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Update and analysis of the University College London Low Density Lipoprotein receptor familial hypercholesterolemia database

Leigh, SEA; Foster, AH; Whittall, RA; Hubbart, CS; Humphries, SE; (2008) Update and analysis of the University College London Low Density Lipoprotein receptor familial hypercholesterolemia database. ANN HUM GENET , 72 485 - 498. 10.1111/j.1469-1809.2008.00436.x.

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Abstract

Familial hypercholesterolemia (FH) (OMIM 143890) is most commonly caused by variations in the LDLR gene which encodes the receptor for Low Density Lipoprotein (LDL) cholesterol particles. We have updated the University College London (UCL) LDLR FH database (http://www.ucl.ac.uk/ldlr) by adding variants reported in the literature since 2001, converting existing entries to standard nomenclature, and transferring the database to the Leiden Open Source Variation Database (LOVD) platform. As of July 2007 the database listed 1066 unique LDLR gene events. Sixty five percent (n = 689) of the variants are DNA substitutions, 24% (n = 260) small DNA rearrangements (< 100bp) and 11% (n = 117) large DNA rearrangements (> 100bp), proportions which are similar to those reported in the 2001 database (n = 683, 62%, 24% and 14% respectively). The DNA substitutions and small rearrangements occur along the length of the gene, with 24 in the promoter region, 86 in intronic sequences and 839 in the exons (93 nonsense variants, 499 missense variants and 247 small rearrangements). These occur in all exons, with the highest proportion (20%) in exon 4 (186/949); this exon is the largest and codes for the critical ligand binding region, where any missense variant is likely to be pathogenic. Using the PolyPhen and SIFT prediction computer programmes 87% of the missense variants are predicted to have a deleterious effect on LDLR activity, and it is probable that at least 48% of the remainder are also pathogenic, but their role in FH causation requires confirmation by in vitro or family studies.

Type:Article
Title:Update and analysis of the University College London Low Density Lipoprotein receptor familial hypercholesterolemia database
DOI:10.1111/j.1469-1809.2008.00436.x
Keywords:familial hypercholesterolaemia, LDLR, nomenclature, database, MOLECULAR-GENETIC ANALYSIS, LDL-RECEPTOR, MESSENGER-RNA, CHOLESTEROL LEVELS, MUTATION ANALYSIS, HUMAN GENOME, SEQUENCE, IDENTIFICATION, NETHERLANDS, SPECTRUM
UCL classification:UCL > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Cardiovascular Science

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