Incidental Mutation 'R2047:Vldlr'
ID 222171
Institutional Source Beutler Lab
Gene Symbol Vldlr
Ensembl Gene ENSMUSG00000024924
Gene Name very low density lipoprotein receptor
Synonyms
MMRRC Submission 040054-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.285) question?
Stock # R2047 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 27193884-27231631 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 27212238 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Phenylalanine at position 84 (C84F)
Ref Sequence ENSEMBL: ENSMUSP00000126730 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025866] [ENSMUST00000047645] [ENSMUST00000164746] [ENSMUST00000165761] [ENSMUST00000167487] [ENSMUST00000172302]
AlphaFold P98156
Predicted Effect probably damaging
Transcript: ENSMUST00000025866
AA Change: C84F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000025866
Gene: ENSMUSG00000024924
AA Change: C84F

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
EGF_like 32 68 7.38e1 SMART
LDLa 32 69 1.69e-16 SMART
LDLa 71 110 5.81e-15 SMART
LDLa 112 151 1.96e-12 SMART
LDLa 153 190 7.15e-15 SMART
LDLa 192 231 1.23e-13 SMART
LDLa 238 275 1.1e-15 SMART
LDLa 277 314 1.13e-12 SMART
LDLa 317 357 3.86e-11 SMART
EGF_CA 356 395 1e-5 SMART
EGF_CA 396 435 6.1e-10 SMART
Blast:LY 461 495 4e-15 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000047645
AA Change: C84F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000049145
Gene: ENSMUSG00000024924
AA Change: C84F

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
EGF_like 32 68 7.38e1 SMART
LDLa 32 69 1.69e-16 SMART
LDLa 71 110 1.25e-14 SMART
LDLa 112 149 7.15e-15 SMART
LDLa 151 190 1.23e-13 SMART
LDLa 197 234 1.1e-15 SMART
LDLa 236 273 1.13e-12 SMART
LDLa 276 316 3.86e-11 SMART
EGF_CA 315 354 1e-5 SMART
EGF_CA 355 394 6.1e-10 SMART
LY 420 462 2.16e-1 SMART
LY 464 506 9.54e-12 SMART
LY 507 550 2.22e-12 SMART
LY 551 593 1.66e-11 SMART
LY 594 637 5.97e-4 SMART
EGF 664 709 2.16e-1 SMART
transmembrane domain 728 750 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000163729
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164509
Predicted Effect probably damaging
Transcript: ENSMUST00000164746
AA Change: C84F

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000128193
Gene: ENSMUSG00000024924
AA Change: C84F

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
LDLa 32 69 1.69e-16 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000165761
SMART Domains Protein: ENSMUSP00000130382
Gene: ENSMUSG00000024924

DomainStartEndE-ValueType
LDLa 1 26 1.58e0 SMART
EGF 28 64 4e-5 SMART
LY 88 130 2.16e-1 SMART
LY 132 174 9.54e-12 SMART
LY 175 218 2.22e-12 SMART
LY 219 258 3.25e-5 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000167487
AA Change: C84F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000127329
Gene: ENSMUSG00000024924
AA Change: C84F

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
EGF_like 32 68 7.38e1 SMART
LDLa 32 69 1.69e-16 SMART
LDLa 71 110 5.81e-15 SMART
LDLa 112 151 1.96e-12 SMART
LDLa 153 190 7.15e-15 SMART
LDLa 192 231 1.23e-13 SMART
LDLa 238 275 1.1e-15 SMART
LDLa 277 314 1.13e-12 SMART
LDLa 317 357 3.86e-11 SMART
EGF_CA 356 395 1e-5 SMART
EGF_CA 396 435 6.1e-10 SMART
LY 461 503 2.16e-1 SMART
LY 505 547 9.54e-12 SMART
LY 548 591 2.22e-12 SMART
LY 592 634 1.66e-11 SMART
LY 635 678 5.97e-4 SMART
EGF 705 750 2.16e-1 SMART
transmembrane domain 797 819 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000172302
AA Change: C84F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000126730
Gene: ENSMUSG00000024924
AA Change: C84F

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
EGF_like 32 68 7.38e1 SMART
LDLa 32 69 1.69e-16 SMART
LDLa 71 110 5.81e-15 SMART
LDLa 112 151 1.96e-12 SMART
LDLa 153 190 7.15e-15 SMART
LDLa 192 231 1.23e-13 SMART
LDLa 238 275 1.1e-15 SMART
LDLa 277 314 1.13e-12 SMART
LDLa 317 357 3.86e-11 SMART
EGF_CA 356 395 1e-5 SMART
EGF_CA 396 435 6.1e-10 SMART
LY 461 503 2.16e-1 SMART
LY 505 547 9.54e-12 SMART
LY 548 591 2.22e-12 SMART
LY 592 634 1.66e-11 SMART
LY 635 678 5.97e-4 SMART
EGF 705 750 2.16e-1 SMART
transmembrane domain 769 791 N/A INTRINSIC
Meta Mutation Damage Score 0.9665 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 100% (57/57)
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. This gene encodes a lipoprotein receptor that is a member of the LDLR family and plays important roles in VLDL-triglyceride metabolism and the reelin signaling pathway. Mutations in this gene cause VLDLR-associated cerebellar hypoplasia. Alternative splicing generates multiple transcript variants encoding distinct isoforms for this gene. [provided by RefSeq, Aug 2009]
PHENOTYPE: Homozygous null mutants exhibit modest reductions in body weight and adiposity. In behavioral tests, mutants display deficits in contextual fear conditioning and long term potentiation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik A G 7: 130,747,836 (GRCm39) F52S probably damaging Het
Acot12 T C 13: 91,931,122 (GRCm39) S457P probably damaging Het
Adcy5 G A 16: 35,110,478 (GRCm39) V882M possibly damaging Het
Ahnak A G 19: 8,991,664 (GRCm39) D4316G possibly damaging Het
Aldh1l2 G A 10: 83,342,607 (GRCm39) A401V probably damaging Het
Apol7e A G 15: 77,601,810 (GRCm39) H136R probably benign Het
Arl5a A G 2: 52,302,072 (GRCm39) probably null Het
Asns G T 6: 7,680,093 (GRCm39) A341E probably damaging Het
C7 A G 15: 5,075,143 (GRCm39) L183P probably damaging Het
Cacng2 C T 15: 78,003,037 (GRCm39) A19T probably damaging Het
Ccdc121rt2 A G 5: 112,598,575 (GRCm39) N374S probably benign Het
Ccr4 A G 9: 114,321,633 (GRCm39) F144S probably damaging Het
Ckap2 A G 8: 22,658,763 (GRCm39) V660A probably benign Het
Cramp1 A T 17: 25,222,189 (GRCm39) Y176* probably null Het
Dgki A G 6: 36,890,581 (GRCm39) S922P possibly damaging Het
Drd5 C T 5: 38,477,679 (GRCm39) S224L probably damaging Het
Ei24 T C 9: 36,691,459 (GRCm39) K341E probably benign Het
Eno2 A T 6: 124,744,659 (GRCm39) probably benign Het
Epb41l4a T C 18: 33,961,259 (GRCm39) N425S probably benign Het
F13b T G 1: 139,435,961 (GRCm39) C256G probably damaging Het
Gp6 A T 7: 4,376,270 (GRCm39) probably benign Het
H2-Q7 A T 17: 35,659,123 (GRCm39) R191S probably damaging Het
Ivns1abp T A 1: 151,227,382 (GRCm39) S63R possibly damaging Het
Kcnj16 A G 11: 110,915,946 (GRCm39) probably null Het
Lpcat4 T C 2: 112,075,142 (GRCm39) probably null Het
Lrrc14b T C 13: 74,511,561 (GRCm39) K173R probably benign Het
Maml3 C A 3: 51,597,866 (GRCm39) R939S probably damaging Het
Mrgpra2b C T 7: 47,113,908 (GRCm39) V249I probably benign Het
Mrpl46 T A 7: 78,431,312 (GRCm39) Y82F probably damaging Het
Mthfs T A 9: 89,097,356 (GRCm39) I71N probably damaging Het
Nectin4 T C 1: 171,212,720 (GRCm39) V351A possibly damaging Het
Npas3 T C 12: 54,115,612 (GRCm39) F827L probably damaging Het
Nrp1 G A 8: 129,224,577 (GRCm39) probably benign Het
Ocln C A 13: 100,671,632 (GRCm39) A242S probably damaging Het
Or10ad1c T A 15: 98,084,920 (GRCm39) T253S probably damaging Het
Or13g1 G A 7: 85,956,012 (GRCm39) T103I probably damaging Het
Or5d37 A T 2: 87,924,237 (GRCm39) N14K probably benign Het
Pappa T C 4: 65,149,378 (GRCm39) probably benign Het
Ptpn6 T C 6: 124,698,752 (GRCm39) T480A probably benign Het
Pycr1 A T 11: 120,532,512 (GRCm39) D168E possibly damaging Het
Rnf6 T C 5: 146,148,674 (GRCm39) T126A probably damaging Het
Slc25a39 G A 11: 102,296,657 (GRCm39) probably benign Het
Slc35f4 G T 14: 49,541,029 (GRCm39) probably benign Het
Sppl2a C T 2: 126,768,772 (GRCm39) A112T probably damaging Het
Sptbn1 A C 11: 30,088,360 (GRCm39) probably benign Het
Sqle T C 15: 59,197,907 (GRCm39) Y376H probably benign Het
Terb1 A T 8: 105,212,094 (GRCm39) Y296N probably damaging Het
Ttbk2 T C 2: 120,579,397 (GRCm39) H506R probably damaging Het
Ttn T C 2: 76,737,879 (GRCm39) D4220G probably benign Het
Tub A G 7: 108,625,939 (GRCm39) D230G probably benign Het
Ube2d3 T A 3: 135,170,967 (GRCm39) I137K probably benign Het
Vmn1r54 A T 6: 90,246,970 (GRCm39) I295F probably damaging Het
Vmn2r56 A G 7: 12,466,918 (GRCm39) S39P probably damaging Het
Zfp358 A G 8: 3,545,934 (GRCm39) H172R probably damaging Het
Zfp619 T C 7: 39,187,062 (GRCm39) C1031R probably damaging Het
Zfp777 A G 6: 48,021,280 (GRCm39) I114T probably benign Het
Other mutations in Vldlr
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01346:Vldlr APN 19 27,217,081 (GRCm39) missense possibly damaging 0.93
IGL01575:Vldlr APN 19 27,224,031 (GRCm39) missense probably benign
IGL01626:Vldlr APN 19 27,221,173 (GRCm39) missense probably damaging 1.00
IGL02213:Vldlr APN 19 27,218,726 (GRCm39) missense probably benign 0.09
IGL02365:Vldlr APN 19 27,223,025 (GRCm39) missense probably damaging 1.00
IGL02488:Vldlr APN 19 27,215,675 (GRCm39) missense probably damaging 1.00
IGL02708:Vldlr APN 19 27,215,485 (GRCm39) missense possibly damaging 0.92
IGL02947:Vldlr APN 19 27,217,120 (GRCm39) missense probably benign 0.03
disturbed UTSW 19 27,216,204 (GRCm39) nonsense probably null
r26 UTSW 19 27,223,054 (GRCm39) missense probably damaging 0.99
spotty UTSW 19 27,216,192 (GRCm39) missense probably damaging 1.00
PIT4142001:Vldlr UTSW 19 27,212,269 (GRCm39) missense probably benign 0.05
R0195:Vldlr UTSW 19 27,215,786 (GRCm39) missense probably damaging 1.00
R0288:Vldlr UTSW 19 27,218,051 (GRCm39) splice site probably benign
R0536:Vldlr UTSW 19 27,217,364 (GRCm39) missense probably damaging 1.00
R0537:Vldlr UTSW 19 27,225,318 (GRCm39) missense probably damaging 1.00
R0542:Vldlr UTSW 19 27,213,655 (GRCm39) missense probably benign 0.01
R0594:Vldlr UTSW 19 27,212,219 (GRCm39) missense probably damaging 1.00
R0624:Vldlr UTSW 19 27,215,663 (GRCm39) missense possibly damaging 0.91
R0726:Vldlr UTSW 19 27,215,786 (GRCm39) missense probably damaging 1.00
R1017:Vldlr UTSW 19 27,218,733 (GRCm39) missense probably damaging 1.00
R1148:Vldlr UTSW 19 27,218,691 (GRCm39) missense probably benign 0.01
R1148:Vldlr UTSW 19 27,218,691 (GRCm39) missense probably benign 0.01
R1443:Vldlr UTSW 19 27,217,121 (GRCm39) missense possibly damaging 0.91
R1493:Vldlr UTSW 19 27,218,691 (GRCm39) missense probably benign 0.01
R1520:Vldlr UTSW 19 27,224,466 (GRCm39) missense possibly damaging 0.96
R1520:Vldlr UTSW 19 27,217,943 (GRCm39) missense probably damaging 0.99
R1657:Vldlr UTSW 19 27,223,070 (GRCm39) missense probably benign 0.00
R1901:Vldlr UTSW 19 27,218,709 (GRCm39) missense probably damaging 1.00
R2258:Vldlr UTSW 19 27,215,786 (GRCm39) missense probably damaging 1.00
R2273:Vldlr UTSW 19 27,225,415 (GRCm39) missense probably damaging 1.00
R2423:Vldlr UTSW 19 27,213,688 (GRCm39) missense possibly damaging 0.49
R3196:Vldlr UTSW 19 27,220,554 (GRCm39) missense probably damaging 0.98
R3752:Vldlr UTSW 19 27,215,731 (GRCm39) missense probably damaging 1.00
R3801:Vldlr UTSW 19 27,195,021 (GRCm39) missense probably damaging 0.99
R3835:Vldlr UTSW 19 27,212,214 (GRCm39) missense probably damaging 1.00
R4027:Vldlr UTSW 19 27,215,713 (GRCm39) missense probably benign
R4301:Vldlr UTSW 19 27,215,802 (GRCm39) missense possibly damaging 0.80
R4470:Vldlr UTSW 19 27,212,219 (GRCm39) missense probably damaging 0.96
R4541:Vldlr UTSW 19 27,216,192 (GRCm39) missense probably damaging 1.00
R4765:Vldlr UTSW 19 27,217,947 (GRCm39) missense probably damaging 1.00
R4771:Vldlr UTSW 19 27,217,290 (GRCm39) missense probably damaging 0.97
R4795:Vldlr UTSW 19 27,216,252 (GRCm39) splice site probably null
R4839:Vldlr UTSW 19 27,215,465 (GRCm39) missense probably damaging 1.00
R5074:Vldlr UTSW 19 27,215,677 (GRCm39) missense probably damaging 1.00
R5134:Vldlr UTSW 19 27,216,212 (GRCm39) nonsense probably null
R5281:Vldlr UTSW 19 27,221,631 (GRCm39) missense probably benign 0.44
R5466:Vldlr UTSW 19 27,217,243 (GRCm39) critical splice acceptor site probably null
R5514:Vldlr UTSW 19 27,221,624 (GRCm39) missense probably damaging 0.97
R5886:Vldlr UTSW 19 27,221,171 (GRCm39) missense probably benign 0.03
R5889:Vldlr UTSW 19 27,217,064 (GRCm39) missense probably damaging 1.00
R6110:Vldlr UTSW 19 27,215,477 (GRCm39) missense possibly damaging 0.92
R6343:Vldlr UTSW 19 27,223,049 (GRCm39) missense probably damaging 0.99
R6833:Vldlr UTSW 19 27,217,974 (GRCm39) missense probably damaging 1.00
R6838:Vldlr UTSW 19 27,225,370 (GRCm39) missense probably damaging 1.00
R7169:Vldlr UTSW 19 27,221,728 (GRCm39) missense probably benign
R7197:Vldlr UTSW 19 27,212,241 (GRCm39) missense probably benign 0.36
R7304:Vldlr UTSW 19 27,216,004 (GRCm39) missense possibly damaging 0.93
R7403:Vldlr UTSW 19 27,213,674 (GRCm39) nonsense probably null
R7658:Vldlr UTSW 19 27,220,536 (GRCm39) missense probably benign 0.33
R7754:Vldlr UTSW 19 27,195,015 (GRCm39) start codon destroyed probably benign 0.01
R8105:Vldlr UTSW 19 27,216,204 (GRCm39) nonsense probably null
R8377:Vldlr UTSW 19 27,212,258 (GRCm39) missense probably damaging 1.00
R8529:Vldlr UTSW 19 27,207,656 (GRCm39) missense probably benign 0.03
R8777:Vldlr UTSW 19 27,217,946 (GRCm39) missense probably benign 0.00
R8777-TAIL:Vldlr UTSW 19 27,217,946 (GRCm39) missense probably benign 0.00
R9380:Vldlr UTSW 19 27,216,192 (GRCm39) missense possibly damaging 0.63
R9400:Vldlr UTSW 19 27,216,175 (GRCm39) missense probably damaging 0.99
R9483:Vldlr UTSW 19 27,224,031 (GRCm39) missense probably benign 0.00
R9502:Vldlr UTSW 19 27,218,742 (GRCm39) missense probably damaging 1.00
R9509:Vldlr UTSW 19 27,221,687 (GRCm39) missense probably benign 0.44
R9630:Vldlr UTSW 19 27,207,623 (GRCm39) missense probably damaging 1.00
R9767:Vldlr UTSW 19 27,212,274 (GRCm39) missense probably damaging 1.00
R9768:Vldlr UTSW 19 27,218,720 (GRCm39) missense possibly damaging 0.47
Predicted Primers PCR Primer
(F):5'- TAGAGCTCAGCCCTAGAGATGC -3'
(R):5'- CAAGTTTCAGGCAGGCAAAG -3'

Sequencing Primer
(F):5'- GCCCTAGAGATGCCAACAATTTG -3'
(R):5'- TTTCAGGCAGGCAAAGAAAAATG -3'
Posted On 2014-08-25