PMID: 25647241

Systematic cell-based phenotyping of missense alleles empowers rare variant association studies: a case for LDLR and myocardial infarction.

PLoS genetics
AS Thormaehlen, C Schuberth, HH Won, P Blattmann, B Joggerst-Thomalla, S Theiss, R Asselta, S Duga, PA Merlini, D Ardissino, ES Lander, S Gabriel, DJ Rader, GM Peloso, R Pepperkok, S Kathiresan, H Runz
2015-02

129 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
10-113933886-A-G GPAM c.414-283T>C - IntronicSNV - 6/21
19-11240282-A-G LDLR c.2483A>G p.Tyr828Cys Missense 17/18 -
19-11217352-G-A LDLR c.806G>A p.Gly269Asp Missense 5/18 -
10-113933886-A-T GPAM c.414-283T>A - IntronicSNV - 6/21
19-11217336-A-T LDLR c.790A>T p.Met264Leu Missense 5/18 -
19-11217336-A-C LDLR c.790A>C p.Met264Leu Missense 5/18 -
6-32412435-G-A HLA-DRA c.*18G>A - 3_prime_UTR_variant 5/5 -
2-21233972-T-C APOB c.5768A>G p.His1923Arg Missense 26/29 -
19-11217264-G-A LDLR c.718G>A p.Glu240Lys Missense 5/18 -
19-11215934-G-T LDLR c.352G>T p.Asp118Tyr Missense 4/18 -
19-11200274-C-G LDLR c.50C>G p.Ala17Gly Missense 1/18 -
19-11227613-G-A LDLR c.1784G>A p.Arg595Gln Missense 12/18 -
19-11216000-G-T LDLR c.418G>T p.Glu140* Nonsense 4/18 -
19-11218190-G-A LDLR c.940G>A p.Gly314Arg Missense 6/18 -
19-11210928-C-T LDLR c.97C>T p.Gln33* Nonsense 2/18 -
19-45411987-G-A APOE c.434G>A p.Gly145Asp Missense 4/4 -
19-11218077-G-C LDLR c.827G>C p.Cys276Ser Missense 6/18 -
1-55529187-G-A PCSK9 c.2009G>A p.Gly670Glu Missense 12/12 -
19-11231159-G-A LDLR c.2101G>A p.Gly701Ser Missense 14/18 -
2-44065739-C-G ABCG5 c.80G>C p.Gly27Ala Missense 1/13 -
19-11200282-G-A LDLR c.58G>A p.Gly20Arg Missense 1/18 -
19-11216244-A-G LDLR c.662A>G p.Asp221Gly Missense 4/18 -
19-11218076-T-A LDLR c.826T>A p.Cys276Ser Missense 6/18 -
7-44574061-A-T NPC1L1 c.2151T>A p.Phe717Leu Missense 6/20 -
19-11224419-G-A LDLR c.1567G>A p.Val523Met Missense 10/18 -
19-11240240-G-A LDLR c.2441G>A p.Arg814Gln Missense 17/18 -
19-11222234-G-A LDLR c.1105G>A p.Val369Met Missense 8/18 -
7-44574061-A-C NPC1L1 c.2151T>G p.Phe717Leu Missense 6/20 -
2-21230858-T-C APOB c.8882A>G p.Asn2961Ser Missense 26/29 -
19-11216112-C-T LDLR c.530C>T p.Ser177Leu Missense 4/18 -
19-11224013-C-T LDLR c.1246C>T p.Arg416Trp Missense 9/18 -
4-100532602-G-A MTTP c.1981G>A p.Gly661Ser Missense 15/19 -
19-11224103-C-G LDLR c.1336C>G p.Leu446Val Missense 9/18 -
19-11226829-G-A LDLR c.1646G>A p.Gly549Asp Missense 11/18 -
19-11224245-T-A LDLR c.1393T>A p.Tyr465Asn Missense 10/18 -
19-11218079-G-A LDLR c.829G>A p.Glu277Lys Missense 6/18 -
19-11231112-C-T LDLR c.2054C>T p.Pro685Leu Missense 14/18 -
1-241661268-A-T FH c.1393T>A p.Tyr465Asn Missense 10/10 -
19-11213453-C-T LDLR c.304C>T p.Gln102* Nonsense 3/18 -
19-11224024-C-A LDLR c.1257C>A p.Tyr419* Nonsense 9/18 -
19-11221357-G-A LDLR c.970G>A p.Gly324Ser Missense 7/18 -
19-11230798-G-A LDLR c.1876G>A p.Glu626Lys Missense 13/18 -
4-100510903-A-G MTTP c.497A>G p.Asn166Ser Missense 5/19 -
6-160578860-T-C SLC22A1 c.1599-688T>C - IntronicSNV - 10/10
19-11221375-A-C LDLR c.988A>C p.Asn330His Missense 7/18 -
11-116661488-C-T APOA5 c.457G>A p.Val153Met Missense 4/4 -
19-11231184-G-A LDLR c.2126G>A p.Arg709Lys Missense 14/18 -
19-11240278-G-A LDLR c.2479G>A p.Val827Ile Missense 17/18 -
19-11221444-G-A LDLR c.1057G>A p.Glu353Lys Missense 7/18 -
19-11216124-C-G LDLR c.542C>G p.Pro181Arg Missense 4/18 -
19-11224422-G-A LDLR c.1570G>A p.Val524Met Missense 10/18 -
19-11226782-G-A LDLR c.1599G>A p.Trp533* Nonsense 11/18 -
19-11213390-C-T LDLR c.241C>T p.Arg81Cys Missense 3/18 -
2-21232455-A-T APOB c.7285T>A p.Ser2429Thr Missense 26/29 -
19-11230873-G-A LDLR c.1951G>A p.Asp651Asn Missense 13/18 -
19-11216127-A-G LDLR c.545A>G p.Gln182Arg Missense 4/18 -
19-11222300-G-A LDLR c.1171G>A p.Ala391Thr Missense 8/18 -
19-11215974-A-G LDLR c.392A>G p.Asp131Gly Missense 4/18 -
19-11222262-A-C LDLR c.1133A>C p.Gln378Pro Missense 8/18 -
19-11224437-G-C LDLR c.1585G>C p.Gly529Arg Missense 10/18 -
2-44072576-G-C ABCG8 c.166-718G>C - IntronicSNV - 2/12
19-11227604-G-A LDLR c.1775G>A p.Gly592Glu Missense 12/18 -
19-11218103-C-T LDLR c.853C>T p.His285Tyr Missense 6/18 -
19-11215992-G-T LDLR c.410G>T p.Gly137Val Missense 4/18 -
19-11230876-A-G LDLR c.1954A>G p.Met652Val Missense 13/18 -
19-11224428-C-T LDLR c.1576C>T p.Pro526Ser Missense 10/18 -
4-100512919-C-G MTTP c.730C>G p.Gln244Glu Missense 7/19 -
19-11224326-G-A LDLR c.1474G>A p.Asp492Asn Missense 10/18 -
19-11218096-C-A LDLR c.846C>A p.Phe282Leu Missense 6/18 -
19-11210974-G-A LDLR c.143G>A p.Gly48Asp Missense 2/18 -
19-11224362-A-G LDLR c.1510A>G p.Lys504Glu Missense 10/18 -
19-11213450-G-A LDLR c.301G>A p.Glu101Lys Missense 3/18 -
7-44579180-G-C NPC1L1 c.816C>G p.Leu272Leu Synonymous 2/20 -
7-44579180-G-A NPC1L1 c.816C>T p.Leu272Leu Synonymous 2/20 -
19-11217256-G-A LDLR c.710G>A p.Arg237His Missense 5/18 -
19-11221334-A-G LDLR c.947A>G p.Asn316Ser Missense 7/18 -
19-11216238-G-A LDLR c.656G>A p.Gly219Asp Missense 4/18 -
14-24883887-G-A NYNRIN c.2932G>A p.Ala978Thr Missense 9/9 -
19-11240197-G-A LDLR c.2398G>A p.Val800Ile Missense 17/18 -
2-44079930-C-T ABCG8 c.887C>T p.Ala296Val Missense 6/13 -
1-241661151-T-C FH c.1510A>G p.Lys504Glu Missense 10/10 -
19-11218158-G-A LDLR c.908G>A p.Arg303Gln Missense 6/18 -
19-11224266-G-T LDLR c.1414G>T p.Asp472Tyr Missense 10/18 -
4-100512392-G-A MTTP c.502G>A p.Val168Ile Missense 6/19 -
19-11211016-C-T LDLR c.185C>T p.Thr62Met Missense 2/18 -
19-11238728-A-G LDLR c.2356A>G p.Ser786Gly Missense 16/18 -
19-11217303-C-T LDLR c.757C>T p.Arg253Trp Missense 5/18 -
19-11224233-G-T LDLR c.1381G>T p.Gly461Cys Missense 10/18 -
19-11226781-G-A LDLR c.1598G>A p.Trp533* Nonsense 11/18 -
19-11221411-G-A LDLR c.1024G>A p.Asp342Asn Missense 7/18 -
19-11215896-C-T LDLR c.314C>T p.Pro105Leu Missense 4/18 -
2-21249716-C-T APOB c.2188G>A p.Val730Ile Missense 15/29 -
19-11231174-A-G LDLR c.2116A>G p.Arg706Gly Missense 14/18 -
19-11221435-C-T LDLR c.1048C>T p.Arg350* Nonsense 7/18 -
19-11224254-G-A LDLR c.1402G>A p.Val468Ile Missense 10/18 -
7-44574063-A-G NPC1L1 c.2149T>C p.Phe717Leu Missense 6/20 -
1-63025942-G-T DOCK7 c.2200-1051C>A - IntronicSNV - 19/48
2-21263869-C-A APOB c.324G>T p.Glu108Asp Missense 4/29 -
19-11221390-G-A LDLR c.1003G>A p.Gly335Ser Missense 7/18 -
2-21263869-C-G APOB c.324G>C p.Glu108Asp Missense 4/29 -
19-11224432-T-C LDLR c.1580T>C p.Val527Ala Missense 10/18 -
19-11233951-G-A LDLR c.2242G>A p.Asp748Asn Missense 15/18 -
19-11216247-G-A LDLR c.665G>A p.Cys222Tyr Missense 4/18 -
19-11227645-G-T LDLR c.1816G>T p.Ala606Ser Missense 12/18 -
19-11221414-G-A LDLR c.1027G>A p.Gly343Ser Missense 7/18 -
19-11233886-C-T LDLR c.2177C>T p.Thr726Ile Missense 15/18 -
2-44072576-G-T ABCG8 c.166-718G>T - IntronicSNV - 2/12
19-11227549-C-T LDLR c.1720C>T p.Arg574Cys Missense 12/18 -
19-11224061-C-G LDLR c.1294C>G p.Leu432Val Missense 9/18 -
1-55518352-C-T PCSK9 c.687C>T p.His229His Synonymous 5/12 -
4-100521805-A-C MTTP c.1151A>C p.Asp384Ala Missense 10/19 -
19-11218096-C-G LDLR c.846C>G p.Phe282Leu Missense 6/18 -
2-21225485-C-G APOB c.12809G>C p.Arg4270Thr Missense 29/29 -
19-11241984-G-A LDLR c.2575G>A p.Val859Met Missense 18/18 -
19-11224399-G-A LDLR c.1547G>A p.Gly516Asp Missense 10/18 -
19-11234017-C-T LDLR c.2308C>T p.Gln770* Nonsense 15/18 -
2-21224853-C-T APOB c.13441G>A p.Ala4481Thr Missense 29/29 -
19-11233991-C-T LDLR c.2282C>T p.Thr761Met Missense 15/18 -
19-11216171-T-C LDLR c.589T>C p.Cys197Arg Missense 4/18 -
19-11216084-G-A LDLR c.502G>A p.Asp168Asn Missense 4/18 -
19-11216047-C-A LDLR c.465C>A p.Cys155* Nonsense 4/18 -
19-11233940-G-A LDLR c.2231G>A p.Arg744Gln Missense 15/18 -
19-11215991-G-A LDLR c.409G>A p.Gly137Ser Missense 4/18 -
19-11218142-A-G LDLR c.892A>G p.Met298Val Missense 6/18 -
19-11227576-C-G LDLR c.1747C>G p.His583Asp Missense 12/18 -
19-11227594-G-C LDLR c.1765G>C p.Asp589His Missense 12/18 -
19-11223962-G-A LDLR c.1195G>A p.Ala399Thr Missense 9/18 -
19-11217344-T-A LDLR c.798T>A p.Asp266Glu Missense 5/18 -
19-11218094-T-C LDLR c.844T>C p.Phe282Leu Missense 6/18 -