Variant and patient data

Database statistics (Summary tables)

A summary of the database statistics can be reached through the "Database statistics" submenu item under the Variants tab, or the "Summary tables" link from the gene homepage.

In the first table, the numbers of variants are shown per exon (and intron, depending on the values in the Exon column). Next to the numbers are horizontal bars showing the relative percentage of variants in this exon or intron. If the Reference Sequence parser has been run using a GenBank file, LOVD knows the actual lengths of the exons and introns, and the percentages are compensated using these exon and intron lengths. LOVD tries to interpret exon values as much as possible to group them together.

The bottom three tables represent the numbers of variants at DNA, RNA and Protein levels, given as absolute numbers and as percentages (bars), categorized according to variant types (e.g. substitutions, deletions). The variant types are links, clicking on them will give you an overview of all those variants counted. Please note that the number of variants shown can deviate from the numbers shown in the database statistics tables. Reasons for these differences can be that a variant is reported more than once (see # Reported field) or a homozygous variant (shown only once but counted twice).
The DNA variants table also displays the number of variants per section of the gene (5' start, coding region, introns, 3' stop). These numbers are always calculated based on textual interpretation of the DNA field. DNA field. Please note that the values "c.=" and "c.0" in the DNA field are not counted as variants.

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Last modified 2014/08/25 14:48:31 CEST

When using or discussing LOVD please refer to:
Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT (2011). LOVD v.2.0: the next generation in gene variant databases. Hum Mutat. 2011 May;32(5):557-63.

LOVD has received funding from the European Community's Seventh Framework Programme
(FP7/2007-2013) under grant agreement nº 200754 - the GEN2PHEN project.
Leiden University Medical Center, Netherlands
Ing. Ivo F.A.C. Fokkema, Dr. Johan T. den Dunnen