JAS:Genes/LDLR: Difference between revisions

(New page: {| class="wikitable" style="float:right" ! Other Links |- | [http://www.ncbi.nlm.nih.gov/gene/3949 NCBI Entrez Gene] |- | [http://genome.ucsc.edu/cgi-bin/hgTracks?position=LDLR UCSD Golden...)
 
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; Well known mutations related with Familial Hypercholesterolemia (FH)
; Well known mutations related with Familial Hypercholesterolemia (FH)
: [[Mutation:LDLR/Mut/1012/T-A|C317S]] in exon 7
: [[JASReference:Funahashi_T:Yamashita_S:Maruyama_T:Ueyama_Y:Menju_M:Nagai_Y:Takemura_K:Miyake_Y:Tajima_S:Matsuzawa_Y:,J_Intern_Med,1996,239,187|LDLR/Mut/1012/T-A (exon7) C338S]]
: [[Mutation:LDLR/Mut/2054/C-T|P664L]] in exon 14
: [[JASReference:Soutar_AK:Knight_BL:Patel_DD:,Proc_Natl_Acad_Sci_U_S_A,1989,86,4166|
: [[Mutation:LDLR/Mut/2431/A-T|K790X]] in exon 17
LDLR/Mut/2054/C-T (exon14) P685L]]
: [[JASReference:Maruyama_T:Miyake_Y:Tajima_S:Harada-Shiba_M:Yamamura_T:Tsushima_M:Kishino_B:Horiguchi_Y:Funahashi_T:Matsuzawa_Y:Yamamoto_A:,Arterioscler_Thromb_Vasc_Biol,1995,15,1713|LDLR/Mut/2431/A-T (exon17) K811X]]


==Statistics==
==Statistics==
; Registered number of mutations ... {{#expr: {{#countTitle:LDLR/Mut/|Mutation}} + {{#countTitle:LDLR/Del/|Mutation}} + {{#countTitle:LDLR/Ins/|Mutation}} + {{#countTitle:LDLR/DelIns/|Mutation}} }}
{{JAS/MutationStat|LDLR}}
* Single nucleotide substitution ... {{#countTitle:LDLR/Mut|Mutation}}
* exon2-exon6 ... ligand binding domain (280 AA)
* Deletion ... {{#countTitle:LDLR/Del|Mutation}}
* exon7-exon14 ... 33 % identical to the human epidermal growth factor (400 AA)
* Insertion ... {{#countTitle:LDLR/Ins|Mutation}}
* exon15 ... O-linked sugar
* Deletion & Insertion ... {{#countTitle:LDLR/DelIns|Mutation}}
* exon16 ... membrane spanning
 
* exon17,18 ... cytoplasmic domain
; Mutation at each exon
{| class="wikitable" style="text-align:center"
!
!colspan="5"|<small>ligand binding domain (280 AA)</small>
!colspan="8"|<small>33 % identical to the human epidermal growth factor (400 AA)</small>
!<small>O-linked sugar</small>
!<small>membrane spanning</small>
!colspan="2"|<small>cytoplasmic domain</small>
|-
| ex1 || ex2 || ex3 || ex4 || ex5 || ex6 || ex7 || ex8 || ex9 || ex10 || ex11 || ex12 || ex13 || ex14 || ex15 || ex16 || ex17 || ex18
|-
| {{#CountLine:^_position=exon1$|Mutation|LDLR/_%}}
| {{#CountLine:position=exon2|Mutation|LDLR/_%}}
| {{#CountLine:position=exon3|Mutation|LDLR/_%}}
| {{#CountLine:position=exon4|Mutation|LDLR/_%}}
| {{#CountLine:position=exon5|Mutation|LDLR/_%}}
| {{#CountLine:position=exon6|Mutation|LDLR/_%}}
| {{#CountLine:position=exon7|Mutation|LDLR/_%}}
| {{#CountLine:position=exon8|Mutation|LDLR/_%}}
| {{#CountLine:position=exon9|Mutation|LDLR/_%}}
| {{#CountLine:position=exon10|Mutation|LDLR/_%}}
| {{#CountLine:position=exon11|Mutation|LDLR/_%}}
| {{#CountLine:position=exon12|Mutation|LDLR/_%}}
| {{#CountLine:position=exon13|Mutation|LDLR/_%}}
| {{#CountLine:position=exon14|Mutation|LDLR/_%}}
| {{#CountLine:position=exon15|Mutation|LDLR/_%}}
| {{#CountLine:position=exon16|Mutation|LDLR/_%}}
| {{#CountLine:position=exon17|Mutation|LDLR/_%}}
| {{#CountLine:position=exon18|Mutation|LDLR/_%}}
|}
 
; Mutation at introns ... {{#CountLine:position=intron|Mutation|LDLR/_%}}


==Reported Mutations==
==Reported Mutations==
{| class="wikitable sortable"
{{JAS/AllMutation|LDLR}}
|+
!Page
!Position
!Structure
!Mutation
!Name
!Nucleotide change
!Effect on coding sequence
!Class
!Author
!Reference
{{#repeat:JAS/Mutation/Table/Row|1|
{{#SearchTitle:LDLR/|Mutation}}
}}
|}

Latest revision as of 18:10, 19 July 2012

Other Links
NCBI Entrez Gene
UCSD GoldenPath

Low-Density Lipoprotein Receptor (LDLR)

Chromosomal Location
19p13.3 (Lindgren V et al. PNAS 1985, 82(24):8567)

LDLR is the most intensively analyzed gene in patients with primary hyperlipidemia. It has 18 exons.

Well known mutations related with Familial Hypercholesterolemia (FH)
LDLR/Mut/1012/T-A (exon7) C338S
LDLR/Mut/2054/C-T (exon14) P685L
LDLR/Mut/2431/A-T (exon17) K811X

Statistics

The number of mutations (E = exon; I = intron)

E1
5

E2
10 		E3
8 		E4
22 		E5
3 		E6
3 		E7
7 		E8
9 		E9
10 		E10
3 		E11
8 		E12
4 		E13
4 		E14
8 		E15
4 		E16
4 		E17
1 		I10
1 		I12
1 		I15
1 		Exon15
1 		promoter
2 		Total
119
The type of mutations

Single-nucleotide
mutation
75

Deletion
30 		Insertion
10 		Del&Ins
1 		Duplication
5 		Others
0 		Total
121
  • exon2-exon6 ... ligand binding domain (280 AA)
  • exon7-exon14 ... 33 % identical to the human epidermal growth factor (400 AA)
  • exon15 ... O-linked sugar
  • exon16 ... membrane spanning
  • exon17,18 ... cytoplasmic domain

Reported Mutations

Mutation Effect Position Reference
LDLR/Mut/223/T-A C75S exon3 Emi (1998) Jpn_Heart_J
LDLR/Mut/1012/T-A C338S exon7 Funahashi (1996) J_Intern_Med
LDLR/Del/578/7 D193fsX11 exon4 Hattori (2002) J_Hum_Genet
LDLR/Ins/682/14 E228fsX42 exon4 Hattori (2002) J_Hum_Genet
LDLR/Del/943/49 N315fsX39 exon7 Hattori (2002) J_Hum_Genet
LDLR/Mut/1072/T-C C358R exon8 Hattori (2002) J_Hum_Genet
LDLR/Ins/1687/C N564QfsX16 exon11 Hattori (2002) J_Hum_Genet
LDLR/Mut/1705+1/G-C 5'splice_donor_mutation intron11 Hattori (2002) J_Hum_Genet
LDLR/Mut/1705+1/G-T 5'splice_donor_mutation intron11 Hattori (2002) J_Hum_Genet
LDLR/Mut/1731/G-T W577C exon12 Hattori (2002) J_Hum_Genet
LDLR/Del/355/7 G119AfsX85 exon4 Hattori (1999) Hum_Mutat
LDLR/Dup/661/21 D221-D227dup exon4 Hattori (1999) Hum_Mutat
LDLR/Dup/1242/5 R416fsX12 exon9 Hattori (1999) Hum_Mutat
LDLR/Mut/1291/G-A A431T exon9 Hattori (1999) Hum_Mutat
LDLR/Mut/1599/G-A W523X exon11 Hattori (1999) Hum_Mutat
LDLR/Ins/1687/C N564QfsX16 exon11 Hattori (1999) Hum_Mutat
LDLR/Mut/1702/C-G L568V exon11 Hattori (1999) Hum_Mutat
LDLR/Ins/2035/T Y679LfsX38 exon14 Hattori (1999) Hum_Mutat
LDLR/Mut/2140/G-A E714K exon14 Hattori (1999) Hum_Mutat
LDLR/Mut/2215/C-T Q739X exon15 Higashikata (1996) Domyakukoka
LDLR/Mut/285/C-A C95X exon3 Hirayama (1998) J_Hum_Genet
LDLR/Mut/1136/G-A C379Y exon8 Hirayama (1998) J_Hum_Genet
LDLR/Ins/1773/G G582fsX11 exon12 Hirayama (1998) J_Hum_Genet
LDLR/Mut/1822/C-T P608S exon12 Hirayama (1998) J_Hum_Genet
LDLR/Del/1963/T F655fsX10 exon11 Hirayama (1998) J_Hum_Genet
LDLR/Ins/327/C S110LfsX20 exon4 Hirota (2002) Ann_Clin_Biochem
LDLR/Del/In1-In3/10k - exon2-3 Kajinami (1989) Circulation
LDLR/Del/Ex2-Ex4/12k - exon2-4 Kajinami (1990) J_Intern_Med
LDLR/Del/Ex7-Ex14/13k - exon7-14 Kajinami (1990) J_Intern_Med
LDLR/Del/Ex15/6k - exon15 Kajinami (1988) Arterioscler_Thromb_Vasc_Biol
LDLR/Del/In14-In15/6k 6 kb deletion Exon15 Kajinami (1988) Atherosclerosis
LDLR/Del/In1-In3/5k - exons2-3 Kigawa (1993) J_Biochem
LDLR/Del/Ex2-3/Ex2-3 - exon2-3 Mabuchi (2011) Atherosclerosis
LDLR/Dup/Ex3-6/Ex3-6 - exon3-6 Mabuchi (2011) Atherosclerosis
LDLR/-/codon159/- W159X exon4 Mabuchi (2011) Atherosclerosis
LDLR/Mut/IVS15-3/C-A - intron15 Mabuchi (2011) Atherosclerosis
LDLR/Mut/1845+2/T-C 5'splice_donor_mutation intron12 Maruyama (1995) Eur_J_Biochem
LDLR/Mut/418/G-A E130K exon4 Maruyama (1995) Arterioscler_Thromb_Vasc_Biol
LDLR/Mut/1845+2/T-C 5'splice donor mutation Mut/1845+2/T-C Maruyama (1995) Arterioscler_Thromb_Vasc_Biol
LDLR/Mut/2054/C-T P685L exon14 Maruyama (1995) Arterioscler_Thromb_Vasc_Biol
LDLR/Mut/2431/A-T K811X exon17 Maruyama (1995) Arterioscler_Thromb_Vasc_Biol
LDLR/Mut/68-1/G-C 3'splice_acceptor_mutation exon1 Maruyama (1998) Hum_Mutat
LDLR/Mut/1502/C-A A501E exon10 Miyake (1997) Domyakukoka
LDLR/Del/Ex7-14/12k - exon7-14 Miyake (1989) J_Biol_Chem
LDLR/Mut/1297/G-C D433H exon9 Miyake (1992) Eur_J_Biochem
LDLR/Del/Ex16-18/7.8k - exon16-18 Miyake (1981) Proc_Natl_Acad_Sci_U_S_A
LDLR/Mut/-137/C-T - promoter Miyake (2009) Atherosclerosis
LDLR/Mut/-134/C-T - promoter Miyake (2009) Atherosclerosis
LDLR/Del/Ex1/Ex1 - exon1 Miyake (2009) Atherosclerosis
LDLR/Mut/1/A-C M1L exon1 Miyake (2009) Atherosclerosis
LDLR/Del/20/AA K7IfsX21 exon1 Miyake (2009) Atherosclerosis
LDLR/Mut/29/G-A W10X exon1 Miyake (2009) Atherosclerosis
LDLR/Del/Ex2-6/Ex2-6 - exon2-6 Miyake (2009) Atherosclerosis
LDLR/Mut/283/T-G C95G exon3 Miyake (2009) Atherosclerosis
LDLR/Mut/301/G-A E101K exon3 Miyake (2009) Atherosclerosis
LDLR/Mut/401/G-T C134F exon4 Miyake (2009) Atherosclerosis
LDLR/Mut/500/G-A C167Y exon4 Miyake (2009) Atherosclerosis
LDLR/Mut/666/C-A C222X exon4 Miyake (2009) Atherosclerosis
LDLR/Dup/667/15 K223-D227dup exon4 Miyake (2009) Atherosclerosis
LDLR/Mut/681/C-A D227E exon4 Miyake (2009) Atherosclerosis
LDLR/Mut/682/G-A E228K exon4 Miyake (2009) Atherosclerosis
LDLR/Del/Ex5/Ex5 - exon5 Miyake (2009) Atherosclerosis
LDLR/Mut/828/C-A C276X exon6 Miyake (2009) Atherosclerosis
LDLR/Mut/883/G-T V295F exon6 Miyake (2009) Atherosclerosis
LDLR/Mut/1028/G-T G343V exon7 Miyake (2009) Atherosclerosis
LDLR/Ins/1062/T I355fsX3 exon8 Miyake (2009) Atherosclerosis
LDLR/Mut/1069/G-T E357X exon8 Miyake (2009) Atherosclerosis
LDLR/Dup/1107/5 L371fsX44 exon8 Miyake (2009) Atherosclerosis
LDLR/Del/1111/21 L371-C377del exon8 Miyake (2009) Atherosclerosis
LDLR/Mut/1265/T-G L422R exon9 Miyake (2009) Atherosclerosis
LDLR/Del/Ex9-10/Ex9-10 - exon9-10 Miyake (2009) Atherosclerosis
LDLR/Mut/1562/C-T A521V exon10 Miyake (2009) Atherosclerosis
LDLR/Mut/1618/G-A A530T exon11 Miyake (2009) Atherosclerosis
LDLR/Mut/1691/A-G N564S exon11 Miyake (2009) Atherosclerosis
LDLR/Mut/1845+1/G-A 5'splice_donor_mutation intron12 Miyake (2009) Atherosclerosis
LDLR/Del/Ex13-15/Ex13-15 - exon13-15 Miyake (2009) Atherosclerosis
LDLR/Del/Ex13-18/Ex13-18 - exon13-18 Miyake (2009) Atherosclerosis
LDLR/Del/Ex16-17/4k - exon16-17 Miyake (2009) Atherosclerosis
LDLR/Mut/2042/G-C C681S exon14 Miyake (2009) Atherosclerosis
LDLR/Mut/2087/G-T C696F exon14 Miyake (2009) Atherosclerosis
LDLR/Del/2102/G G701fsX8 exon14 Miyake (2009) Atherosclerosis
LDLR/Mut/2389/G-A V797M exon16 Miyake (2009) Atherosclerosis
LDLR/Mut/137/G-C C25S exon2 Takahashi (2001) Clin_Genet
LDLR/Del/2201/CA F74SfsX47 exon15 Tashiro (1988) Eur_J_Clin_Invest
LDLR/Mut/139/G-A D47N exon2 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/344/G-A R115H exon4 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1012/T-C C338R exon7 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1066/G-C D356H exon8 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1207/T-C F403L exon9 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1285/G-A V429M exon9 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1784/G-A R595Q exon12 Varret (1998) Nucleic_Acids_Res
LDLR/Mut/1246/C-T R416W exon9 Yagi (1994) Domyakukoka
LDLR/Ins/1247/5 R416fsX12 exon9 Yamakawa (1993) Hum_Genet
LDLR/Del/1655/T I552TfsX15 exon11 Yamakawa (1993) Hum_Genet
LDLR/DelIns/1115-1123/AGGGTGGCT-CACTGA E372-Y375delinsALN exon8 Yamakawa (1994) Hum_Genet
LDLR/Del/In1-In3/5k - exon2-3 Yamakawa (1989) Hum_Genet
LDLR/Del/Ex15-16/5.5k - exon15-16 Yamakawa (1989) Hum_Genet
LDLR/Del/Ex16-17/4k - exon16-17 Yamakawa (1989) Hum_Genet
LDLR/Mut/131/G-A W44X exon2 Yu (2002) Atherosclerosis
LDLR/Mut/137/G-A C46Y exon2 Yu (2002) Atherosclerosis
LDLR/Del/230/G G77AfsX53 exon3 Yu (2002) Atherosclerosis
LDLR/Mut/244/G-T C82F exon3 Yu (2002) Atherosclerosis
LDLR/Mut/288/G-T C95F exon3 Yu (2002) Atherosclerosis
LDLR/Mut/361/T-G C121G exon4 Yu (2002) Atherosclerosis
LDLR/Mut/388/T-A S130T exon4 Yu (2002) Atherosclerosis
LDLR/Ins/389/C S130fsX50 exon4 Yu (2002) Atherosclerosis
LDLR/Mut/463/T-C C155R exon4 Yu (2002) Atherosclerosis
LDLR/Mut/478/T-C C160R exon4 Yu (2002) Atherosclerosis
LDLR/Mut/550/T-C C184R exon4 Yu (2002) Atherosclerosis
LDLR/Mut/565/G-A V189M exon4 Yu (2002) Atherosclerosis
LDLR/Mut/611/G-C C204S exon4 Yu (2002) Atherosclerosis
LDLR/Mut/796/G-A D266N exon5 Yu (2002) Atherosclerosis
LDLR/Mut/797/A-G D266G exon5 Yu (2002) Atherosclerosis
LDLR/Mut/901/G-T D301Y exon6 Yu (2002) Atherosclerosis
LDLR/Mut/1048/C-T R340X exon7 Yu (2002) Atherosclerosis
LDLR/Ins/1061/T D354fsX4 exon8 Yu (2002) Atherosclerosis
LDLR/Mut/1252/G-A E418K exon9 Yu (2002) Atherosclerosis
LDLR/Mut/1567/G-A V523M exon10 Yu (2002) Atherosclerosis
LDLR/Mut/1587-1/G-A 3'splice_acceptor_mutation intron10 Yu (2002) Atherosclerosis
LDLR/Del/1871/TCA I624del exon13 Yu (2002) Atherosclerosis
LDLR/Mut/1925/T-C L642S exon13 Yu (2002) Atherosclerosis
LDLR/Mut/2026/G-A G676S exon14 Yu (2002) Atherosclerosis
LDLR/Del/2055/G P685fsX24 exon14 Yu (2002) Atherosclerosis
LDLR/Mut/2312-3/C-A 3'splice_acceptor_mutation intron15 Yu (2002) Atherosclerosis
LDLR/Ins/2416/G V806fsX11 exon17 Yu (2002) Atherosclerosis
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