Incidental Mutation 'R3835:Vldlr'
ID 275612
Institutional Source Beutler Lab
Gene Symbol Vldlr
Ensembl Gene ENSMUSG00000024924
Gene Name very low density lipoprotein receptor
Synonyms
MMRRC Submission 040890-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.285) question?
Stock # R3835 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 27193884-27231631 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 27212214 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 76 (D76G)
Ref Sequence ENSEMBL: ENSMUSP00000128193 (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: D76G

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000025866
Gene: ENSMUSG00000024924
AA Change: D76G

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 possibly damaging
Transcript: ENSMUST00000047645
AA Change: D76G

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000049145
Gene: ENSMUSG00000024924
AA Change: D76G

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: D76G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000128193
Gene: ENSMUSG00000024924
AA Change: D76G

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 possibly damaging
Transcript: ENSMUST00000167487
AA Change: D76G

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000127329
Gene: ENSMUSG00000024924
AA Change: D76G

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 possibly damaging
Transcript: ENSMUST00000172302
AA Change: D76G

PolyPhen 2 Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000126730
Gene: ENSMUSG00000024924
AA Change: D76G

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 0.4453 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 98% (43/44)
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl4 T C 3: 151,216,254 (GRCm39) I479T probably damaging Het
Adh6a G A 3: 138,033,275 (GRCm39) probably null Het
Anapc7 A G 5: 122,581,940 (GRCm39) T528A possibly damaging Het
Ap5b1 A G 19: 5,618,918 (GRCm39) T113A possibly damaging Het
Apaf1 G A 10: 90,895,449 (GRCm39) R439C probably benign Het
Apoa5 A T 9: 46,181,878 (GRCm39) H318L probably damaging Het
Bltp2 A G 11: 78,169,911 (GRCm39) R1545G probably benign Het
Btnl9 T G 11: 49,071,512 (GRCm39) T104P probably damaging Het
Cimip3 AC A 17: 47,744,348 (GRCm39) probably benign Het
Dennd5a T C 7: 109,533,449 (GRCm39) K107R probably benign Het
Dthd1 A T 5: 63,007,128 (GRCm39) R610W probably damaging Het
Eno1 T C 4: 150,331,119 (GRCm39) S186P probably benign Het
Gipc2 C A 3: 151,833,823 (GRCm39) V153F probably damaging Het
Gpt A G 15: 76,582,783 (GRCm39) Y295C probably damaging Het
Kcnh5 T A 12: 74,945,044 (GRCm39) Q735L probably benign Het
Lrrc10 A G 10: 116,881,691 (GRCm39) N122D possibly damaging Het
Lrrc37 C A 11: 103,510,836 (GRCm39) L377F unknown Het
Meis2 T C 2: 115,752,228 (GRCm39) H301R probably damaging Het
Muc5b A T 7: 141,412,918 (GRCm39) I1955F unknown Het
Nalcn A T 14: 123,530,834 (GRCm39) probably benign Het
Nmt2 T C 2: 3,315,723 (GRCm39) probably benign Het
Nnt C T 13: 119,509,031 (GRCm39) G403R probably damaging Het
Or4a79 T G 2: 89,551,799 (GRCm39) I219L possibly damaging Het
Or4d6 T A 19: 12,086,764 (GRCm39) I49F possibly damaging Het
Or5b109 A T 19: 13,212,103 (GRCm39) D163V probably benign Het
Ovgp1 A G 3: 105,893,631 (GRCm39) E468G probably benign Het
Pax6 G A 2: 105,526,795 (GRCm39) E234K probably benign Het
Prkdc A G 16: 15,609,810 (GRCm39) E3138G probably damaging Het
Prmt6 T C 3: 110,158,121 (GRCm39) D56G possibly damaging Het
Ptprt A G 2: 161,389,307 (GRCm39) V1261A probably damaging Het
Qtrt2 A G 16: 43,701,435 (GRCm39) S42P probably damaging Het
Rab9b C T X: 135,762,259 (GRCm39) R47Q possibly damaging Het
Rpgrip1 A G 14: 52,384,710 (GRCm39) E606G probably damaging Het
Setx C T 2: 29,035,072 (GRCm39) S519L possibly damaging Het
Slc15a2 A T 16: 36,592,490 (GRCm39) C191* probably null Het
Snrk T C 9: 121,966,069 (GRCm39) probably benign Het
St6galnac1 T C 11: 116,657,109 (GRCm39) D422G probably damaging Het
Stag1 C T 9: 100,620,035 (GRCm39) T46I probably damaging Het
Tagln T C 9: 45,843,008 (GRCm39) I18V probably benign Het
Tasor2 T C 13: 3,625,292 (GRCm39) T1553A probably benign Het
Tbx18 C A 9: 87,611,689 (GRCm39) A114S probably benign Het
Ttc16 T C 2: 32,659,322 (GRCm39) D259G probably damaging Het
Vmn2r24 G T 6: 123,764,412 (GRCm39) D430Y probably benign Het
Xlr3a T C X: 72,138,644 (GRCm39) E5G probably damaging 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
R2047:Vldlr UTSW 19 27,212,238 (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
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'- TAGAGCTCAGCCCTAGAGATG -3'
(R):5'- TCAAGTTTCAGGCAGGCAAAG -3'

Sequencing Primer
(F):5'- GCCCTAGAGATGCCAACAATTTG -3'
(R):5'- TGTCAAGCAATCGATAAAGCATC -3'
Posted On 2015-04-06