All variants in the LDLR gene

Information The variants shown are described using the NM_000527.4 transcript reference sequence.

3731 entries on 38 pages. Showing entries 1 - 100.
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Effect     

Exon     

AscendingDNA change (cDNA)     

Protein     

RNA change     

DNA/Legacy     

Predict/MutationTaster     

P-domain     

Predict/PolyPhen     

Predict/SIFT     

Conservation     

Predict/Splice     

Enzyme activity     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Owner     
+/+ 4 c.[649_654dup;657_661del] p.([Asp217_Gly218dup; Gly219fs*7]) r.(?) [D196_G197dup;G198fsX7] - LDL-receptor class A5 - - - - - ACGS pathogenic g.[11216231_11216236dup;11216239_11216243del] - - - LDLR_000370 predicted trucated protein; 6bp duplication (GATGGT) & 5bp deletion (CCCCG) PubMed: Giesel 1995 - - Germline - - - 0 - Sarah Leigh
+/+ _1_2i c.-1823_190+566del p.0? r.(?) - - Promoter - exon 2 - - - - - ACGS pathogenic g.11198402_11211587del g.11087726_11100911del - - LDLR_000005 predicted no protein; Deletion of exons 1 & 2; May be the same as c.1-?_190+?del PubMed: Goldmann 2010 - - Germline - 1/37 patients with LDLR mutation. 1/1945 FH patients. Variant not present in controls - 0 - Sarah Leigh
+/. _1_1i c.-1818_67+1091delinsTTC p.0? r.0? - - - - - - - - - pathogenic (dominant) g.11198407_11201382delinsTTC g.11087731_11090706delinsTTC 11198406_11201384del, insTTCG - LDLR_002172 2977 del exon 1 PubMed: Wong 2019, Journal: Wong 2019 - - Germline yes - - 0 - Karen HY Wong
-?/-? _1 c.-268G>T p.? r.(=) - - FP2 cis acting regulatory element - - 7/8 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Transient transfection in HepG2 cells demonstrated ACGS likely benign g.11199957G>T g.11089281G>T - - LDLR_000374 Hobb's numbering -175. Probably rare African non-disease causing variant. Found in FH and normal, may contribute to FH when present with other FH alleles (c.1222G>A, p.E408K) PubMed: Scholtz 1999 - - Germline - - - 0 - Sarah Leigh
-?/-? _1 c.-268G>T p.? r.(=) - - FP2 cis acting regulatory element - - 7/8 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - limited effect on LDLR activity ACGS likely benign g.11199957G>T g.11089281G>T - - LDLR_000374 - PubMed: Whittall 2002 - - Germline - - - 0 - Sarah Leigh
-?/. - c.-268G>T p.(=) r.(?) - - - - - - - - - likely benign g.11199957G>T g.11089281G>T LDLR(NM_000527.4):c.-268G>T - LDLR_000374 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/? _1 c.-221_-220insA p.? r.(=) - - FP1 cis acting regulatory element - - - - - ACGS VUS g.11200005dup g.11089329dup - - LDLR_000950 - PubMed: Bodamer 2002 - - Germline - - - 0 - Sarah Leigh
-?/-? _1 c.-217C>T p.? r.(=) - - FP1 cis acting regulatory element - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 160% luciferase activity compared to wt {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS likely benign g.11200008C>T g.11089332C>T - - LDLR_000015 predicted enhanced transcription; Hobb's numbering -124; Within 2bp of cis-acting regulatory element FP1; Found with c.-149C>T (Hobb's numbering -59) in normal son of proband for c.-149C>T PubMed: Scholtz 1999 - - Germline - - - 0 - Sarah Leigh
-?/? _1 c.-217C>T p.? r.(=) IVS1-217C>T - FP1 cis acting regulatory element - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 160% luciferase activity compared to wt {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS likely benign g.11200008C>T g.11089332C>T - - LDLR_000015 predicted enhanced transcription; Hobb's numbering -124; Within 2bp of cis-acting regulatory element FP1; Found on same allele as c.2041T>G, p.(Cys681Gly); increased expression of this pathogenic variant under the influence of c.-217C>T may explain the Hmz phenotype of this patient. PubMed: Snozek 2009 - - Germline - - - 0 - Sarah Leigh
-?/? _1 c.-215A>G p.? r.(=) - - FP1 cis acting regulatory element - - 11/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 100% luciferase activity compared to wt {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS likely benign g.11200010A>G g.11089334A>G - - LDLR_000006 prediction no effect on transcription PubMed: Usifo 2012 - - Germline - - - 0 - Sarah Leigh
-?/-? _1 c.-208A>T p.? r.(=) - - SREBP1/FP1 - - 12/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 100% of wt trascriptional activity (luciferase assay). ACGS likely benign g.11200017A>T g.11089341A>T - - LDLR_001268 prediction no effect on transcription PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
?/? _1 c.-206C>T p.? r.(=) - - SREBP1/FP1 - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200019C>T g.11089343C>T - - LDLR_001010 - PubMed: Lind 2002 - - Germline - - - 0 - Sarah Leigh
?/? _1 c.-193_-186delinsTG p.? r.(=) - - SREBP1 binding site - - - - not tested ACGS VUS g.11200032_11200039delinsTG g.11089356_11089363delinsTG - - LDLR_001024 - PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
?/? _1 c.-188C>T p.? r.(=) - - SREBP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200037C>T g.11089361C>T - - LDLR_001023 - PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+?/. - c.-187C>T p.(=) r.(?) - - - - - - - - - likely pathogenic g.11200038C>T g.11089362C>T LDLR(NM_000527.4):c.-187C>T - LDLR_002180 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - promotor & exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; 13kb deletion of promotor & exon 1; Predicted to be pathogenic according to criteria set by Huijgen et al European Heart Journal (2012) 33, 2325–2330. Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) FH Valencia-5 - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; 6.8kb deletion of promotor & exon 1; Similar to FH Denver-1 (6kb deletion of promotor & exon 1); No mRNA Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Chaves 2001 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; 13kb deletion of exon 1 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion of promoter & exon 1; Found in one proband Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Tichy 2012 - - Germline - 0.19 in this study - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion of exon 1; No details given of size, could be the same as other exon 1 deletions. Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Koeijvoets 2005 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promoter - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; 9325bp deletion of promotor & exon 1 (see original paper for genomic breakpoints); Not the same as FH French Canadian-1 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Nissen 2006 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) FH Denver-1 - Promotor - exon 1 - - - - <2% LDLR activity when Htz with unknown FH allele ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion of promotor & exon 1 (6kb); No detectable mRNA Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Hobbs 1988 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) FH French Canadian-1 - Promotor - exon 1 - - - - <2% LDLR activity in Hmz ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion of promotor & exon 1 (>10kb); Found in 60% French Canadian FH Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Hobbs 1987 - - Germline - - - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion of promotor & exon 1, size of deletion not stated; Reported in 2 probands but may be different deletions in each. Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Marduel 2010 - - Germline - NA - 0 - Sarah Leigh
+/+ _1_1i c.(?_-187)_(67+1_68-1)del p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS pathogenic g.11200038_11200292del - c.-187-?_67+?del - LDLR_000007 predicted no protein; Deletion >30 kb upstream of promotor & exon 1 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Sharifi 2016 - - Germline - NA - 0 - Sarah Leigh
+?/+? _1_1i c.(?_-187)_(67+1_68-1)dup p.0? r.(?) - - Promotor - exon 1 - - - - - ACGS likely pathogenic g.11200038_11200292dup - c.-187-?_67+?dup - LDLR_001273 predicted no protein; Duplication of promotor & exon 1 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Sharifi 2016 - - Germline - NA - 0 - Sarah Leigh
+/+ _1_2i c.(?_-187)_(190+1_191-1)del p.0? r.(?) - - Promotor - exon 2 - - - - - ACGS pathogenic g.11200038_11211022del - c.-187-?_190+?del - LDLR_000008 predicted no protein; Deletion of exons 1 & 2 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Chmara 2010 - - Germline - 4/169 patients with LDLR mutation. 4/378 FH patients. Variant not present in Normal Non FH patients - 0 - Sarah Leigh
+/+ _1_2i c.(?_-187)_(190+1_191-1)del p.0? r.(?) FH Valencia-1 - Promotor - exon 2 - - - - - ACGS pathogenic g.11200038_11211022del - c.-187-?_190+?del - LDLR_000008 predicted no protein; 18kb deletion of promotor - exon 2; Similar to FH Siracusa (20kb deletion of promotor - exon 2) Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Chaves 2001 - - Germline - - - 0 - Sarah Leigh
+/+ _1_2i c.(?_-187)_(190+1_191-1)del p.0? r.(?) - - Promotor - exon 2 - - - - - ACGS pathogenic g.11200038_11211022del - c.-187-?_190+?del - LDLR_000008 predicted no protein; Deletion of exons 1-2; No details given of size could be the same as other deletions. Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Koeijvoets 2005 - - Germline - - - 0 - Sarah Leigh
+/+ _1_2i c.(?_-187)_(190+1_191-1)del p.0? r.(?) FH Siracusa - Promotor - exon 2 - - - - 45% LDLR activity in Htz fibroblasts ACGS pathogenic g.11200038_11211022del - c.-187-?_190+?del - LDLR_000008 predicted no protein; 20kb deletion of promotor and exons 1-2; Similar to FH Valencia-1 (18kb deletion of prom-exon2) Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Garuti 1996 - - Germline - - - 0 - Sarah Leigh
+/+ _1_6i c.(?_-187)_(940+1_941-1)del p.0? r.(?) FH Bologna-1 - Promoter - exon 6 - - - - - ACGS pathogenic g.11200038_11218191del - c.-187-?_940+?del - LDLR_001274 predicted no protein; >10kb deletion of promotor & exons 1-6 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Sun 1992 - - Germline - - - 0 - Sarah Leigh
+/+ _1_6i c.(?_-187)_(940+1_941-1)del p.0? r.(?) FH Bari-3 - Promoter - exon 6 - - - - - ACGS pathogenic g.11200038_11218191del - c.-187-?_940+?del - LDLR_001274 predicted no protein; 24kb deletion the promotor - exon 6 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Bertolini 2000 - - Germline - - - 0 - Sarah Leigh
+/+ _1_6i c.(?_-187)_(940+1_941-1)del p.0? r.(?) FH Bologna-1 - Promoter - exon 6 - - - - 40-50% LDLR activity in Htz ACGS pathogenic g.11200038_11218191del - c.-187-?_940+?del - LDLR_001274 predicted no protein; >25kb deletion of promotor & exons 1-6 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Lelli 1991 - - Germline - - - 0 - Sarah Leigh
+/+ _1_7i c.(?_-187)_(1060+1_1061-1)del p.0? r.(?) - - Promoter - exon 7 - - - - - ACGS pathogenic g.11200038_11221448del - c.-187-?_1060+?del - LDLR_001271 predicted no protein; Deletion of promoter - exon 7; Found in 1 proband, segregates with FH in 2 affected relatives and not in 2 unaffected relatives Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Marduel 2010 - - Germline - - - 0 - Sarah Leigh
+/+ _1_8i c.(?_-187)_(1186+1_1187-1)del p.0? r.(?) - - Promoter - exon 8 - - - - - ACGS pathogenic g.11200038_11222316del - c.-187-?_1186+?del - LDLR_001091 predicted no protein; 23kb deletion of promotor and exons 1-8 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+/+ _1_12i c.(?_-187)_(1845+1_1846-1)del p.0? r.(?) - - Promoter - exon 12 - - - - - ACGS pathogenic g.11200038_11227675del - c.-187-?_1845+?del - LDLR_001167 predicted no protein; Deletion of exons 1-12 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Shin 2015 - - Germline - - - 0 - Sarah Leigh
+/+ _1_14i c.(?_-187)_(2140+1_2141-1)del p.0? r.(?) - - Promoter - exon 14 - - - - - ACGS pathogenic g.11200038_11231199del - c.-187-?_2140+?del - LDLR_000009 predicted no protein; Deletion of exons 1-14 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Van der Graaf 2011 - - Germline - - - 0 - Sarah Leigh
+/+ _1_15i c.(?_-187)_(2311+1_2312-1)del p.0? r.(?) - - Promoter - exon 15 - - - - - ACGS pathogenic g.11200038_11234021del - c.-187-?_2311+?del - LDLR_001272 predicted no protein; >36kb htz deletion of exons 1-15 Variant Error [EMISMATCH/EUNCERTAIN]: This transcript variant has an error. Please fix this entry and then remove this message. PubMed: Bertolini 2013 - - Germline - - - 0 - Sarah Leigh
+/+ _1_18_ c.(?_-187)_(*2584_?)del p.0? r.(?) - - whole gene - - - - - ACGS pathogenic g.11200038_11244576del g.11089362_11133900del c.-187-?_*2584del - LDLR_000010 predicted no protein; deletion of whole gene; found in 1 proband, segregates with FH in 2 affected relatives and not in 2 unaffected relatives PubMed: Marduel 2010 - - Germline - - - 0 - Sarah Leigh
+/+ _1_18_ c.(?_-187)_(*2584_?)del p.0? r.(?) - - whole gene - - - - - ACGS pathogenic g.11200038_11244577del g.11089362_11133901del c.-187-?_*2584del - LDLR_000010 predicted no protein; deletion of whole gene PubMed: Usifo 2012 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-185_-183del p.(=) r.(=) FH Pedi-2 - SREBP1 binding site - - - - 5-15% LDLR activity when Htz with FH Pedi-1 (c.172delG, p.(Glu58Serfs*148)). 10% of wt luciferase activity ACGS likely pathogenic g.11200040_11200042del g.11089364_11089366del c.-185_-183delCTT - LDLR_000103 predicted reduced transcription; Hobb's numbering: -92_-90del; Variant reduces activity in luciferase assay without presence of FH Pedi-1 (c.172delG, p.(Glu58Serfs*148)); DNase I footprinting indicated that this variant abolished Sp1 binding to SREBP repeat 1 in the LDLR promoter PubMed: Peeters 1998 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-156C>T p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested ACGS likely pathogenic g.11200069C>T g.11089393C>T - - LDLR_001112 Hobbs' numbering -63C>T. Hmz, first report of Hmz variant in promotor. Co-segragated with FH in 1 affected sibling, not present in 1 unaffected sibling, 5 affected siblings not tested PubMed: Dedoussis 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-155_-154delinsTTCTGCAAACTCCT p.(=) r.(=) - - SREBP2 binding site - - - - 11% of wt trascriptional activity (luciferase assay) ACGS likely pathogenic g.11200070_11200071delinsTTCTGCAAACTCCT g.11089394_11089395delinsTTCTGCAAACTCCT - - LDLR_001267 predicted reduced transcription; Nomenclature corrected from article (c; 155_-150delACCCCinsTTCTGCAAACTCCTCCC) PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
?/? 1 c.-153C>T p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested ACGS VUS g.11200072C>T g.11089396C>T - - LDLR_001116 Hobb's numbering -60C>T. Authors assumed this variant has a causal effect on the basis of its position in the promoter sequence, no evidence provided in this study. PubMed: Francova 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-152C>T p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 40% of wt transcription using luciferase assay ACGS likely pathogenic g.11200073C>T g.11089397C>T - - LDLR_001266 predicted reduced transcription; Hobb's numbering: -59C>T. PubMed: Scholtz 1999 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-152C>T p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 40% of wt transcription using luciferase assay ACGS likely pathogenic g.11200073C>T g.11089397C>T - - LDLR_001266 predicted reduced transcription; Hobb's numbering: -59C>T. PubMed: Khoo 2000 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-152C>T p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 40% of wt transcription using luciferase assay ACGS likely pathogenic g.11200073C>T g.11089397C>T - - LDLR_001266 predicted reduced transcription; Hobb's numbering: -59C>T. PubMed: Brusgaard 2006 - - Germline - - - 0 - Sarah Leigh
+/. - c.-152C>T p.(=) r.(?) - - - - - - - - - pathogenic g.11200073C>T g.11089397C>T LDLR(NM_000527.4):c.-152C>T - LDLR_001266 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_AMC
+?/. - c.-150A>G p.(=) r.(?) - - - - - - - - - likely pathogenic g.11200075A>G g.11089399A>G LDLR(NM_000527.4):c.-150A>G - LDLR_002040 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/? 1 c.-149C>A p.(=) r.(=) - - SREBP2 binding site - - - - not tested ACGS VUS g.11200076C>A g.11089400C>A - - LDLR_001264 Hobb's numbering: -56C>A. PubMed: Tichy 2012 - - Germline - - - 0 - Sarah Leigh
?/? 1 c.-146C>A p.(=) r.(=) - - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested ACGS VUS g.11200079C>A g.11089403C>A - - LDLR_001263 Hobb's numbering -53C>A PubMed: Day 1997 - - Germline - not in ExAC, June 2015 - 0 - Sarah Leigh
?/. - c.-143A>C p.(=) r.(?) - - - - - - - - - VUS g.11200082A>C g.11089406A>C LDLR(NM_000527.4):c.-143A>C - LDLR_002041 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+/. - c.-142C>G p.(=) r.(?) - - - - - - - - - pathogenic g.11200083C>G g.11089407C>G LDLR(NM_000527.4):c.-142C>G - LDLR_001923 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_AMC
?/? 1 c.-142C>T p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 20% of wt transcription using luciferase assay & blocks ability to bind Sp1 (gel retardation assays). ACGS VUS g.11200083C>T g.11089407C>T - - LDLR_000857 predicted reduced transcription; Hobb's numbering -49; Reduced expression in luciferase reporter assay & blocks ability to bind Sp1 (gel retardation assays); No other variants found in proband, but some relatives with c.-142C>T do not have FH. PubMed: Mozas 2002 - - Germline - - - 0 - Sarah Leigh
?/? 1 c.-142C>T p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 20% of wt transcription using luciferase assay & blocks ability to bind Sp1 (gel retardation assays). ACGS VUS g.11200083C>T g.11089407C>T - - LDLR_000857 predicted reduced transcription; Hobb's numbering -49; Reduced expression in luciferase reporter assay & blocks ability to bind Sp1 (gel retardation assays); {PMID11792717:Mozas et al 2002 J Lipid Res 43 13} PubMed: Leren 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-140C>G p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 7% transcriptional activity (luciferase assay). 25% reduction nuclear protein binding (EMSA assay){PMID21538688: De Castro-Oros 2011} ACGS likely pathogenic g.11200085C>G g.11089409C>G - - LDLR_000322 prediction reduced transcription PubMed: Alonso 2009 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-140C>G p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 7% of wt trascriptional activity (luciferase assay). 25% reduction of nuclear protein binding (EMSA assay) ACGS likely pathogenic g.11200085C>G g.11089409C>G - - LDLR_000322 prediction reduced transcription PubMed: De Castro-Oros 2011 - - Germline - 0.3 in this study - 0 - Sarah Leigh
+?/+? 1 c.-140C>T p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 6% of wt trascriptional activity (luciferase assay). 25% reduction of nuclear protein binding in (EMSA assay) ACGS likely pathogenic g.11200085C>T g.11089409C>T - - LDLR_000323 predicted reduced transcription; Proband also carries c.858C>A, p.(Ser286Arg)(probably pathogenic) PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
?/? 1 c.-139C>A p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested ACGS VUS g.11200086C>A g.11089410C>A - - LDLR_001025 - PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-139C>G p.(=) r.(=) - - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 26% of wt using luciferase assay ACGS likely pathogenic g.11200086C>G g.11089410C>G - - LDLR_001190 predicted reduced transcription; Proband compound Htz with c.762_763inv, p.(Q254_C255delinsHG), inherited from mother & c.-22delC from father; Not found in 50 normals; Creates new initiation site, which could result in an novel peptide of 35aa. PubMed: Smith 2007 - - Germline - - - 0 - Sarah Leigh
+/. - c.-139C>G p.(=) r.(?) - - - - - - - - - pathogenic g.11200086C>G g.11089410C>G LDLR(NM_000527.4):c.-139C>G - LDLR_001190 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+?/+? 1 c.-138del p.(=) r.(=) FH Pyrgos - SP1 binding site - - 12/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 24% LDLR activity in Htz lymphocytes. Reduced level of expression ACGS likely pathogenic g.11200087del g.11089411del c.-138delT - LDLR_000959 predicted reduced levels of transcription; Hobbs' numbering: -45delT. PubMed: Dedoussis 2003 - - Germline - - - 0 - Sarah Leigh
+/. - c.-138del p.(=) r.(?) - - - - - - - - - pathogenic g.11200087del g.11089411del LDLR(NM_000527.4):c.-138delT - LDLR_000959 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_AMC
+?/+? 1 c.-138T>C p.(=) r.(=) - - SP1 binding site - - 12/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Luciferase assay 43% of normal in the presence & 25% in the absence of sterols in the medium. ACGS likely pathogenic g.11200087T>C g.11089411T>C - - LDLR_000438 predicted reduced transcription; Hobbs' numbering: -45T>C PubMed: Sun 1995 - - Germline - - - 0 - Sarah Leigh
?/? 1 c.-137C>T p.(=) r.(=) FH Albuquerque - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 5-15% LDLR activity when Htz with c.1222G>A, p.(Glu408Lys), FH Algeria-1, FH Osaka ACGS VUS g.11200088C>T g.11089412C>T - - LDLR_001262 Hobb's numbering: -44C>T. Found as compound Htz with c.1222G>A, p.(Glu408Lys) (FH-Algeria-1)(likely pathogenic). PubMed: Dedoussis 2003 - - Germline - - - 0 - Sarah Leigh
?/? 1 c.-137C>T p.(=) r.(=) FH Albuquerque - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested ACGS VUS g.11200088C>T g.11089412C>T - - LDLR_001262 Hobb's numbering: -44C>T. Found as compound Htz with c.2054C>T, p.(Pro685Leu)(likely pathogenic). PubMed: Mak 1998 - - Germline - - - 0 - Sarah Leigh
+/. - c.-137C>T p.(=) r.(?) - - - - - - - - - pathogenic g.11200088C>T g.11089412C>T LDLR(NM_000527.4):c.-137C>T - LDLR_001262 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+?/+? 1 c.-136C>G p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 22% of wt trascriptional activity (luciferase assay). 30% reduction of nuclear protein binding in (EMSA assay) ACGS likely pathogenic g.11200089C>G g.11089413C>G - - LDLR_001260 prediction reduced transcription PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
+?/+? 1 c.-136C>T p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 50% reduction of binding, internalization & degradation of labeled LDL in Htz fibroblasts compared with wt. Reduced mRNA levels; SP1 binding inhibited ACGS likely pathogenic g.11200089C>T g.11089413C>T - - LDLR_001261 predicted reduced transcription; co-segregated with the FH phenotype in six available family members; Abolished binding of Spi transcription factor to this site. PubMed: Koivisto 1994 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-136C>T p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - - ACGS likely pathogenic g.11200089C>T g.11089413C>T - - LDLR_001261 prediction reduced transcription PubMed: Kim 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-136C>T p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - - ACGS likely pathogenic g.11200089C>T g.11089413C>T - - LDLR_001261 prediction reduced transcription PubMed: Leren 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-136C>T p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - - ACGS likely pathogenic g.11200089C>T g.11089413C>T - - LDLR_001261 prediction reduced transcription PubMed: Fouchier 2005 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-136C>T p.(=) r.(=) Hobb’s -43C>T - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Transcription level of variant reduced to <5% of wt ACGS likely pathogenic g.11200089C>T g.11089413C>T - - LDLR_001261 prediction reduced transcription PubMed: Jensen 1996 - - Germline - - - 0 - Sarah Leigh
+/. - c.-136C>T p.(=) r.(?) - - - - - - - - - pathogenic g.11200089C>T g.11089413C>T LDLR(NM_000527.4):c.-136C>T - LDLR_001261 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/. _1 c.-135C>A p.(?) r.(=) - Disease causing - - - - - - ACMG VUS g.11200090C>A g.11089414C>A g.5034C>A - LDLR_001906 - Journal: Banares 2017 - - Germline - 1/33 cases - 0 - Virginia Bañares
+?/+? 1 c.-135C>G p.(=) r.(=) Hobb’s -42C>T; FH Columbia-2 - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 5-15% LDLR activity in Hmz. 11% trascriptional activity (luciferase assay){PMID21538688: De Castro-Oros 2011} ACGS likely pathogenic g.11200090C>G g.11089414C>G - - LDLR_000003 prediction reduced transcription PubMed: Hobbs 1992 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-135C>G p.(=) r.(=) Hobb’s -42C>T; FH Columbia-2 - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 11% of wt trascriptional activity (luciferase assay){PMID21538688: De Castro-Oros et al, Hum Mutat. 2011 Aug;32(8):868-72} ACGS likely pathogenic g.11200090C>G g.11089414C>G - - LDLR_000003 prediction reduced transcription PubMed: Mozas 2004 - - Germline - - - 0 - Sarah Leigh
+?/+ 1 c.-135C>G p.(0) r.(=) Hobb’s -42C>T; FH Columbia-2 - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 11% of wt trascriptional activity (luciferase assay){PMID21538688: De Castro-Oros et al, Hum Mutat. 2011 Aug;32(8):868-72} ACGS likely pathogenic g.11200090C>G g.11089414C>G - - LDLR_000003 predicted reduced transcription; On the same allele as c.1185G>C, p.(Val395Val) PubMed: Bourbon 2009 - - Germline - - - 0 - Sarah Leigh
+?/? 1 c.-135C>G p.(=) r.(=) Hobb’s -42C>T; FH Columbia-2 - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 11% of wt trascriptional activity (luciferase assay){PMID21538688: De Castro-Oros et al, Hum Mutat. 2011 Aug;32(8):868-72} ACGS likely pathogenic g.11200090C>G g.11089414C>G - - LDLR_000003 prediction reduced transcription PubMed: Medeiros 2010 - - Germline - - - 0 - Sarah Leigh
+/. - c.-135C>G p.(=) r.(?) - - - - - - - - - pathogenic g.11200090C>G g.11089414C>G LDLR(NM_000527.4):c.-135C>G - LDLR_000003 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_AMC
?/. 1 c.-134C>A p.(=) r.(=) - - - - - - - - - VUS g.11200091C>A g.11089415C>A - - LDLR_002179 - Journal: Gomez 2017 - - Germline/De novo (untested) - - - 0 - Andrea Gomez
?/. - c.-122C>T p.(=) r.(?) - - - - - - - - - VUS g.11200103C>T g.11089427C>T LDLR(NM_000527.4):c.-122C>T - LDLR_002042 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+?/+? 1 c.-121T>C p.(=) r.(=) - - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 72% of WT promoter activity (luciferase assay) {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS likely pathogenic g.11200104T>C g.11089428T>C - - LDLR_000002 predicted reduced transcription; 72% of WT promoter activity {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} PubMed: Taylor 2010 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-121T>C p.(=) r.(=) - - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 72% of WT promoter activity (luciferase assay) {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS likely pathogenic g.11200104T>C g.11089428T>C - - LDLR_000002 predicted reduced transcription; 72% of WT promoter activity {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} PubMed: Hooper 2012 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-120C>T p.(=) r.(=) Hobb’s -27C>T - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 3% of WT promoter activity (luciferase assay) ACGS likely pathogenic g.11200105C>T g.11089429C>T - - LDLR_001115 predicted reduced transcription; co-segregated with FH in 3 siblings, father not available on not present in mother; Not present in 50 normal controls PubMed: Francova 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-120C>T p.(=) r.(=) Hobb’s -27C>T - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 3% of WT promoter activity (luciferase assay) ACGS likely pathogenic g.11200105C>T g.11089429C>T - - LDLR_001115 predicted reduced transcription; co-segregated with FH in 3 siblings, father not available on not present in mother; Not present in 50 normal controls PubMed: Francova 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-120C>T p.(=) r.(=) Hobb’s -27C>T - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 3% of WT promoter activity (luciferase assay) ACGS likely pathogenic g.11200105C>T g.11089429C>T - - LDLR_001115 predicted reduced transcription; co-segregated with FH in 3 siblings, father not available on not present in mother; Not present in 50 normal controls PubMed: Francova 2004 - - Germline - - - 0 - Sarah Leigh
+?/+? 1 c.-120C>T p.(=) r.(=) Hobb’s -27C>T - TATA box/SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 3% of WT promoter activity (luciferase assay) ACGS likely pathogenic g.11200105C>T g.11089429C>T - - LDLR_001115 prediction reduced transcription PubMed: Alonso 2009 - - Germline - - - 0 - Sarah Leigh
+?/. - c.-120C>T p.(=) r.(?) - - - - - - - - - likely pathogenic g.11200105C>T g.11089429C>T LDLR(NM_000527.4):c.-120C>T - LDLR_001115 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_AMC
?/+? 1 c.-101T>C p.(=) r.(=) - - TATA box - - 12/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 64% of WT promoter activity (luciferase assay) {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} ACGS VUS g.11200124T>C g.11089448T>C - - LDLR_000001 predicted reduced transcription; 64% of WT promoter activity (luciferase assay) {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} PubMed: Usifo 2012 - - Germline - - - 0 - Sarah Leigh
?/. - c.-98C>T p.(=) r.(?) - - - - - - - - - VUS g.11200127C>T g.11089451C>T LDLR(NM_000527.4):c.-98C>T - LDLR_001925 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - VKGL-NL_Groningen
-?/-? 1 c.-88G>A p.(=) r.(=) - - 5'UTR - - 12/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Normal levels of transcription (luciferase assay in HEPG2 cells) ACGS likely benign g.11200137G>A g.11089461G>A - - LDLR_001270 prediction no effect on transcription PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
?/? 1 c.-68A>C p.(=) r.(=) - - 5'UTR - - 5/11 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200157A>C g.11089481A>C - - LDLR_001121 - PubMed: Laurie 2004 - - Germline - - - 0 - Sarah Leigh
?/. - c.-48A>G p.(=) r.(?) - - - - - - - - - VUS g.11200177A>G g.11089501A>G LDLR(NM_000527.4):c.-48A>G - LDLR_002216 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
-?/. - c.-47G>T p.(=) r.(?) - - - - - - - - - likely benign g.11200178G>T - LDLR(NM_000527.4):c.-47G>T - LDLR_002221 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
-?/-? 1 c.-36T>G p.(=) r.(=) - - 5'UTR - - 6/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Normal levels of transcription (luciferase assay in HEPG2 cells) ACGS likely benign g.11200189T>G g.11089513T>G - - LDLR_001269 prediction no effect on transcription PubMed: De Castro-Oros 2011 - - Germline - 0.06 in this study - 0 - Sarah Leigh
?/? 1 c.-23A>C p.(=) r.(=) - - 5'UTR - - 7/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200202A>C g.11089526A>C - - LDLR_000815 - PubMed: Mozas 2004 - - Germline - - - 0 - Sarah Leigh
?/. - c.-22C>T p.(=) r.(?) - - - - - - - - - VUS g.11200203C>T g.11089527C>T LDLR(NM_000527.4):c.-22C>T - LDLR_002181 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/? 1 c.-22del p.(=) r.(=) - - 5'UTR - - 10/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200203del g.11089527del c.-22delC - LDLR_001139 Proband compound Htz with c.762_763inv, p.(Q254_C255delinsHG), inherited from mother & c.-22delC from father. Not found in 50 normals. Creates new initiation site, which could result in an novel peptide of 35aa. PubMed: Sozen 2005 - - Germline - - - 0 - Sarah Leigh
?/? 1 c.-14C>A p.(=) r.(=) - - 5'UTR - - 9/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested ACGS VUS g.11200211C>A g.11089535C>A - - LDLR_001265 - PubMed: Day 1997 - - Germline - - - 0 - Sarah Leigh
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