporting data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'UniProt', 'domain': 'uniprot.org'})">UniProt</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimGeneInfo">
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<span class="panel-title">
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<span class="small">
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<a href="#mimGeneInfoLinksFold" id="mimGeneInfoLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<div style="display: table-row">
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<div id="mimGeneInfoLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Gene Info</div>
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</div>
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</a>
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</span>
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</span>
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</div>
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<div id="mimGeneInfoLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="http://biogps.org/#goto=genereport&id=3198" 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>
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<div><a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000105991;t=ENST00000643460" 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>
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<div><a href="https://www.genecards.org/cgi-bin/carddisp.pl?gene=HOXA1" 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>
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<div><a href="http://amigo.geneontology.org/amigo/search/annotation?q=HOXA1" 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>
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<div><a href="https://www.genome.jp/dbget-bin/www_bget?hsa+3198" 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>
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<dd><a href="http://v1.marrvel.org/search/gene/HOXA1" 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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<dd><a href="https://monarchinitiative.org/NCBIGene:3198" class="mim-tip-hint" title="Monarch Initiative." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Monarch', 'domain': 'monarchinitiative.org'})">Monarch</a></dd>
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<div><a href="https://www.ncbi.nlm.nih.gov/gene/3198" class="mim-tip-hint" title="Gene-specific map, sequence, expression, structure, function, citation, and homology data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Gene', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Gene</a></div>
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<div><a href="https://genome.ucsc.edu/cgi-bin/hgGene?db=hg38&hgg_chrom=chr7&hgg_gene=ENST00000643460.2&hgg_start=27092993&hgg_end=27096000&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>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimClinicalResources">
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<span class="panel-title">
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<span class="small">
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<a href="#mimClinicalResourcesLinksFold" id="mimClinicalResourcesLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<div style="display: table-row">
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<div id="mimClinicalResourcesLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Clinical Resources</div>
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</div>
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</a>
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</span>
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</span>
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</div>
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<div id="mimClinicalResourcesLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel" aria-labelledby="clinicalResources">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://search.clinicalgenome.org/kb/genes/HGNC:5099" class="mim-tip-hint" title="A ClinGen curated resource of ratings for the strength of evidence supporting or refuting the clinical validity of the claim(s) that variation in a particular gene causes disease." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ClinGen Validity', 'domain': 'search.clinicalgenome.org'})">ClinGen Validity</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/gtr/all/tests/?term=142955[mim]" class="mim-tip-hint" title="Genetic Testing Registry." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GTR', 'domain': 'ncbi.nlm.nih.gov'})">GTR</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimVariation">
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<span class="panel-title">
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<span class="small">
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<a href="#mimVariationLinksFold" id="mimVariationLinksToggle" class=" mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<span id="mimVariationLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5">▼</span> Variation
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</a>
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</span>
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</span>
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</div>
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<div id="mimVariationLinksFold" class="panel-collapse collapse in mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.ncbi.nlm.nih.gov/clinvar?term=142955[MIM]" class="mim-tip-hint" title="ClinVar aggregates information about sequence variation and its relationship to human health." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">ClinVar</a></div>
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<div><a href="https://gnomad.broadinstitute.org/gene/ENSG00000105991" class="mim-tip-hint" title="The Genome Aggregation Database (gnomAD), Broad Institute." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'gnomAD', 'domain': 'gnomad.broadinstitute.org'})">gnomAD</a></div>
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<div><a href="https://www.ebi.ac.uk/gwas/search?query=HOXA1" class="mim-tip-hint" title="GWAS Catalog; NHGRI-EBI Catalog of published genome-wide association studies." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'GWAS Catalog', 'domain': 'gwascatalog.org'})">GWAS Catalog </a></div>
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<div><a href="https://www.gwascentral.org/search?q=HOXA1" 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 </a></div>
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<div><a href="http://www.hgmd.cf.ac.uk/ac/gene.php?gene=HOXA1" class="mim-tip-hint" title="Human Gene Mutation Database; published mutations causing or associated with human inherited disease; disease-associated/functional polymorphisms." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HGMD', 'domain': 'hgmd.cf.ac.uk'})">HGMD</a></div>
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<div><a href="https://evs.gs.washington.edu/EVS/PopStatsServlet?searchBy=Gene+Hugo&target=HOXA1&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="https://www.pharmgkb.org/gene/PA29376" class="mim-tip-hint" title="Pharmacogenomics Knowledge Base; curated and annotated information regarding the effects of human genetic variations on drug response." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PharmGKB', 'domain': 'pharmgkb.org'})">PharmGKB</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimAnimalModels">
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<span class="panel-title">
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<span class="small">
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<a href="#mimAnimalModelsLinksFold" id="mimAnimalModelsLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
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<div style="display: table-row">
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<div id="mimAnimalModelsLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Animal Models</div>
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</div>
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</a>
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</span>
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</span>
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</div>
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<div id="mimAnimalModelsLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.alliancegenome.org/gene/HGNC:5099" class="mim-tip-hint" title="Search Across Species; explore model organism and human comparative genomics." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'Alliance Genome', 'domain': 'alliancegenome.org'})">Alliance Genome</a></div>
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<div><a href="https://flybase.org/reports/FBgn0002522.html" class="mim-tip-hint" title="A Database of Drosophila Genes and Genomes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'FlyBase', 'domain': 'flybase.org'})">FlyBase</a></div>
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<div><a href="https://www.mousephenotype.org/data/genes/MGI:96170" class="mim-tip-hint" title="International Mouse Phenotyping Consortium." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'IMPC', 'domain': 'knockoutmouse.org'})">IMPC</a></div>
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<div><a href="http://v1.marrvel.org/search/gene/HOXA1#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="http://www.informatics.jax.org/marker/MGI:96170" class="mim-tip-hint" title="Mouse Genome Informatics; international database resource for the laboratory mouse, including integrated genetic, genomic, and biological data." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MGI Mouse Gene', 'domain': 'informatics.jax.org'})">MGI Mouse Gene</a></div>
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<div><a href="https://www.mmrrc.org/catalog/StrainCatalogSearchForm.php?search_query=" class="mim-tip-hint" title="Mutant Mouse Resource & Research Centers." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'MMRRC', 'domain': 'mmrrc.org'})">MMRRC</a></div>
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<div><a href="https://www.ncbi.nlm.nih.gov/gene/3198/ortholog/" class="mim-tip-hint" title="Orthologous genes at NCBI." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'NCBI Orthologs', 'domain': 'ncbi.nlm.nih.gov'})">NCBI Orthologs</a></div>
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<div><a href="https://www.orthodb.org/?ncbi=3198" 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://wormbase.org/db/gene/gene?name=WBGene00000437;class=Gene" class="mim-tip-hint" title="Database of the biology and genome of Caenorhabditis elegans and related nematodes." target="_blank" onclick="gtag('event', 'mim_outbound', {'name'{'name': 'Wormbase Gene', 'domain': 'wormbase.org'})">Wormbase Gene</a></div>
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<div><a href="https://zfin.org/ZDB-GENE-000823-5" class="mim-tip-hint" title="The Zebrafish Model Organism Database." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ZFin', 'domain': 'zfin.org'})">ZFin</a></div>
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</div>
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</div>
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</div>
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<div class="panel panel-default" style="margin-top: 0px; border-radius: 0px">
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<div class="panel-heading mim-panel-heading" role="tab" id="mimCellularPathways">
|
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<span class="panel-title">
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<span class="small">
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<a href="#mimCellularPathwaysLinksFold" id="mimCellularPathwaysLinksToggle" class="collapsed mimSingletonTriangleToggle" role="button" data-toggle="collapse" data-parent="#mimExternalLinksAccordion">
|
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<div style="display: table-row">
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<div id="mimCellularPathwaysLinksToggleTriangle" class="small mimSingletonTriangle" style="color: #337CB5; display: table-cell;">►</div>
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<div style="display: table-cell;">Cellular Pathways</div>
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</div>
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</a>
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</span>
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</span>
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</div>
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<div id="mimCellularPathwaysLinksFold" class="panel-collapse collapse mimLinksFold" role="tabpanel">
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<div class="panel-body small mim-panel-body">
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<div><a href="https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:3198" 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>
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<div><a href="https://reactome.org/content/query?q=HOXA1&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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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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<span>
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<span class="mim-tip-bottom" qtip_title="<strong>Looking for this gene or this phenotype in other resources?</strong>" qtip_text="Select a related resource from the dropdown menu and click for a targeted link to information directly relevant.">
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</span>
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</span>
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</div>
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<div class="col-lg-8 col-lg-pull-2 col-md-8 col-md-pull-2 col-sm-8 col-sm-pull-2 col-xs-12">
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<div>
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<a id="title" class="mim-anchor"></a>
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<div>
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<a id="number" class="mim-anchor"></a>
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<div class="text-right">
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<a href="#" class="mim-tip-icd" qtip_title="<strong>ICD+</strong>" qtip_text="
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<strong>SNOMEDCT:</strong> 720518006, 720567008<br />
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">ICD+</a>
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</div>
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<div>
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<span class="h3">
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<span class="mim-font mim-tip-hint" title="Gene description">
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<span class="text-danger"><strong>*</strong></span>
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142955
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</span>
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</span>
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</div>
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</div>
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<div>
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<a id="preferredTitle" class="mim-anchor"></a>
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<h3>
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<span class="mim-font">
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HOMEOBOX A1; HOXA1
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</span>
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</h3>
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</div>
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<div>
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<br />
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</div>
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<div>
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<a id="alternativeTitles" class="mim-anchor"></a>
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<div>
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<p>
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<span class="mim-font">
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<em>Alternative titles; symbols</em>
|
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</span>
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</p>
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</div>
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<div>
|
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<h4>
|
|
<span class="mim-font">
|
|
HOMEOBOX 1F; HOX1F<br />
|
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Hox-1.6, MOUSE, HOMOLOG OF<br />
|
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lab, DROSOPHILA, HOMOLOG OF
|
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</span>
|
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</h4>
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</div>
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</div>
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<div>
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<br />
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</div>
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</div>
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<div>
|
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<a id="approvedGeneSymbols" class="mim-anchor"></a>
|
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<p>
|
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<span class="mim-text-font">
|
|
<strong><em>HGNC Approved Gene Symbol: <a href="https://www.genenames.org/tools/search/#!/genes?query=HOXA1" class="mim-tip-hint" title="HUGO Gene Nomenclature Committee." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'HGNC', 'domain': 'genenames.org'})">HOXA1</a></em></strong>
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</span>
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</p>
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</div>
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<div>
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<a id="cytogeneticLocation" class="mim-anchor"></a>
|
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<p>
|
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<span class="mim-text-font">
|
|
<strong>
|
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<em>
|
|
Cytogenetic location: <a href="/geneMap/7/131?start=-3&limit=10&highlight=131">7p15.2</a>
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|
Genomic coordinates <span class="small">(GRCh38)</span> : <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr7:27092993-27096000&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'})">7:27,092,993-27,096,000</a> </span>
|
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</em>
|
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</strong>
|
|
<a href="https://www.ncbi.nlm.nih.gov/" target="_blank" class="small"> (from NCBI) </a>
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</span>
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</p>
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</div>
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<div>
|
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<br />
|
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</div>
|
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<div>
|
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<a id="geneMap" class="mim-anchor"></a>
|
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<div style="margin-bottom: 10px;">
|
|
<span class="h4 mim-font">
|
|
<strong>Gene-Phenotype Relationships</strong>
|
|
</span>
|
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</div>
|
|
<div>
|
|
<table class="table table-bordered table-condensed table-hover small mim-table-padding">
|
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<thead>
|
|
<tr class="active">
|
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<th>
|
|
Location
|
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</th>
|
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<th>
|
|
Phenotype
|
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</th>
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<th>
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|
Phenotype <br /> MIM number
|
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</th>
|
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<th>
|
|
Inheritance
|
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</th>
|
|
<th>
|
|
Phenotype <br /> mapping key
|
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</th>
|
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</tr>
|
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</thead>
|
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<tbody>
|
|
|
|
<tr>
|
|
<td rowspan="2">
|
|
<span class="mim-font">
|
|
<a href="/geneMap/7/131?start=-3&limit=10&highlight=131">
|
|
7p15.2
|
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</a>
|
|
</span>
|
|
</td>
|
|
|
|
|
|
<td>
|
|
<span class="mim-font">
|
|
Athabaskan brainstem dysgenesis syndrome
|
|
|
|
</span>
|
|
</td>
|
|
<td>
|
|
<span class="mim-font">
|
|
|
|
<a href="/entry/601536"> 601536 </a>
|
|
|
|
</span>
|
|
</td>
|
|
<td>
|
|
<span class="mim-font">
|
|
|
|
<abbr class="mim-tip-hint" title="Autosomal recessive">AR</abbr>
|
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|
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</span>
|
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</td>
|
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<td>
|
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<span class="mim-font">
|
|
|
|
<abbr class="mim-tip-hint" title="3 - The molecular basis of the disorder is known">3</abbr>
|
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</span>
|
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</td>
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</tr>
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<tr>
|
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<td>
|
|
<span class="mim-font">
|
|
Bosley-Salih-Alorainy syndrome
|
|
|
|
</span>
|
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</td>
|
|
<td>
|
|
<span class="mim-font">
|
|
|
|
<a href="/entry/601536"> 601536 </a>
|
|
|
|
</span>
|
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</td>
|
|
<td>
|
|
<span class="mim-font">
|
|
|
|
<abbr class="mim-tip-hint" title="Autosomal recessive">AR</abbr>
|
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|
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</span>
|
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</td>
|
|
<td>
|
|
<span class="mim-font">
|
|
|
|
<abbr class="mim-tip-hint" title="3 - The molecular basis of the disorder is known">3</abbr>
|
|
|
|
</span>
|
|
</td>
|
|
</tr>
|
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</tbody>
|
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</table>
|
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</div>
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</div>
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<div>
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<div class="btn-group">
|
|
<button type="button" class="btn btn-success dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
|
|
PheneGene Graphics <span class="caret"></span>
|
|
</button>
|
|
<ul class="dropdown-menu" style="width: 17em;">
|
|
<li><a href="/graph/linear/142955" target="_blank" onclick="gtag('event', 'mim_graph', {'destination': 'Linear'})"> Linear </a></li>
|
|
<li><a href="/graph/radial/142955" target="_blank" onclick="gtag('event', 'mim_graph', {'destination': 'Radial'})"> Radial </a></li>
|
|
</ul>
|
|
</div>
|
|
<span class="glyphicon glyphicon-question-sign mim-tip-hint" title="OMIM PheneGene graphics depict relationships between phenotypes, groups of related phenotypes (Phenotypic Series), and genes.<br /><a href='/static/omim/pdf/OMIM_Graphics.pdf' target='_blank'>A quick reference overview and guide (PDF)</a>"></span>
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</div>
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<p>In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on 4 separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. <a href="#3" class="mim-tip-reference" title="Hong, Y. S., Kim, S. Y., Bhattacharya, A., Pratt, D. R., Hong, W. K., Tainsky, M. A. <strong>Structure and function of the HOX A1 human homeobox gene cDNA.</strong> Gene 159: 209-214, 1995.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/7622051/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">7622051</a>] [<a href="https://doi.org/10.1016/0378-1119(95)92712-g" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="7622051">Hong et al. (1995)</a> determined the structure of the first gene in the homeobox A cluster, HOXA1, by cloning its full-length cDNA, which predicts a protein of 335 amino acids. In vitro translation produced the expected 36-kD protein. An alternatively spliced cDNA was also obtained. In PA-1 teratocarcinoma cells, HOXA1 was induced by retinoic acid earlier than other HOXA cluster genes. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=7622051" 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>HOX genes are required during the morphogenesis of both vertebrate digits and external genitals. <a href="#6" class="mim-tip-reference" title="Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D. <strong>Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci.</strong> Science 346: 1004-1006, 2014.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/25414315/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">25414315</a>] [<a href="https://doi.org/10.1126/science.1257493" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="25414315">Lonfat et al. (2014)</a> investigated whether transcription in such distinct contexts involves a shared enhancer-containing landscape. They showed that the same regulatory topology is used, albeit with some tissue-specific enhancer-promoter interactions, which suggested the hijacking of a regulatory backbone from one context to another. In addition, comparable organizations were observed at both HOXA1 and HOXD1 (<a href="/entry/142987">142987</a>) clusters, which separated through genome duplication in an ancestral invertebrate animal. <a href="#6" class="mim-tip-reference" title="Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D. <strong>Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci.</strong> Science 346: 1004-1006, 2014.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/25414315/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">25414315</a>] [<a href="https://doi.org/10.1126/science.1257493" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="25414315">Lonfat et al. (2014)</a> proposed that this convergent regulatory evolution was triggered by the preexistence of some chromatin architecture, thus facilitating the subsequent recruitment of the appropriate transcription factors. <a href="#6" class="mim-tip-reference" title="Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D. <strong>Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci.</strong> Science 346: 1004-1006, 2014.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/25414315/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">25414315</a>] [<a href="https://doi.org/10.1126/science.1257493" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="25414315">Lonfat et al. (2014)</a> argued that regulatory topologies may have both favored and constrained the evolution of pleiotropic developmental loci in vertebrates. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=25414315" 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="#13" class="mim-tip-reference" title="Xiong, Z., Xia, P., Zhu, X., Geng, J., Wang, S., Ye, B., Qin, X., Qu, Y., He, L., Fan, D., Du, Y., Tian, Y., Fan, Z. <strong>Glutamylation of deubiquitinase BAP1 controls self-renewal of hematopoietic stem cells and hematopoiesis.</strong> J. Exp. Med. 217: e20190974, 2020. Note: Electronic Article.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/31699823/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">31699823</a>] [<a href="https://doi.org/10.1084/jem.20190974" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="31699823">Xiong et al. (2020)</a> found that Bap1 (<a href="/entry/603089">603089</a>) facilitated expression of Hoxa1, which was required for self-renewal of mouse hematopoietic stem cells (HSCs). Ttll5 (<a href="/entry/612268">612268</a>) and Ttll7 (<a href="/entry/618813">618813</a>) glutamylated Bap1 at glu651 in HSCs, whereas Ccp3 (<a href="/entry/617346">617346</a>) removed Bap1 glutamylation. Bap1 glutamylation promoted its interaction with Ube2o (<a href="/entry/617649">617649</a>) and accelerated lys48-linked ubiquitination of Bap1 for its degradation. Degradation of Bap1 suppressed Hoxa1 expression, thereby enhancing HSC self-renewal and hematopoiesis. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=31699823" 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="#1" class="mim-tip-reference" title="Apiou, F., Flagiello, D., Cillo, C., Malfoy, B., Poupon, M.-F., Dutrillaux, B. <strong>Fine mapping of human HOX gene clusters.</strong> Cytogenet. Cell Genet. 73: 114-115, 1996.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/8646877/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">8646877</a>] [<a href="https://doi.org/10.1159/000134320" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="8646877">Apiou et al. (1996)</a> used fluorescence in situ hybridization to localize the HOXA gene cluster precisely to 7p15.3. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=8646877" 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 href="#4" class="mim-tip-reference" title="Ingram, J. L., Stodgell, C. J., Hyman, S. L., Figlewicz, D. A., Weitkamp, L. R., Rodier, P. M. <strong>Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders.</strong> Teratology 62: 393-405, 2000.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/11091361/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">11091361</a>] [<a href="https://doi.org/10.1002/1096-9926(200012)62:6<393::AID-TERA6>3.0.CO;2-V" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="11091361">Ingram et al. (2000)</a> identified a common polymorphism in the HOXA1 gene: an A-to-G substitution at codon 218, changing the codon for one histidine in a series of histidine repeats to an arginine at position 73. The frequency of the G allele was 20 to 60% among the Coriell Human Diversity Panel, but was not identified in any individuals of Asian origin including Indians, Japanese, and Chinese. The frequency of the G allele was 0.202 in 57 probands with autism spectrum disorders and 0.203 in their 32 affected relatives. The frequency of the G allele in 134 unaffected relatives of subjects with an Asperger spectrum disorder was 0.164. The frequency of the G allele in the convenience population for this study was 0.109. In the autism spectrum disorder families, there was a significant deviation from the HOXA1 genotype ratios expected from Hardy-Weinberg proportions. Among affected offspring, a significant deviation from mendelian expectation in gene transmission was observed. <a href="#4" class="mim-tip-reference" title="Ingram, J. L., Stodgell, C. J., Hyman, S. L., Figlewicz, D. A., Weitkamp, L. R., Rodier, P. M. <strong>Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders.</strong> Teratology 62: 393-405, 2000.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/11091361/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">11091361</a>] [<a href="https://doi.org/10.1002/1096-9926(200012)62:6<393::AID-TERA6>3.0.CO;2-V" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="11091361">Ingram et al. (2000)</a> suggested that there was evidence of an interaction between HOXA1, HOXB1, and gender in susceptibility to autism spectrum disorders. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=11091361" 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><strong><em>Bosley-Salih-Alorainy/Athabaskan Brainstem Dysgenesis Syndromes</em></strong></p><p>
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<a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> carried out SNP-based linkage analysis in a Saudi Arabian family with Bosley-Salih-Alorainy syndrome (BSAS; <a href="/entry/601536">601536</a>) and identified a single, fully informative 8.5-Mb region on 7p15.3-p14.3 in which only the affected children were homozygous. Further analysis narrowed the linkage to a region of homozygosity of approximately 300 kb on 7p15.2. Because of similarities between the BSAS phenotype and the pathology of the Hoxa1 -/- mouse, and because the HOXA cluster falls in the haploidentical region, <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> analyzed the HOXA1 gene in Saudi Arabian individuals with BSAS and found a homozygous guanine insertion, 175_176insG, predicted to result in a reading frameshift and the introduction of a premature stop codon (<a href="#0001">142955.0001</a>). A Turkish individual with BSAS had a homozygous 84C-G transversion resulting in the substitution of a stop codon for a tyrosine residue (Y28X; <a href="#0002">142955.0002</a>). Noting the phenotypic overlap of BSAS, the Hoxa1 knockout mouse, and Athabaskan brainstem dysgenesis syndrome, <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> analyzed genomic DNA from 5 of the reported individuals with ABDS and 4 of their phenotypically normal parents. All 5 affected individuals were homozygous across the HOXA1 locus and carried a homozygous 76C-T HOXA1 mutation resulting in substitution of a stop codon for arginine (R26X; <a href="#0003">142955.0003</a>). <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> pointed out that to their knowledge this was the first report of viable homozygous truncating mutations in any human HOX gene and of a mendelian disorder resulting from mutations in a human HOX gene critical for development of the central nervous system. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16155570" 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>Because 1 of the patients of <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> with a mutation in HOXA1 had Duane anomaly and asymptomatic left carotid hypoplasia (see <a href="#0001">142955.0001</a>), <a href="#12" class="mim-tip-reference" title="Tischfield, M. A., Chan, W.-M., Grunert, J.-F., Andrews, C., Engle, E. C. <strong>HOXA1 mutations are not a common cause of Duane anomaly.</strong> Am. J. Med. Genet. 140A: 900-902, 2006.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16528738/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16528738</a>] [<a href="https://doi.org/10.1002/ajmg.a.31167" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16528738">Tischfield et al. (2006)</a> analyzed the HOXA1 gene in 101 probands with isolated Duane anomaly (DA) and 30 with DA and other symptoms. None in this group harbored a mutation in SALL4 (<a href="/entry/607343">607343</a>) or ROBO3 (<a href="/entry/608630">608630</a>), and none were members of a pedigree whose phenotype maps to the DURS2 (<a href="/entry/604356">604356</a>) locus. No mutation was detected in any proband; the authors concluded that HOXA1 mutations are a rare cause of isolated Duane anomaly. <a href="https://pubmed.ncbi.nlm.nih.gov/?term=16155570+16528738" 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="#7" class="mim-tip-reference" title="Lufkin, T., Dierich, A., LeMeur, M., Mark, M., Chambon, P. <strong>Disruption of the Hox-1.6 homeobox gene results in defects in a region corresponding to its rostral domain of expression.</strong> Cell 66: 1105-1119, 1991.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/1680563/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">1680563</a>] [<a href="https://doi.org/10.1016/0092-8674(91)90034-v" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="1680563">Lufkin et al. (1991)</a> generated mice deficient in Hoxa1 by homologous recombination. Heterozygous mice were normal but homozygous mice died at birth from anoxia and had numerous defects that were centered at the levels of rhombomeres 4 to 7 and included delayed hindbrain neural tube closure, absence of certain cranial nerves and ganglia, and malformed inner ears and bones of the skull. <a href="#9" class="mim-tip-reference" title="Mark, M., Lufkin, T., Vonesch, J.-L., Ruberte, E., Olivo, J.-C., Dolle, P., Gorry, P., Lumsden, A., Chambon, P. <strong>Two rhombomeres are altered in Hoxa-1 mutant mice.</strong> Development 119: 319-338, 1993.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/8287791/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">8287791</a>] [<a href="https://doi.org/10.1242/dev.119.2.319" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="8287791">Mark et al. (1993)</a> further characterized the anatomic defects in Hoxa1 -/- mutant mice. Three-dimensional reconstructions of Hoxa1 -/- rhombencephalon revealed that it bears only 5 rhombomeric structures instead of the normal 7. The first 3 of these rhombomeres appeared normal as judged from the distribution pattern of Crabp1 (<a href="/entry/180230">180230</a>) transcripts in the neuroectoderm and from histologic analysis of the cranial nerve components derived from these structures. In contrast, the neural crest cell-free region normally located opposite rhombomere-5 is absent in Hoxa1 -/- embryos, and motor neurons of the facial and abducens nerves, which normally differentiate within rhombomeres 4, 5, and 6, are missing in Hoxa1 -/- fetuses. These data suggested that rhombomere 4 is markedly reduced, whereas rhombomere 5 is almost absent, in Hoxa1 -/- embryos. Remnants of rhombomeres 4 and 5 appeared to be fused caudally with rhombomere 6 to form a single fourth rhombomeric structure. <a href="#9" class="mim-tip-reference" title="Mark, M., Lufkin, T., Vonesch, J.-L., Ruberte, E., Olivo, J.-C., Dolle, P., Gorry, P., Lumsden, A., Chambon, P. <strong>Two rhombomeres are altered in Hoxa-1 mutant mice.</strong> Development 119: 319-338, 1993.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/8287791/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">8287791</a>] [<a href="https://doi.org/10.1242/dev.119.2.319" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="8287791">Mark et al. (1993)</a> found that the mutual relationship along the rostrocaudal axis between the otic pit and the neuroepithelial site of int2 protein secretion was not significantly changed in Hoxa1 -/- embryos. However, the abnormal relationship between the rhombencephalon and the epithelial inner ear may account for the aplasia and faulty differentiation of the membranous labyrinth, the disruption of the cartilaginous otic capsule, and the disorganization of some middle ear structures. <a href="https://pubmed.ncbi.nlm.nih.gov/?term=1680563+8287791" 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="#10" class="mim-tip-reference" title="Pasqualetti, M., Neun, R., Davenne, M., Rijli, F. M. <strong>Retinoic acid rescues inner ear defects in Hoxa1 deficient mice.</strong> Nature Genet. 29: 34-39, 2001.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/11528388/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">11528388</a>] [<a href="https://doi.org/10.1038/ng702" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="11528388">Pasqualetti et al. (2001)</a> demonstrated that a single maternal administration of a low dose of the vitamin A metabolite retinoic acid was sufficient to compensate the requirement for Hoxa1 function in Hoxa1-deficient mice. A single dose of retinoic acid rescued cochlear and vestibular defects in mutant fetuses without affecting the development of wildtype fetuses. These results identified a temporal window of susceptibility to retinoids that is critical for mammalian inner ear specification, and provided the first evidence that a subteratogenic dose of vitamin A derivative can be effective in rescuing a congenital defect in the mammalian embryo. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=11528388" 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="#5" class="mim-tip-reference" title="Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C. J., Duboule, D. <strong>Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function.</strong> Nature 435: 1113-1116, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15973411/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15973411</a>] [<a href="https://doi.org/10.1038/nature03648" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="15973411">Kmita et al. (2005)</a> described mice that were lacking all Hoxa and Hoxd functions in their forelimbs. They showed that such limbs are arrested early in their developmental patterning and display severe truncations of distal elements, partly owing to the absence of Sonic hedgehog (<a href="/entry/600725">600725</a>) expression. These results indicated that the evolutionary recruitment of Hox gene function into growing appendages might have been crucial in implementing hedgehog signaling, subsequently leading to the distal extension of tetrapod appendages. Accordingly, <a href="#5" class="mim-tip-reference" title="Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C. J., Duboule, D. <strong>Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function.</strong> Nature 435: 1113-1116, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15973411/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15973411</a>] [<a href="https://doi.org/10.1038/nature03648" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="15973411">Kmita et al. (2005)</a> suggested these mutant limbs may be reminiscent of an ancestral trunk extension, related to that proposed for arthropods. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15973411" 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="#8" class="mim-tip-reference" title="Makki, N., Capecchi, M. R. <strong>Cardiovascular defects in a mouse model of HOXA1 syndrome.</strong> Hum. Molec. Genet. 21: 26-31, 2012.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/21940751/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">21940751</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=21940751[PMID]&report=imagesdocsum" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Image', 'domain': 'ncbi.nlm.nih.gov'})">images</a>] [<a href="https://doi.org/10.1093/hmg/ddr434" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="21940751">Makki and Capecchi (2012)</a> found that deletion of Hoxa1 in mice caused a variety of malformations of the cardiac outflow tract and great arteries in late-stage embryos. Defects showed variable penetrance and included interrupted aortic arch type B, aberrant subclavian artery, and tetralogy of Fallot (see <a href="/entry/187500">187500</a>). During early mouse embryogenesis, Hoxa1 was expressed in precursors of cardiac neural crest cells, and it directed expression of genes important for neural crest specification. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=21940751" 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>ALLELIC VARIANTS (<a href="/help/faq#1_4"></strong>
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<a href="https://www.ncbi.nlm.nih.gov/clinvar?term=142955[MIM]" class="btn btn-default mim-tip-hint" role="button" title="ClinVar aggregates information about sequence variation and its relationship to human health." target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">ClinVar</a>
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<div class="btn-group"> <button type="button" class="btn btn-default btn-xs dropdown-toggle mim-font" data-toggle="dropdown"><span class="text-primary">●</span> rs769152039 <span class="caret"></span></button> <ul class="dropdown-menu"> <li><a href="https://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs769152039;toggle_HGVS_names=open" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'ensembl.org'})">Ensembl</a></li> <li><a href="https://gnomad.broadinstitute.org/variant/rs769152039?dataset=gnomad_r2_1" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'gnomad.broadinstitute.org'})" style="padding-left: 8px;"><span class="text-primary">●</span> gnomAD</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/snp/?term=rs769152039" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'www.ncbi.nlm.nih.gov'})">NCBI</a></li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&clinvar=pack&omimAvSnp=pack&position=rs769152039" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'genome.ucsc.edu'})">UCSC</a></li> </ul> </div>
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<p>In affected members of 3 consanguineous Saudi Arabian families with Bosley-Salih-Alorainy syndrome and in a 4-year-old Saudi Arabian boy, born of consanguineous parents, with Duane anomaly and hypoplastic left carotid artery (BSAS; see <a href="/entry/601536">601536</a>), <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> identified homozygosity for a guanine insertion, 175_176insG. The mutation segregated with the disorder in the families; haplotype analysis indicated a founder effect. The mutation was predicted to result in a frameshift and premature termination, although functional studies of the variant and studies of patient cells were not performed. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16155570" 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="#2" class="mim-tip-reference" title="Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu-Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., Erickson, R. P. <strong>The clinical spectrum of homozygous HOXA1 mutations.</strong> Am. J. Med. Genet. 146A: 1235-1240, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18412118/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18412118</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=18412118[PMID]&report=imagesdocsum" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Image', 'domain': 'ncbi.nlm.nih.gov'})">images</a>] [<a href="https://doi.org/10.1002/ajmg.a.32262" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18412118">Bosley et al. (2008)</a> identified the 175_176insG mutation in affected members of 2 additional consanguineous Saudi Arabian families with BSAS. The mutation was predicted to result in a truncated protein and absence of HOXA1 activity. Five patients had conotruncal or septal heart defects. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18412118" 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 class="btn-group"> <button type="button" class="btn btn-default btn-xs dropdown-toggle mim-font" data-toggle="dropdown">rs104894017 <span class="caret"></span></button> <ul class="dropdown-menu"> <li><a href="https://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs104894017;toggle_HGVS_names=open" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'ensembl.org'})">Ensembl</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/snp/?term=rs104894017" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'www.ncbi.nlm.nih.gov'})">NCBI</a></li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&clinvar=pack&omimAvSnp=pack&position=rs104894017" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'genome.ucsc.edu'})">UCSC</a></li> </ul> </div>
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<a href="https://www.ncbi.nlm.nih.gov/clinvar?term=RCV000016028" target="_blank" class="btn btn-default btn-xs mim-tip-hint" title="RCV000016028" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">RCV000016028</a>
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<p>In an individual with Bosley-Salih-Alorainy syndrome (BSAS; see <a href="/entry/601536">601536</a>) from a Turkish family, <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> found homozygosity for an 84C-G transversion resulting in substitution of a stop codon for a tyrosine residue (Y28X). Functional studies of the variant were not performed, but it was predicted to result in a loss of function. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16155570" 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 class="btn-group"> <button type="button" class="btn btn-default btn-xs dropdown-toggle mim-font" data-toggle="dropdown"><span class="text-primary">●</span> rs104894018 <span class="caret"></span></button> <ul class="dropdown-menu"> <li><a href="https://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs104894018;toggle_HGVS_names=open" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'ensembl.org'})">Ensembl</a></li> <li><a href="https://gnomad.broadinstitute.org/variant/rs104894018?dataset=gnomad_r2_1" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'gnomad.broadinstitute.org'})" style="padding-left: 8px;"><span class="text-primary">●</span> gnomAD</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/snp/?term=rs104894018" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'www.ncbi.nlm.nih.gov'})">NCBI</a></li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&clinvar=pack&omimAvSnp=pack&position=rs104894018" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'genome.ucsc.edu'})">UCSC</a></li> </ul> </div>
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<a href="https://www.ncbi.nlm.nih.gov/clinvar?term=RCV000016029 OR RCV002466406" target="_blank" class="btn btn-default btn-xs mim-tip-hint" title="RCV000016029, RCV002466406" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">RCV000016029...</a>
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<p>In individuals with Athabaskan brainstem dysgenesis syndrome (ABDS; <a href="/entry/601536">601536</a>), reported in Native American tribes, <a href="#11" class="mim-tip-reference" title="Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C. <strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong> Nature Genet. 37: 1035-1037, 2005.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>] [<a href="https://doi.org/10.1038/ng1636" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="16155570">Tischfield et al. (2005)</a> found homozygosity for a 76C-T transition in the HOXA1 gene, predicted to result in the substitution of a stop codon for an arginine residue (arg26 to ter; R26X). The mutation was heterozygous in the parents and absent from 344 control chromosomes; haplotype analysis was consistent with a founder effect. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16155570" 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="#2" class="mim-tip-reference" title="Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu-Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., Erickson, R. P. <strong>The clinical spectrum of homozygous HOXA1 mutations.</strong> Am. J. Med. Genet. 146A: 1235-1240, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18412118/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18412118</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=18412118[PMID]&report=imagesdocsum" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Image', 'domain': 'ncbi.nlm.nih.gov'})">images</a>] [<a href="https://doi.org/10.1002/ajmg.a.32262" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18412118">Bosley et al. (2008)</a> identified the R26X mutation in 3 patients from 3 families of Native American origin with ABDS. All had deafness, horizontal gaze palsy, and developmental delay, and 2 had congenital cardiac defects. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18412118" 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>.0004 BOSLEY-SALIH-ALORAINY SYNDROME</strong>
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HOXA1, 1-BP DEL, 185G
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<div class="btn-group"> <button type="button" class="btn btn-default btn-xs dropdown-toggle mim-font" data-toggle="dropdown">rs1562700083 <span class="caret"></span></button> <ul class="dropdown-menu"> <li><a href="https://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs1562700083;toggle_HGVS_names=open" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'ensembl.org'})">Ensembl</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/snp/?term=rs1562700083" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'www.ncbi.nlm.nih.gov'})">NCBI</a></li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&clinvar=pack&omimAvSnp=pack&position=rs1562700083" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'dbSNP', 'domain': 'genome.ucsc.edu'})">UCSC</a></li> </ul> </div>
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<a href="https://www.ncbi.nlm.nih.gov/clinvar?term=RCV000016030" target="_blank" class="btn btn-default btn-xs mim-tip-hint" title="RCV000016030" onclick="gtag('event', 'mim_outbound', {'name': 'ClinVar', 'domain': 'ncbi.nlm.nih.gov'})">RCV000016030</a>
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<p>In a Saudi Arabian patient, born of consanguineous parents, with Bosley-Salih-Alorainy syndrome (BSAS; <a href="/entry/601536">601536</a>), <a href="#2" class="mim-tip-reference" title="Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu-Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., Erickson, R. P. <strong>The clinical spectrum of homozygous HOXA1 mutations.</strong> Am. J. Med. Genet. 146A: 1235-1240, 2008.[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18412118/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18412118</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=18412118[PMID]&report=imagesdocsum" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Image', 'domain': 'ncbi.nlm.nih.gov'})">images</a>] [<a href="https://doi.org/10.1002/ajmg.a.32262" target="_blank" onclick="gtag('event', 'mim_outbound', {'destination': 'Publisher'})">Full Text</a>]" pmid="18412118">Bosley et al. (2008)</a> identified a homozygous 1-bp deletion (185delG) in the HOXA1 gene, predicted to result in a frameshift and premature termination. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function. The patient had Duane retraction anomaly, horizontal gaze restriction, and deafness, but normal cognition. <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=18412118" 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>REFERENCES</strong>
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<a id="Apiou1996" class="mim-anchor"></a>
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Apiou, F., Flagiello, D., Cillo, C., Malfoy, B., Poupon, M.-F., Dutrillaux, B.
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<strong>Fine mapping of human HOX gene clusters.</strong>
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[<a href="https://doi.org/10.1159/000134320" target="_blank">Full Text</a>]
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Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu-Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., Erickson, R. P.
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<strong>The clinical spectrum of homozygous HOXA1 mutations.</strong>
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Am. J. Med. Genet. 146A: 1235-1240, 2008.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/18412118/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">18412118</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=18412118[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=18412118" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1002/ajmg.a.32262" target="_blank">Full Text</a>]
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<a id="Hong1995" class="mim-anchor"></a>
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Hong, Y. S., Kim, S. Y., Bhattacharya, A., Pratt, D. R., Hong, W. K., Tainsky, M. A.
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<strong>Structure and function of the HOX A1 human homeobox gene cDNA.</strong>
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/7622051/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">7622051</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=7622051" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1016/0378-1119(95)92712-g" target="_blank">Full Text</a>]
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Ingram, J. L., Stodgell, C. J., Hyman, S. L., Figlewicz, D. A., Weitkamp, L. R., Rodier, P. M.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/11091361/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">11091361</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=11091361" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1002/1096-9926(200012)62:6<393::AID-TERA6>3.0.CO;2-V" target="_blank">Full Text</a>]
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Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C. J., Duboule, D.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/15973411/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">15973411</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=15973411" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1038/nature03648" target="_blank">Full Text</a>]
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Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D.
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<strong>Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci.</strong>
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Science 346: 1004-1006, 2014.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/25414315/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">25414315</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=25414315" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1126/science.1257493" target="_blank">Full Text</a>]
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Lufkin, T., Dierich, A., LeMeur, M., Mark, M., Chambon, P.
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<strong>Disruption of the Hox-1.6 homeobox gene results in defects in a region corresponding to its rostral domain of expression.</strong>
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/1680563/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">1680563</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=1680563" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1016/0092-8674(91)90034-v" target="_blank">Full Text</a>]
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Makki, N., Capecchi, M. R.
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<strong>Cardiovascular defects in a mouse model of HOXA1 syndrome.</strong>
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Hum. Molec. Genet. 21: 26-31, 2012.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/21940751/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">21940751</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=21940751[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=21940751" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1093/hmg/ddr434" target="_blank">Full Text</a>]
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Mark, M., Lufkin, T., Vonesch, J.-L., Ruberte, E., Olivo, J.-C., Dolle, P., Gorry, P., Lumsden, A., Chambon, P.
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[<a href="https://doi.org/10.1242/dev.119.2.319" target="_blank">Full Text</a>]
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Pasqualetti, M., Neun, R., Davenne, M., Rijli, F. M.
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<strong>Retinoic acid rescues inner ear defects in Hoxa1 deficient mice.</strong>
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Nature Genet. 29: 34-39, 2001.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/11528388/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">11528388</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=11528388" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1038/ng702" target="_blank">Full Text</a>]
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<a id="Tischfield2005" class="mim-anchor"></a>
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<div class="">
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<p class="mim-text-font">
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Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C.
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<strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong>
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Nature Genet. 37: 1035-1037, 2005.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16155570/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16155570</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16155570" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1038/ng1636" target="_blank">Full Text</a>]
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<a id="12" class="mim-anchor"></a>
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<a id="Tischfield2006" class="mim-anchor"></a>
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<div class="">
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<p class="mim-text-font">
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Tischfield, M. A., Chan, W.-M., Grunert, J.-F., Andrews, C., Engle, E. C.
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<strong>HOXA1 mutations are not a common cause of Duane anomaly.</strong>
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Am. J. Med. Genet. 140A: 900-902, 2006.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/16528738/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">16528738</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=16528738" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1002/ajmg.a.31167" target="_blank">Full Text</a>]
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</p>
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<a id="13" class="mim-anchor"></a>
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<a id="Xiong2020" class="mim-anchor"></a>
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<div class="">
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<p class="mim-text-font">
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Xiong, Z., Xia, P., Zhu, X., Geng, J., Wang, S., Ye, B., Qin, X., Qu, Y., He, L., Fan, D., Du, Y., Tian, Y., Fan, Z.
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<strong>Glutamylation of deubiquitinase BAP1 controls self-renewal of hematopoietic stem cells and hematopoiesis.</strong>
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J. Exp. Med. 217: e20190974, 2020. Note: Electronic Article.
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[PubMed: <a href="https://pubmed.ncbi.nlm.nih.gov/31699823/" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">31699823</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=31699823" target="_blank" onclick="gtag('event', 'mim_outbound', {'name': 'PubMed Related', 'domain': 'pubmed.ncbi.nlm.nih.gov'})">related citations</a>]
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[<a href="https://doi.org/10.1084/jem.20190974" target="_blank">Full Text</a>]
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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<span class="mim-text-font">
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Bao Lige - updated : 03/16/2020
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<div class="row collapse" id="mimCollapseContributors">
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<span class="mim-text-font">
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Ada Hamosh - updated : 01/14/2015<br>Patricia A. Hartz - updated : 12/15/2014<br>Cassandra L. Kniffin - updated : 6/18/2008<br>Marla J. F. O'Neill - updated : 8/9/2006<br>Victor A. McKusick - updated : 9/21/2005<br>Ada Hamosh - updated : 7/27/2005<br>Ada Hamosh - updated : 8/27/2001<br>Ada Hamosh - updated : 12/5/2000<br>Alan F. Scott - updated : 8/22/1995
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<div class="col-lg-2 col-md-2 col-sm-4 col-xs-4">
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<span class="text-nowrap mim-text-font">
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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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<span class="mim-text-font">
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Victor A. McKusick : 8/22/1990
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<a href="#mimCollapseEditHistory" role="button" data-toggle="collapse"> Edit History: </a>
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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alopez : 08/27/2020
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<div class="row collapse" id="mimCollapseEditHistory">
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<span class="mim-text-font">
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ckniffin : 08/05/2020<br>carol : 03/18/2020<br>carol : 03/17/2020<br>mgross : 03/16/2020<br>alopez : 01/14/2015<br>mgross : 12/16/2014<br>mcolton : 12/15/2014<br>carol : 9/18/2013<br>wwang : 6/30/2008<br>ckniffin : 6/18/2008<br>carol : 1/26/2007<br>alopez : 8/9/2006<br>alopez : 8/9/2006<br>alopez : 10/14/2005<br>alopez : 9/26/2005<br>terry : 9/21/2005<br>alopez : 7/28/2005<br>terry : 7/27/2005<br>terry : 3/18/2004<br>alopez : 9/4/2001<br>terry : 8/27/2001<br>carol : 12/5/2000<br>terry : 12/5/2000<br>dkim : 7/21/1998<br>dkim : 6/26/1998<br>mark : 3/2/1998<br>terry : 2/17/1998<br>alopez : 6/4/1997<br>mark : 8/19/1996<br>marlene : 8/15/1996<br>mark : 8/22/1995<br>carol : 9/26/1994<br>supermim : 3/16/1992<br>carol : 8/22/1990
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<span class="mim-font">
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<strong>*</strong> 142955
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<h3>
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HOMEOBOX A1; HOXA1
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<span class="mim-font">
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<em>Alternative titles; symbols</em>
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<h4>
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<span class="mim-font">
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HOMEOBOX 1F; HOX1F<br />
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Hox-1.6, MOUSE, HOMOLOG OF<br />
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lab, DROSOPHILA, HOMOLOG OF
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<strong><em>HGNC Approved Gene Symbol: HOXA1</em></strong>
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<strong>SNOMEDCT:</strong> 720518006, 720567008;
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Cytogenetic location: 7p15.2
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Genomic coordinates <span class="small">(GRCh38)</span> : 7:27,092,993-27,096,000 </span>
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</em>
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</strong>
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<span class="small">(from NCBI)</span>
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<strong>Gene-Phenotype Relationships</strong>
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Location
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Phenotype
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Phenotype <br /> MIM number
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Inheritance
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Phenotype <br /> mapping key
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<span class="mim-font">
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7p15.2
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<span class="mim-font">
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Athabaskan brainstem dysgenesis syndrome
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601536
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Autosomal recessive
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<span class="mim-font">
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3
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<span class="mim-font">
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Bosley-Salih-Alorainy syndrome
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<span class="mim-font">
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601536
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<span class="mim-font">
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Autosomal recessive
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<td>
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<span class="mim-font">
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3
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<strong>TEXT</strong>
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<h4>
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<strong>Cloning and Expression</strong>
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<span class="mim-text-font">
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<p>In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on 4 separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. Hong et al. (1995) determined the structure of the first gene in the homeobox A cluster, HOXA1, by cloning its full-length cDNA, which predicts a protein of 335 amino acids. In vitro translation produced the expected 36-kD protein. An alternatively spliced cDNA was also obtained. In PA-1 teratocarcinoma cells, HOXA1 was induced by retinoic acid earlier than other HOXA cluster genes. </p>
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<span class="mim-font">
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<strong>Gene Function</strong>
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<p>HOX genes are required during the morphogenesis of both vertebrate digits and external genitals. Lonfat et al. (2014) investigated whether transcription in such distinct contexts involves a shared enhancer-containing landscape. They showed that the same regulatory topology is used, albeit with some tissue-specific enhancer-promoter interactions, which suggested the hijacking of a regulatory backbone from one context to another. In addition, comparable organizations were observed at both HOXA1 and HOXD1 (142987) clusters, which separated through genome duplication in an ancestral invertebrate animal. Lonfat et al. (2014) proposed that this convergent regulatory evolution was triggered by the preexistence of some chromatin architecture, thus facilitating the subsequent recruitment of the appropriate transcription factors. Lonfat et al. (2014) argued that regulatory topologies may have both favored and constrained the evolution of pleiotropic developmental loci in vertebrates. </p><p>Xiong et al. (2020) found that Bap1 (603089) facilitated expression of Hoxa1, which was required for self-renewal of mouse hematopoietic stem cells (HSCs). Ttll5 (612268) and Ttll7 (618813) glutamylated Bap1 at glu651 in HSCs, whereas Ccp3 (617346) removed Bap1 glutamylation. Bap1 glutamylation promoted its interaction with Ube2o (617649) and accelerated lys48-linked ubiquitination of Bap1 for its degradation. Degradation of Bap1 suppressed Hoxa1 expression, thereby enhancing HSC self-renewal and hematopoiesis. </p>
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<div>
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<br />
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<h4>
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<span class="mim-font">
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<strong>Mapping</strong>
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</div>
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<span class="mim-text-font">
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<p>Apiou et al. (1996) used fluorescence in situ hybridization to localize the HOXA gene cluster precisely to 7p15.3. </p>
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<div>
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<br />
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</div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>Molecular Genetics</strong>
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</h4>
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</div>
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<span class="mim-text-font">
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<p><strong><em>Autism Spectrum Disorder Susceptibility</em></strong></p><p>
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Ingram et al. (2000) identified a common polymorphism in the HOXA1 gene: an A-to-G substitution at codon 218, changing the codon for one histidine in a series of histidine repeats to an arginine at position 73. The frequency of the G allele was 20 to 60% among the Coriell Human Diversity Panel, but was not identified in any individuals of Asian origin including Indians, Japanese, and Chinese. The frequency of the G allele was 0.202 in 57 probands with autism spectrum disorders and 0.203 in their 32 affected relatives. The frequency of the G allele in 134 unaffected relatives of subjects with an Asperger spectrum disorder was 0.164. The frequency of the G allele in the convenience population for this study was 0.109. In the autism spectrum disorder families, there was a significant deviation from the HOXA1 genotype ratios expected from Hardy-Weinberg proportions. Among affected offspring, a significant deviation from mendelian expectation in gene transmission was observed. Ingram et al. (2000) suggested that there was evidence of an interaction between HOXA1, HOXB1, and gender in susceptibility to autism spectrum disorders. </p><p><strong><em>Bosley-Salih-Alorainy/Athabaskan Brainstem Dysgenesis Syndromes</em></strong></p><p>
|
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Tischfield et al. (2005) carried out SNP-based linkage analysis in a Saudi Arabian family with Bosley-Salih-Alorainy syndrome (BSAS; 601536) and identified a single, fully informative 8.5-Mb region on 7p15.3-p14.3 in which only the affected children were homozygous. Further analysis narrowed the linkage to a region of homozygosity of approximately 300 kb on 7p15.2. Because of similarities between the BSAS phenotype and the pathology of the Hoxa1 -/- mouse, and because the HOXA cluster falls in the haploidentical region, Tischfield et al. (2005) analyzed the HOXA1 gene in Saudi Arabian individuals with BSAS and found a homozygous guanine insertion, 175_176insG, predicted to result in a reading frameshift and the introduction of a premature stop codon (142955.0001). A Turkish individual with BSAS had a homozygous 84C-G transversion resulting in the substitution of a stop codon for a tyrosine residue (Y28X; 142955.0002). Noting the phenotypic overlap of BSAS, the Hoxa1 knockout mouse, and Athabaskan brainstem dysgenesis syndrome, Tischfield et al. (2005) analyzed genomic DNA from 5 of the reported individuals with ABDS and 4 of their phenotypically normal parents. All 5 affected individuals were homozygous across the HOXA1 locus and carried a homozygous 76C-T HOXA1 mutation resulting in substitution of a stop codon for arginine (R26X; 142955.0003). Tischfield et al. (2005) pointed out that to their knowledge this was the first report of viable homozygous truncating mutations in any human HOX gene and of a mendelian disorder resulting from mutations in a human HOX gene critical for development of the central nervous system. </p><p>Because 1 of the patients of Tischfield et al. (2005) with a mutation in HOXA1 had Duane anomaly and asymptomatic left carotid hypoplasia (see 142955.0001), Tischfield et al. (2006) analyzed the HOXA1 gene in 101 probands with isolated Duane anomaly (DA) and 30 with DA and other symptoms. None in this group harbored a mutation in SALL4 (607343) or ROBO3 (608630), and none were members of a pedigree whose phenotype maps to the DURS2 (604356) locus. No mutation was detected in any proband; the authors concluded that HOXA1 mutations are a rare cause of isolated Duane anomaly. </p>
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</span>
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<div>
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<br />
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</div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>Animal Model</strong>
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</span>
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</h4>
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</div>
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<span class="mim-text-font">
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<p>Lufkin et al. (1991) generated mice deficient in Hoxa1 by homologous recombination. Heterozygous mice were normal but homozygous mice died at birth from anoxia and had numerous defects that were centered at the levels of rhombomeres 4 to 7 and included delayed hindbrain neural tube closure, absence of certain cranial nerves and ganglia, and malformed inner ears and bones of the skull. Mark et al. (1993) further characterized the anatomic defects in Hoxa1 -/- mutant mice. Three-dimensional reconstructions of Hoxa1 -/- rhombencephalon revealed that it bears only 5 rhombomeric structures instead of the normal 7. The first 3 of these rhombomeres appeared normal as judged from the distribution pattern of Crabp1 (180230) transcripts in the neuroectoderm and from histologic analysis of the cranial nerve components derived from these structures. In contrast, the neural crest cell-free region normally located opposite rhombomere-5 is absent in Hoxa1 -/- embryos, and motor neurons of the facial and abducens nerves, which normally differentiate within rhombomeres 4, 5, and 6, are missing in Hoxa1 -/- fetuses. These data suggested that rhombomere 4 is markedly reduced, whereas rhombomere 5 is almost absent, in Hoxa1 -/- embryos. Remnants of rhombomeres 4 and 5 appeared to be fused caudally with rhombomere 6 to form a single fourth rhombomeric structure. Mark et al. (1993) found that the mutual relationship along the rostrocaudal axis between the otic pit and the neuroepithelial site of int2 protein secretion was not significantly changed in Hoxa1 -/- embryos. However, the abnormal relationship between the rhombencephalon and the epithelial inner ear may account for the aplasia and faulty differentiation of the membranous labyrinth, the disruption of the cartilaginous otic capsule, and the disorganization of some middle ear structures. </p><p>Pasqualetti et al. (2001) demonstrated that a single maternal administration of a low dose of the vitamin A metabolite retinoic acid was sufficient to compensate the requirement for Hoxa1 function in Hoxa1-deficient mice. A single dose of retinoic acid rescued cochlear and vestibular defects in mutant fetuses without affecting the development of wildtype fetuses. These results identified a temporal window of susceptibility to retinoids that is critical for mammalian inner ear specification, and provided the first evidence that a subteratogenic dose of vitamin A derivative can be effective in rescuing a congenital defect in the mammalian embryo. </p><p>Kmita et al. (2005) described mice that were lacking all Hoxa and Hoxd functions in their forelimbs. They showed that such limbs are arrested early in their developmental patterning and display severe truncations of distal elements, partly owing to the absence of Sonic hedgehog (600725) expression. These results indicated that the evolutionary recruitment of Hox gene function into growing appendages might have been crucial in implementing hedgehog signaling, subsequently leading to the distal extension of tetrapod appendages. Accordingly, Kmita et al. (2005) suggested these mutant limbs may be reminiscent of an ancestral trunk extension, related to that proposed for arthropods. </p><p>Makki and Capecchi (2012) found that deletion of Hoxa1 in mice caused a variety of malformations of the cardiac outflow tract and great arteries in late-stage embryos. Defects showed variable penetrance and included interrupted aortic arch type B, aberrant subclavian artery, and tetralogy of Fallot (see 187500). During early mouse embryogenesis, Hoxa1 was expressed in precursors of cardiac neural crest cells, and it directed expression of genes important for neural crest specification. </p>
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<div>
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<h4>
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<span class="mim-font">
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<strong>ALLELIC VARIANTS</strong>
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</span>
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<strong>4 Selected Examples):</strong>
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</span>
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</h4>
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<div>
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<p />
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</div>
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<div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>.0001 BOSLEY-SALIH-ALORAINY SYNDROME</strong>
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</span>
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</h4>
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</div>
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<span class="mim-text-font">
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HOXA1, 1-BP INS, 175G
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<br />
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SNP: rs769152039,
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gnomAD: rs769152039,
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ClinVar: RCV000016027, RCV000984930, RCV001008325
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</span>
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<p>In affected members of 3 consanguineous Saudi Arabian families with Bosley-Salih-Alorainy syndrome and in a 4-year-old Saudi Arabian boy, born of consanguineous parents, with Duane anomaly and hypoplastic left carotid artery (BSAS; see 601536), Tischfield et al. (2005) identified homozygosity for a guanine insertion, 175_176insG. The mutation segregated with the disorder in the families; haplotype analysis indicated a founder effect. The mutation was predicted to result in a frameshift and premature termination, although functional studies of the variant and studies of patient cells were not performed. </p><p>Bosley et al. (2008) identified the 175_176insG mutation in affected members of 2 additional consanguineous Saudi Arabian families with BSAS. The mutation was predicted to result in a truncated protein and absence of HOXA1 activity. Five patients had conotruncal or septal heart defects. </p>
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</span>
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<div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>.0002 BOSLEY-SALIH-ALORAINY SYNDROME</strong>
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</span>
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</h4>
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</div>
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<div>
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<span class="mim-text-font">
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HOXA1, TYR28TER
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<br />
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SNP: rs104894017,
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ClinVar: RCV000016028
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</span>
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<div>
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<span class="mim-text-font">
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<p>In an individual with Bosley-Salih-Alorainy syndrome (BSAS; see 601536) from a Turkish family, Tischfield et al. (2005) found homozygosity for an 84C-G transversion resulting in substitution of a stop codon for a tyrosine residue (Y28X). Functional studies of the variant were not performed, but it was predicted to result in a loss of function. </p>
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</span>
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</div>
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<div>
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<br />
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</div>
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</div>
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<div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>.0003 ATHABASKAN BRAINSTEM DYSGENESIS SYNDROME</strong>
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</span>
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</h4>
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</div>
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<div>
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<span class="mim-text-font">
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HOXA1, ARG26TER
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<br />
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SNP: rs104894018,
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gnomAD: rs104894018,
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ClinVar: RCV000016029, RCV002466406
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</span>
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</div>
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<div>
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<span class="mim-text-font">
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<p>In individuals with Athabaskan brainstem dysgenesis syndrome (ABDS; 601536), reported in Native American tribes, Tischfield et al. (2005) found homozygosity for a 76C-T transition in the HOXA1 gene, predicted to result in the substitution of a stop codon for an arginine residue (arg26 to ter; R26X). The mutation was heterozygous in the parents and absent from 344 control chromosomes; haplotype analysis was consistent with a founder effect. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function. </p><p>Bosley et al. (2008) identified the R26X mutation in 3 patients from 3 families of Native American origin with ABDS. All had deafness, horizontal gaze palsy, and developmental delay, and 2 had congenital cardiac defects. </p>
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</span>
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</div>
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</div>
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</div>
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<div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>.0004 BOSLEY-SALIH-ALORAINY SYNDROME</strong>
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</span>
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</h4>
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</div>
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<div>
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<span class="mim-text-font">
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HOXA1, 1-BP DEL, 185G
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<br />
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SNP: rs1562700083,
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ClinVar: RCV000016030
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</span>
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</div>
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<div>
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<span class="mim-text-font">
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<p>In a Saudi Arabian patient, born of consanguineous parents, with Bosley-Salih-Alorainy syndrome (BSAS; 601536), Bosley et al. (2008) identified a homozygous 1-bp deletion (185delG) in the HOXA1 gene, predicted to result in a frameshift and premature termination. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function. The patient had Duane retraction anomaly, horizontal gaze restriction, and deafness, but normal cognition. </p>
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</span>
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</div>
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<div>
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<br />
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</div>
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</div>
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</div>
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<div>
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<h4>
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<span class="mim-font">
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<strong>REFERENCES</strong>
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</span>
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</h4>
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<div>
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<p />
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</div>
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<div>
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<ol>
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<li>
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<p class="mim-text-font">
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Apiou, F., Flagiello, D., Cillo, C., Malfoy, B., Poupon, M.-F., Dutrillaux, B.
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<strong>Fine mapping of human HOX gene clusters.</strong>
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Cytogenet. Cell Genet. 73: 114-115, 1996.
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[PubMed: 8646877]
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[Full Text: https://doi.org/10.1159/000134320]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu-Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., Erickson, R. P.
|
|
<strong>The clinical spectrum of homozygous HOXA1 mutations.</strong>
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Am. J. Med. Genet. 146A: 1235-1240, 2008.
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[PubMed: 18412118]
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[Full Text: https://doi.org/10.1002/ajmg.a.32262]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Hong, Y. S., Kim, S. Y., Bhattacharya, A., Pratt, D. R., Hong, W. K., Tainsky, M. A.
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<strong>Structure and function of the HOX A1 human homeobox gene cDNA.</strong>
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Gene 159: 209-214, 1995.
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[PubMed: 7622051]
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[Full Text: https://doi.org/10.1016/0378-1119(95)92712-g]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Ingram, J. L., Stodgell, C. J., Hyman, S. L., Figlewicz, D. A., Weitkamp, L. R., Rodier, P. M.
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<strong>Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders.</strong>
|
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Teratology 62: 393-405, 2000.
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[PubMed: 11091361]
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[Full Text: https://doi.org/10.1002/1096-9926(200012)62:6<393::AID-TERA6>3.0.CO;2-V]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C. J., Duboule, D.
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<strong>Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function.</strong>
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Nature 435: 1113-1116, 2005.
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[PubMed: 15973411]
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[Full Text: https://doi.org/10.1038/nature03648]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D.
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<strong>Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci.</strong>
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Science 346: 1004-1006, 2014.
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[PubMed: 25414315]
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[Full Text: https://doi.org/10.1126/science.1257493]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Lufkin, T., Dierich, A., LeMeur, M., Mark, M., Chambon, P.
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<strong>Disruption of the Hox-1.6 homeobox gene results in defects in a region corresponding to its rostral domain of expression.</strong>
|
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Cell 66: 1105-1119, 1991.
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[PubMed: 1680563]
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[Full Text: https://doi.org/10.1016/0092-8674(91)90034-v]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Makki, N., Capecchi, M. R.
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<strong>Cardiovascular defects in a mouse model of HOXA1 syndrome.</strong>
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Hum. Molec. Genet. 21: 26-31, 2012.
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[PubMed: 21940751]
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[Full Text: https://doi.org/10.1093/hmg/ddr434]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Mark, M., Lufkin, T., Vonesch, J.-L., Ruberte, E., Olivo, J.-C., Dolle, P., Gorry, P., Lumsden, A., Chambon, P.
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<strong>Two rhombomeres are altered in Hoxa-1 mutant mice.</strong>
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Development 119: 319-338, 1993.
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[PubMed: 8287791]
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[Full Text: https://doi.org/10.1242/dev.119.2.319]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Pasqualetti, M., Neun, R., Davenne, M., Rijli, F. M.
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<strong>Retinoic acid rescues inner ear defects in Hoxa1 deficient mice.</strong>
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Nature Genet. 29: 34-39, 2001.
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[PubMed: 11528388]
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[Full Text: https://doi.org/10.1038/ng702]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Tischfield, M. A., Bosley, T. M., Salih, M. A. M., Alorainy, I. A., Sener, E. C., Nester, M. J., Oystreck, D. T., Chan, W.-M., Andrews, C., Erickson, R. P., Engle, E. C.
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<strong>Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.</strong>
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Nature Genet. 37: 1035-1037, 2005.
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[PubMed: 16155570]
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[Full Text: https://doi.org/10.1038/ng1636]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Tischfield, M. A., Chan, W.-M., Grunert, J.-F., Andrews, C., Engle, E. C.
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<strong>HOXA1 mutations are not a common cause of Duane anomaly.</strong>
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Am. J. Med. Genet. 140A: 900-902, 2006.
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[PubMed: 16528738]
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[Full Text: https://doi.org/10.1002/ajmg.a.31167]
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</p>
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</li>
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<li>
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<p class="mim-text-font">
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Xiong, Z., Xia, P., Zhu, X., Geng, J., Wang, S., Ye, B., Qin, X., Qu, Y., He, L., Fan, D., Du, Y., Tian, Y., Fan, Z.
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<strong>Glutamylation of deubiquitinase BAP1 controls self-renewal of hematopoietic stem cells and hematopoiesis.</strong>
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J. Exp. Med. 217: e20190974, 2020. Note: Electronic Article.
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[PubMed: 31699823]
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[Full Text: https://doi.org/10.1084/jem.20190974]
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</li>
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</ol>
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<div>
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<br />
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</div>
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</div>
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<div>
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<div class="row">
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<div class="col-lg-1 col-md-1 col-sm-2 col-xs-2">
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<span class="text-nowrap mim-text-font">
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Contributors:
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</span>
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</div>
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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<span class="mim-text-font">
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Bao Lige - updated : 03/16/2020<br>Ada Hamosh - updated : 01/14/2015<br>Patricia A. Hartz - updated : 12/15/2014<br>Cassandra L. Kniffin - updated : 6/18/2008<br>Marla J. F. O'Neill - updated : 8/9/2006<br>Victor A. McKusick - updated : 9/21/2005<br>Ada Hamosh - updated : 7/27/2005<br>Ada Hamosh - updated : 8/27/2001<br>Ada Hamosh - updated : 12/5/2000<br>Alan F. Scott - updated : 8/22/1995
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</span>
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</div>
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</div>
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</div>
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<div>
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<br />
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</div>
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<div>
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<div class="row">
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<div class="col-lg-1 col-md-1 col-sm-2 col-xs-2">
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<span class="text-nowrap mim-text-font">
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Creation Date:
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</span>
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</div>
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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<span class="mim-text-font">
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Victor A. McKusick : 8/22/1990
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</span>
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</div>
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</div>
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<div class="col-lg-1 col-md-1 col-sm-2 col-xs-2">
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<span class="text-nowrap mim-text-font">
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Edit History:
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</span>
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</div>
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<div class="col-lg-6 col-md-6 col-sm-6 col-xs-6">
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<span class="mim-text-font">
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alopez : 08/27/2020<br>ckniffin : 08/05/2020<br>carol : 03/18/2020<br>carol : 03/17/2020<br>mgross : 03/16/2020<br>alopez : 01/14/2015<br>mgross : 12/16/2014<br>mcolton : 12/15/2014<br>carol : 9/18/2013<br>wwang : 6/30/2008<br>ckniffin : 6/18/2008<br>carol : 1/26/2007<br>alopez : 8/9/2006<br>alopez : 8/9/2006<br>alopez : 10/14/2005<br>alopez : 9/26/2005<br>terry : 9/21/2005<br>alopez : 7/28/2005<br>terry : 7/27/2005<br>terry : 3/18/2004<br>alopez : 9/4/2001<br>terry : 8/27/2001<br>carol : 12/5/2000<br>terry : 12/5/2000<br>dkim : 7/21/1998<br>dkim : 6/26/1998<br>mark : 3/2/1998<br>terry : 2/17/1998<br>alopez : 6/4/1997<br>mark : 8/19/1996<br>marlene : 8/15/1996<br>mark : 8/22/1995<br>carol : 9/26/1994<br>supermim : 3/16/1992<br>carol : 8/22/1990
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