Incidental Mutation 'R5044:Ldlr'
ID 394262
Institutional Source Beutler Lab
Gene Symbol Ldlr
Ensembl Gene ENSMUSG00000032193
Gene Name low density lipoprotein receptor
Synonyms
MMRRC Submission 042634-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5044 (G1)
Quality Score 166
Status Validated
Chromosome 9
Chromosomal Location 21634872-21661215 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 21646538 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Threonine at position 235 (A235T)
Ref Sequence ENSEMBL: ENSMUSP00000149431 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034713] [ENSMUST00000213114]
AlphaFold P35951
Predicted Effect probably benign
Transcript: ENSMUST00000034713
AA Change: A235T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000034713
Gene: ENSMUSG00000032193
AA Change: A235T

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
LDLa 26 65 1.89e-14 SMART
LDLa 67 106 9.81e-13 SMART
EGF_like 108 144 6.81e1 SMART
LDLa 108 145 3.77e-14 SMART
LDLa 147 186 6.67e-15 SMART
LDLa 197 234 1.16e-14 SMART
LDLa 236 273 3.24e-13 SMART
LDLa 276 316 1e-9 SMART
EGF 318 354 3.2e-4 SMART
EGF_CA 355 394 4.09e-11 SMART
LY 420 462 1.11e-3 SMART
LY 466 508 4.7e-11 SMART
LY 509 552 5.23e-9 SMART
LY 553 595 7.86e-13 SMART
LY 596 639 3.25e-5 SMART
EGF 666 713 7.64e-2 SMART
low complexity region 799 811 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000213114
AA Change: A235T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000214359
Predicted Effect noncoding transcript
Transcript: ENSMUST00000215917
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217111
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217613
Meta Mutation Damage Score 0.1949 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.3%
Validation Efficiency 96% (73/76)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygous targeted mutants exhibit 2X higher total plasma cholesterol and 7-9X higher IDL and LDL levels on a normal diet compared to controls. On a high cholesterol diet, mutant effects dramatically increase and mice develop xanthomatosis and atherosclerosis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T A 11: 9,323,323 (GRCm39) F3387I possibly damaging Het
Acacb T A 5: 114,304,088 (GRCm39) S170R probably benign Het
Adamtsl4 A G 3: 95,588,960 (GRCm39) probably null Het
Adgrv1 A G 13: 81,637,050 (GRCm39) C3464R probably benign Het
Apbb1 A T 7: 105,214,889 (GRCm39) probably benign Het
Cad A G 5: 31,212,365 (GRCm39) T23A probably benign Het
Cdca7 A G 2: 72,313,759 (GRCm39) R183G probably benign Het
Cdpf1 T C 15: 85,693,513 (GRCm39) T5A probably benign Het
Cep85 T C 4: 133,883,490 (GRCm39) D133G probably damaging Het
Chrna9 T C 5: 66,128,359 (GRCm39) L189P probably damaging Het
Clca3a1 A C 3: 144,713,689 (GRCm39) probably null Het
Cntn1 G T 15: 92,140,876 (GRCm39) V201F probably damaging Het
Col4a3 A G 1: 82,644,267 (GRCm39) E352G unknown Het
Ddhd2 T C 8: 26,242,164 (GRCm39) Y237C probably damaging Het
Dnah6 A C 6: 73,014,605 (GRCm39) F3609V probably benign Het
Epha3 T C 16: 63,422,650 (GRCm39) K580R possibly damaging Het
Fam135b T C 15: 71,334,560 (GRCm39) N878S probably benign Het
Fbn1 T G 2: 125,171,022 (GRCm39) T1938P probably damaging Het
Foxg1 T C 12: 49,431,969 (GRCm39) V234A probably damaging Het
Garin5b T C 7: 4,761,660 (GRCm39) N351D probably benign Het
Glt1d1 A T 5: 127,721,478 (GRCm39) N55I probably benign Het
Gm17641 C A 3: 68,776,807 (GRCm39) probably benign Het
Gm7665 A G 18: 16,407,788 (GRCm39) noncoding transcript Het
Hgf A C 5: 16,819,892 (GRCm39) N541T probably benign Het
Hipk2 G A 6: 38,795,814 (GRCm39) P152S probably benign Het
Jarid2 C T 13: 45,060,041 (GRCm39) L720F probably damaging Het
Kifc5b A G 17: 27,143,761 (GRCm39) E511G probably damaging Het
Lmln A G 16: 32,894,550 (GRCm39) D231G possibly damaging Het
Lrp1 A G 10: 127,403,364 (GRCm39) C2070R probably damaging Het
Mbl1 A G 14: 40,880,681 (GRCm39) T190A possibly damaging Het
Mpdz A T 4: 81,299,934 (GRCm39) S355T probably benign Het
Muc19 C T 15: 91,772,332 (GRCm39) noncoding transcript Het
Mycbp2 A C 14: 103,376,671 (GRCm39) probably null Het
Naa20 T C 2: 145,757,762 (GRCm39) S164P probably damaging Het
Nme4 A T 17: 26,312,807 (GRCm39) probably benign Het
Npas2 A T 1: 39,386,587 (GRCm39) R619* probably null Het
Nudt19 G A 7: 35,255,171 (GRCm39) T20I possibly damaging Het
Or4c119 T A 2: 88,987,283 (GRCm39) K79* probably null Het
Or5b97 A G 19: 12,878,365 (GRCm39) Y260H probably damaging Het
Pitpnc1 A G 11: 107,187,054 (GRCm39) Y90H possibly damaging Het
Rcor2 A G 19: 7,247,150 (GRCm39) T6A probably benign Het
Rif1 T A 2: 51,999,940 (GRCm39) S1131R probably damaging Het
Rtkn T A 6: 83,127,972 (GRCm39) D377E probably benign Het
Rtn4rl2 T A 2: 84,702,846 (GRCm39) N242I probably damaging Het
Sbno2 G A 10: 79,898,022 (GRCm39) L719F probably benign Het
Scn11a G T 9: 119,648,897 (GRCm39) D55E probably damaging Het
Setd1b T A 5: 123,289,929 (GRCm39) I632N unknown Het
Spaca6 A G 17: 18,051,458 (GRCm39) T45A probably benign Het
Srpk2 A T 5: 23,729,390 (GRCm39) D416E possibly damaging Het
Sspo A T 6: 48,443,889 (GRCm39) probably null Het
Sycp1 A T 3: 102,752,370 (GRCm39) I804N probably benign Het
Tdp2 G A 13: 25,015,809 (GRCm39) R32Q probably benign Het
Tgfbr3 A G 5: 107,284,795 (GRCm39) V618A possibly damaging Het
Tmc3 C T 7: 83,258,326 (GRCm39) P439S probably benign Het
Tnxb A T 17: 34,936,457 (GRCm39) D2740V probably damaging Het
Tspyl4 A G 10: 34,173,933 (GRCm39) T142A probably benign Het
Ttn T C 2: 76,710,785 (GRCm39) probably benign Het
Tubgcp4 T C 2: 121,004,061 (GRCm39) L34P probably damaging Het
Tubgcp6 G T 15: 88,983,748 (GRCm39) probably benign Het
Unc79 T A 12: 103,078,962 (GRCm39) V1690E probably benign Het
Vps4b T C 1: 106,724,148 (GRCm39) probably null Het
Wtap A G 17: 13,186,525 (GRCm39) S341P possibly damaging Het
Wwc1 T C 11: 35,774,172 (GRCm39) T363A probably benign Het
Zbtb8a G A 4: 129,254,293 (GRCm39) T67M probably damaging Het
Zfp865 T C 7: 5,037,668 (GRCm39) probably benign Het
Other mutations in Ldlr
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00501:Ldlr APN 9 21,646,657 (GRCm39) critical splice donor site probably null
IGL01975:Ldlr APN 9 21,644,993 (GRCm39) missense probably benign 0.05
IGL02043:Ldlr APN 9 21,644,795 (GRCm39) missense probably benign 0.03
IGL02524:Ldlr APN 9 21,644,977 (GRCm39) missense probably damaging 1.00
IGL03049:Ldlr APN 9 21,657,115 (GRCm39) missense probably benign 0.00
IGL03113:Ldlr APN 9 21,651,124 (GRCm39) missense possibly damaging 0.85
R0240:Ldlr UTSW 9 21,649,295 (GRCm39) splice site probably benign
R0586:Ldlr UTSW 9 21,651,040 (GRCm39) missense probably benign 0.00
R1398:Ldlr UTSW 9 21,650,838 (GRCm39) missense probably benign 0.01
R1587:Ldlr UTSW 9 21,649,209 (GRCm39) missense probably damaging 0.99
R2198:Ldlr UTSW 9 21,643,698 (GRCm39) missense probably damaging 1.00
R3730:Ldlr UTSW 9 21,643,097 (GRCm39) missense probably benign 0.09
R4422:Ldlr UTSW 9 21,649,248 (GRCm39) missense probably damaging 1.00
R5046:Ldlr UTSW 9 21,657,203 (GRCm39) critical splice donor site probably null
R6186:Ldlr UTSW 9 21,635,055 (GRCm39) start gained probably benign
R6195:Ldlr UTSW 9 21,643,077 (GRCm39) nonsense probably null
R6523:Ldlr UTSW 9 21,648,549 (GRCm39) missense probably damaging 1.00
R6682:Ldlr UTSW 9 21,643,671 (GRCm39) missense probably benign
R7256:Ldlr UTSW 9 21,657,040 (GRCm39) missense probably benign 0.01
R7384:Ldlr UTSW 9 21,651,090 (GRCm39) missense probably benign 0.07
R7823:Ldlr UTSW 9 21,653,602 (GRCm39) critical splice donor site probably null
R8065:Ldlr UTSW 9 21,649,241 (GRCm39) missense probably damaging 1.00
R8223:Ldlr UTSW 9 21,658,546 (GRCm39) missense probably damaging 1.00
R8732:Ldlr UTSW 9 21,650,985 (GRCm39) missense probably benign 0.00
R8931:Ldlr UTSW 9 21,643,108 (GRCm39) missense probably damaging 0.99
R8954:Ldlr UTSW 9 21,650,828 (GRCm39) missense possibly damaging 0.87
R9315:Ldlr UTSW 9 21,644,782 (GRCm39) splice site probably benign
R9489:Ldlr UTSW 9 21,646,626 (GRCm39) missense probably damaging 1.00
R9517:Ldlr UTSW 9 21,655,240 (GRCm39) missense possibly damaging 0.90
R9605:Ldlr UTSW 9 21,646,626 (GRCm39) missense probably damaging 1.00
R9709:Ldlr UTSW 9 21,657,135 (GRCm39) missense probably benign 0.00
X0024:Ldlr UTSW 9 21,651,114 (GRCm39) missense probably damaging 1.00
Z1177:Ldlr UTSW 9 21,651,126 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- ATCCCCTGCGTGATTTAGTG -3'
(R):5'- TTTACAGAAATGCAAGGCACTGAG -3'

Sequencing Primer
(F):5'- GCAGCTCCTGACAGTGAG -3'
(R):5'- GCACTGAGAAGTGGGACC -3'
Posted On 2016-06-15