The UCL low-density lipoprotein receptor gene variant database: pathogenicity update.
Familial hypercholesterolaemia (OMIM 143890) is most frequently caused by variations in the low-density lipoprotein receptor (LDLR) gene. Predicting whether novel variants are pathogenic may not be straightforward, especially for missense and synonymous variants. In 2013, the Association of Clinical Genetic Scientists published guidelines for the classification of variants, with categories 1 and 2 representing clearly not or unlikely pathogenic, respectively, 3 representing variants of unknown significance (VUS), and 4 and 5 representing likely to be or clearly pathogenic, respectively. Here, we update the University College London (UCL)LDLRvariant database according to these guidelines.



PubMed searches and alerts were used to identify novelLDLRvariants for inclusion in the database. Standardin silicotools were used to predict potential pathogenicity. Variants were designated as class 4/5 only when the predictions from the different programs were concordant and as class 3 when predictions were discordant.



The updated database (http://www.lovd.nl/LDLR) now includes 2925 curated variants, representing 1707 independent events. All 129 nonsense variants, 337 small frame-shifting and 117/118 large rearrangements were classified as 4 or 5. Of the 795 missense variants, 115 were in classes 1 and 2, 605 in class 4 and 75 in class 3. 111/181 intronic variants, 4/34 synonymous variants and 14/37 promoter variants were assigned to classes 4 or 5. Overall, 112 (7%) of reported variants were class 3.



This study updates theLDLRvariant database and identifies a number of reported VUS where additional family andin vitrostudies will be required to confirm or refute their pathogenicity.
Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
Sarah
0000-0003-3368-7059
S
Leigh
Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
Marta
M
Futema
Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
Ros
R
Whittall
NE Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK.
Alison
A
Taylor-Beadling
Bristol Genetics Laboratory, Pathology Sciences, Blood Sciences and Bristol Genetics, Southmead Hospital, Bristol, UK.
Maggie
M
Williams
Clinical Genetics and Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Johan T
JT
den Dunnen
Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
Steve E
SE
Humphries
D030541:Databases, Genetic; D014644:Genetic Variation; D006801:Humans; D006938:Hyperlipoproteinemia Type II / Q000235:genetics* / Q000473:pathology; D020125:Mutation, Missense / Q000235:genetics; D010641:Phenotype; D011401:Promoter Regions, Genetic; D011973:Receptors, LDL / Q000235:genetics*
C573412:LDLR protein, human; D011973:Receptors, LDL
Familial Hypercholesterolemia; LDLR; database; in silico pathogenicity predictions; locus specific variant