Incidental Mutation 'R4301:Vldlr'
ID 322440
Institutional Source Beutler Lab
Gene Symbol Vldlr
Ensembl Gene ENSMUSG00000024924
Gene Name very low density lipoprotein receptor
Synonyms
MMRRC Submission 041088-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.250) question?
Stock # R4301 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 27193884-27231631 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 27215802 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 266 (D266E)
Ref Sequence ENSEMBL: ENSMUSP00000127329 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025866] [ENSMUST00000047645] [ENSMUST00000164746] [ENSMUST00000165761] [ENSMUST00000167487] [ENSMUST00000172302]
AlphaFold P98156
Predicted Effect possibly damaging
Transcript: ENSMUST00000025866
AA Change: D266E

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000025866
Gene: ENSMUSG00000024924
AA Change: D266E

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: D225E

PolyPhen 2 Score 0.474 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000049145
Gene: ENSMUSG00000024924
AA Change: D225E

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: ENSMUST00000164509
Predicted Effect probably benign
Transcript: ENSMUST00000164746
SMART Domains Protein: ENSMUSP00000128193
Gene: ENSMUSG00000024924

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: D266E

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000127329
Gene: ENSMUSG00000024924
AA Change: D266E

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 benign
Transcript: ENSMUST00000172302
AA Change: D266E

PolyPhen 2 Score 0.295 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000126730
Gene: ENSMUSG00000024924
AA Change: D266E

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (43/43)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi3bp T A 16: 56,377,266 (GRCm39) V95D probably damaging Het
Adamtsl2 A G 2: 26,977,295 (GRCm39) D252G probably null Het
Adgra3 T C 5: 50,118,420 (GRCm39) R1043G possibly damaging Het
Atxn7l1 A G 12: 33,417,237 (GRCm39) D562G probably damaging Het
Ccdc70 T C 8: 22,463,228 (GRCm39) V6A possibly damaging Het
Cdc25a T C 9: 109,718,810 (GRCm39) V337A probably benign Het
Chil4 G A 3: 106,111,043 (GRCm39) P284S possibly damaging Het
Crb1 A G 1: 139,176,568 (GRCm39) S472P probably benign Het
Fam193b G A 13: 55,690,417 (GRCm39) R740* probably null Het
Fer G T 17: 64,385,905 (GRCm39) L292F probably damaging Het
Gmppa G A 1: 75,419,140 (GRCm39) R349H possibly damaging Het
Hspa1a T C 17: 35,189,482 (GRCm39) I474V probably benign Het
Kcnh8 GAGACCAACGAGCAGCTGATGCTTCAGA GAGA 17: 53,032,934 (GRCm39) 74 probably benign Het
Lrrc30 A G 17: 67,939,563 (GRCm39) S6P probably damaging Het
Lzts3 A G 2: 130,478,358 (GRCm39) S133P probably damaging Het
Mrtfb T C 16: 13,216,169 (GRCm39) Y294H probably damaging Het
Mtmr12 T A 15: 12,236,106 (GRCm39) F122I possibly damaging Het
Mypn A G 10: 62,954,263 (GRCm39) Y124H probably damaging Het
Nfat5 T C 8: 108,082,327 (GRCm39) probably benign Het
Npr2 T C 4: 43,641,332 (GRCm39) probably null Het
Or5a3 T C 19: 12,400,081 (GRCm39) L136P probably damaging Het
Pgm2 G A 5: 64,261,140 (GRCm39) W51* probably null Het
Phip G A 9: 82,841,766 (GRCm39) R48* probably null Het
Piezo2 T C 18: 63,217,911 (GRCm39) T1075A probably damaging Het
Ppat G T 5: 77,076,348 (GRCm39) probably benign Het
Ppp2r2b T A 18: 43,031,811 (GRCm39) E23D probably null Het
Prickle1 T C 15: 93,406,517 (GRCm39) I169V possibly damaging Het
Rab37 T A 11: 115,049,390 (GRCm39) D95E possibly damaging Het
Sash1 A G 10: 8,627,234 (GRCm39) V50A probably benign Het
Siae C A 9: 37,545,009 (GRCm39) Q335K possibly damaging Het
Snx14 A T 9: 88,292,676 (GRCm39) I217K probably damaging Het
Son A G 16: 91,455,299 (GRCm39) T1349A possibly damaging Het
Sptb A G 12: 76,659,471 (GRCm39) L1143S probably damaging Het
Trim80 T C 11: 115,335,939 (GRCm39) probably null Het
Trpm3 T C 19: 22,964,656 (GRCm39) S1374P probably benign Het
Vmn2r79 A G 7: 86,651,099 (GRCm39) H166R possibly damaging Het
Zbtb10 A T 3: 9,330,220 (GRCm39) Q526L probably damaging Het
Zfr2 T C 10: 81,078,018 (GRCm39) probably benign Het
Zswim8 G A 14: 20,763,977 (GRCm39) R449H possibly damaging Het
Zzef1 T C 11: 72,779,861 (GRCm39) V1878A 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
R3835:Vldlr UTSW 19 27,212,214 (GRCm39) missense probably damaging 1.00
R4027:Vldlr UTSW 19 27,215,713 (GRCm39) missense probably benign
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'- AGTGATGAGCTGGACTGTGC -3'
(R):5'- TCAACACAGTCTCGGATGCC -3'

Sequencing Primer
(F):5'- AGTTCCAGTGCAGCACCTC -3'
(R):5'- ACAGTCTCGGATGCCATTGC -3'
Posted On 2015-06-20