Mutalyzer

<h2 id="background">Background</h2>
<p><a href="/facts/Genetic_testing/H21wH0ze">Genetic testing</a> is generally performed in families with <a href="/facts/Genetic_disorder/hFqt2NLn">hereditary disease</a>. Any sequence variant identified in a gene can be described in test reports using the position of the change and the <a href="/facts/Nucleobase/zj1Vl9Qh">nucleotide</a> or <a href="/facts/Amino_acid/WDxYwBny">amino acid</a> involved. With this simple rule, a deletion of the nucleotide <a href="/facts/Guanine/hoTSpz0x">guanine</a> (G) in a stretch of 4 G nucleotides might be described in 4 different ways, when each of the G positions is used. Although different descriptions do not affect the functional consequences of the change,  they may obfuscate the fact that two persons share the same variant or the real frequency of a variant in the population. The standard human sequence variant nomenclature proposed by the Human Genome Variation Society was developed to solve this problem.<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> Proper variant descriptions are expected to facilitate searches for more information about the functional consequences in the literature and in gene variant or locus-specific databases (LSDBs).
</p><p>Mutalyzer is used by the Leiden Open Variation Database (<a href="/facts/LOVD/q2alPnHb">LOVD</a>), which stores sequence variant information for many human genes, to check variant descriptions before submission of new data.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> This helps data sharing, display and integration with other <a href="/facts/Genetic_resources/MCxvURf8">genetic resources</a> (e.g., <a href="/facts/Ensembl/dEhjvNaA">Ensembl</a>, <a href="/facts/UCSC_Genome_Browser/kwumPyLb">UCSC Genome Browser</a>, NCBI sequence viewer)
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<h2 id="external-links">External links</h2>
<ul><li><a href="https://mutalyzer.nl/">Mutalyzer website</a></li>
<li><a href="http://www.hgvs.org/mutnomen">HGVS sequence variant nomenclature website</a></li>
<li><a href="http://www.LOVD.nl/2.0/">LOVD 2.0 website</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide">GenBank website</a></li>
<li><a href="http://www.lrg-sequence.org/">Locus Reference Genomic website</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/RefSeq">RefSeq website</a></li></ul>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Wildeman, Martin; Van Ophuizen, Ernest; Den Dunnen, Johan T.; Taschner, Peter E.M. (2008). "Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker". Human Mutation. 29 (1): 6–13. doi:10.1002/humu.20654. PMID 18000842. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>Den Dunnen, Johan T.; Antonarakis, Stylianos E. (2000). "Mutation Nomenclature Extensions and Suggestions to Describe Complex Mutations: A Discussion". Human Mutation. 15 (1): 7–12. doi:10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N. PMID 10612815. <a href="https://doi.org/10.1002%2F%28SICI%291098-1004%28200001%2915%3A1%3C7%3A%3AAID-HUMU4%3E3.0.CO%3B2-N" target="_blank">https://doi.org/10.1002%2F%28SICI%291098-1004%28200001%2915%3A1%3C7%3A%3AAID-HUMU4%3E3.0.CO%3B2-N</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>Fokkema, Ivo F.A.C.; Den Dunnen, Johan T.; Taschner, Peter E.M. (2005). "LOVD: Easy creation of a locus-specific sequence variation database using an 'LSDB-in-a-box' approach". Human Mutation. 26 (2): 63–8. doi:10.1002/humu.20201. PMID 15977173. <a href="https://doi.org/10.1002%2Fhumu.20201" target="_blank">https://doi.org/10.1002%2Fhumu.20201</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
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Mutalyzer open-in-new

Mutalyzer