Transcript #00011039 (NM_000527.4, LDLR gene)

Transcript name transcript variant 1
Gene name LDLR (low density lipoprotein receptor)
Chromosome 19
Transcript - NCBI ID NM_000527.4
Transcript - Ensembl ID -
Protein - NCBI ID NP_000518.1
Protein - Ensembl ID -
Protein - Uniprot ID -
Exon/intron information Exon/intron information table: HTML, Txt
Remarks -


Variants

3931 entries on 40 pages. Showing entries 1 - 100.
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Affects function     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

Predict/MutationTaster     

P-domain     

Predict/PolyPhen     

Predict/SIFT     

Conservation     

Predict/Splice     

Enzyme activity     
+/+ 4 c.[649_654dup;657_661del] r.(?) p.([Asp217_Gly218dup; Gly219fs*7]) - LDL-receptor class A5 - - - - -
+/+ _1_2i c.-1823_190+566del r.(?) p.0? - Promoter - exon 2 - - - - -
+/. _1_1i c.-1818_67+1091delinsTTC r.0? p.0? - - - - - - -
?/. - c.-283G>C r.(?) p.(=) - - - - - - -
-?/. - c.-268G>T r.(?) p.(=) - - - - - - -
-?/-? _1 c.-268G>T r.(=) p.? - 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
-?/-? _1 c.-268G>T r.(=) p.? - 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
?/? _1 c.-221_-220insA r.(=) p.? - FP1 cis acting regulatory element - - - - -
-?/. - c.-217C>T r.(?) p.(=) - - - - - - -
-?/-? _1 c.-217C>T r.(=) p.? - 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}
-?/? _1 c.-217C>T r.(=) p.? - 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}
-?/? _1 c.-215A>G r.(=) p.? - 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}
-?/-? _1 c.-208A>T r.(=) p.? - 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).
?/? _1 c.-206C>T r.(=) p.? - SREBP1/FP1 - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested
?/? _1 c.-193_-186delinsTG r.(=) p.? - SREBP1 binding site - - - - not tested
?/? _1 c.-188C>T r.(=) p.? - SREBP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested
+?/. - c.-187C>T r.(?) p.(=) - - - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - promotor & exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promoter - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - <2% LDLR activity when Htz with unknown FH allele
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - <2% LDLR activity in Hmz
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_1i c.(?_-187)_(67+1_68-1)del r.(?) p.0? - Promotor - exon 1 - - - - -
+?/+? _1_1i c.(?_-187)_(67+1_68-1)dup r.(?) p.0? - Promotor - exon 1 - - - - -
+/+ _1_2i c.(?_-187)_(190+1_191-1)del r.(?) p.0? - Promotor - exon 2 - - - - -
+/+ _1_2i c.(?_-187)_(190+1_191-1)del r.(?) p.0? - Promotor - exon 2 - - - - -
+/+ _1_2i c.(?_-187)_(190+1_191-1)del r.(?) p.0? - Promotor - exon 2 - - - - -
+/+ _1_2i c.(?_-187)_(190+1_191-1)del r.(?) p.0? - Promotor - exon 2 - - - - 45% LDLR activity in Htz fibroblasts
+/+ _1_6i c.(?_-187)_(940+1_941-1)del r.(?) p.0? - Promoter - exon 6 - - - - -
+/+ _1_6i c.(?_-187)_(940+1_941-1)del r.(?) p.0? - Promoter - exon 6 - - - - -
+/+ _1_6i c.(?_-187)_(940+1_941-1)del r.(?) p.0? - Promoter - exon 6 - - - - 40-50% LDLR activity in Htz
+/+ _1_7i c.(?_-187)_(1060+1_1061-1)del r.(?) p.0? - Promoter - exon 7 - - - - -
+/+ _1_8i c.(?_-187)_(1186+1_1187-1)del r.(?) p.0? - Promoter - exon 8 - - - - -
+/+ _1_12i c.(?_-187)_(1845+1_1846-1)del r.(?) p.0? - Promoter - exon 12 - - - - -
+/+ _1_14i c.(?_-187)_(2140+1_2141-1)del r.(?) p.0? - Promoter - exon 14 - - - - -
+/+ _1_15i c.(?_-187)_(2311+1_2312-1)del r.(?) p.0? - Promoter - exon 15 - - - - -
+/+ _1_18_ c.(?_-187)_(*2584_?)del r.(?) p.0? - whole gene - - - - -
+/+ _1_18_ c.(?_-187)_(*2584_?)del r.(?) p.0? - whole gene - - - - -
+?/+? 1 c.-185_-183del r.(=) p.(=) - SREBP1 binding site - - - - 5-15% LDLR activity when Htz with FH Pedi-1 (c.172delG, p.(Glu58Serfs*148)). 10% of wt luciferase activity
+?/+? 1 c.-156C>T r.(=) p.(=) - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested
+?/+? 1 c.-155_-154delinsTTCTGCAAACTCCT r.(=) p.(=) - SREBP2 binding site - - - - 11% of wt trascriptional activity (luciferase assay)
?/? 1 c.-153C>T r.(=) p.(=) - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested
+/. - c.-152C>T r.(?) p.(=) - - - - - - -
+?/+? 1 c.-152C>T r.(=) p.(=) - 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
+?/+? 1 c.-152C>T r.(=) p.(=) - 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
+?/+? 1 c.-152C>T r.(=) p.(=) - 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
+?/. - c.-150A>G r.(?) p.(=) - - - - - - -
?/? 1 c.-149C>A r.(=) p.(=) - SREBP2 binding site - - - - not tested
?/? 1 c.-146C>A r.(=) p.(=) - SREBP2 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested
?/. - c.-143A>C r.(?) p.(=) - - - - - - -
+/. - c.-142C>G r.(?) p.(=) - - - - - - -
?/? 1 c.-142C>T r.(=) p.(=) - 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).
?/? 1 c.-142C>T r.(=) p.(=) - 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).
+?/+? 1 c.-140C>G r.(=) p.(=) - 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}
+?/+? 1 c.-140C>G r.(=) p.(=) - 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)
+?/+? 1 c.-140C>T r.(=) p.(=) - 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)
?/? 1 c.-139C>A r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested
+/. - c.-139C>G r.(?) p.(=) - - - - - - -
+?/+? 1 c.-139C>G r.(=) p.(=) - 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
+/. - c.-138del r.(?) p.(=) - - - - - - -
+?/+? 1 c.-138del r.(=) p.(=) - 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
+?/+? 1 c.-138T>C r.(=) p.(=) - 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.
+/. - c.-137C>T r.(?) p.(=) - - - - - - -
?/? 1 c.-137C>T r.(=) p.(=) - 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
?/? 1 c.-137C>T r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - Not tested
+?/+? 1 c.-136C>G r.(=) p.(=) - 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)
+/. - c.-136C>T r.(?) p.(=) - - - - - - -
+?/+? 1 c.-136C>T r.(=) p.(=) - 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
+?/+? 1 c.-136C>T r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - -
+?/+? 1 c.-136C>T r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - -
+?/+? 1 c.-136C>T r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - -
+?/+? 1 c.-136C>T r.(=) p.(=) - 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
?/. _1 c.-135C>A r.(=) p.(?) Disease causing - - - - - -
+/. - c.-135C>G r.(?) p.(=) - - - - - - -
+?/+? 1 c.-135C>G r.(=) p.(=) - 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}
+?/+? 1 c.-135C>G r.(=) p.(=) - 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}
+?/+ 1 c.-135C>G r.(=) p.(0) - 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}
+?/? 1 c.-135C>G r.(=) p.(=) - 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}
?/. 1 c.-134C>A r.(=) p.(=) - - - - - - -
?/. - c.-122C>T r.(?) p.(=) - - - - - - -
+?/+? 1 c.-121T>C r.(=) p.(=) - 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}
+?/+? 1 c.-121T>C r.(=) p.(=) - 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}
+?/. - c.-120C>T r.(?) p.(=) - - - - - - -
+?/+? 1 c.-120C>T r.(=) p.(=) - 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)
+?/+? 1 c.-120C>T r.(=) p.(=) - 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)
+?/+? 1 c.-120C>T r.(=) p.(=) - 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)
+?/+? 1 c.-120C>T r.(=) p.(=) - 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)
?/+? 1 c.-101T>C r.(=) p.(=) - 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}
?/. - c.-98C>T r.(?) p.(=) - - - - - - -
-?/-? 1 c.-88G>A r.(=) p.(=) - 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)
?/? 1 c.-68A>C r.(=) p.(=) - 5'UTR - - 5/11 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested
?/. - c.-48A>G r.(?) p.(=) - - - - - - -
-?/. - c.-47G>T r.(?) p.(=) - - - - - - -
-?/-? 1 c.-36T>G r.(=) p.(=) - 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)
?/? 1 c.-23A>C r.(=) p.(=) - 5'UTR - - 7/12 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - not tested
?/. - c.-22C>T r.(?) p.(=) - - - - - - -
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