Incidental Mutation 'R9793:Vim'
ID 734730
Institutional Source Beutler Lab
Gene Symbol Vim
Ensembl Gene ENSMUSG00000026728
Gene Name vimentin
Synonyms
MMRRC Submission
Accession Numbers
Essential gene? Possibly essential (E-score: 0.635) question?
Stock # R9793 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 13579122-13587637 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 13579598 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 119 (D119G)
Ref Sequence ENSEMBL: ENSMUSP00000028062 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028062] [ENSMUST00000141365] [ENSMUST00000193675]
AlphaFold P20152
Predicted Effect probably benign
Transcript: ENSMUST00000028062
AA Change: D119G

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000028062
Gene: ENSMUSG00000026728
AA Change: D119G

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 7.8e-23 PFAM
Filament 102 410 6.65e-150 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000141365
AA Change: D119G

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000114742
Gene: ENSMUSG00000026728
AA Change: D119G

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 1.8e-23 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000193675
AA Change: D119G

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000141494
Gene: ENSMUSG00000026728
AA Change: D119G

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 3.8e-19 PFAM
Pfam:Filament 102 410 3.6e-116 PFAM
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.8%
  • 10x: 99.5%
  • 20x: 98.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the intermediate filament family. Intermediate filamentents, along with microtubules and actin microfilaments, make up the cytoskeleton. The protein encoded by this gene is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. It is also involved in the immune response, and controls the transport of low-density lipoprotein (LDL)-derived cholesterol from a lysosome to the site of esterification. It functions as an organizer of a number of critical proteins involved in attachment, migration, and cell signaling. Mutations in this gene causes a dominant, pulverulent cataract.[provided by RefSeq, Jun 2009]
PHENOTYPE: Homozygous null mutants exhibit impaired performance in motor coordination tests; cerebellum shows underdeveloped/abnormal Bergman glia and stunted, poorly branched Purkinje cells. Mutants are unable to survive experimental 75% reduction of kidney mass. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Add2 A T 6: 86,078,135 (GRCm39) probably null Het
Afap1l1 T C 18: 61,874,822 (GRCm39) D453G possibly damaging Het
Agrn A G 4: 156,261,129 (GRCm39) V656A probably benign Het
Aldh3a1 T C 11: 61,108,927 (GRCm39) Y443H probably damaging Het
Alpk3 T C 7: 80,750,881 (GRCm39) probably null Het
Ano1 A T 7: 144,175,434 (GRCm39) W495R probably damaging Het
Apc T A 18: 34,447,628 (GRCm39) L1508Q probably damaging Het
Cald1 A T 6: 34,723,071 (GRCm39) M52L Het
Ccdc9b T C 2: 118,587,784 (GRCm39) S517G unknown Het
Cdk11b T A 4: 155,732,378 (GRCm39) H510Q unknown Het
Cdk12 T A 11: 98,102,051 (GRCm39) D636E unknown Het
Cfap53 A G 18: 74,438,741 (GRCm39) D306G probably benign Het
Cntln C T 4: 84,985,798 (GRCm39) L951F probably benign Het
Cntnap4 T C 8: 113,608,357 (GRCm39) V1259A probably benign Het
Cntnap5c A T 17: 58,409,192 (GRCm39) T477S probably benign Het
Cyp4a30b A G 4: 115,316,167 (GRCm39) T298A probably benign Het
Dop1b T A 16: 93,598,503 (GRCm39) D2006E probably benign Het
Ermard T C 17: 15,281,441 (GRCm39) L617P probably damaging Het
Glipr1l2 A G 10: 111,942,905 (GRCm39) I253M probably benign Het
Gm40460 CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG 7: 141,794,554 (GRCm39) probably benign Het
Grik3 A G 4: 125,526,315 (GRCm39) T183A probably damaging Het
Hao1 T A 2: 134,372,552 (GRCm39) Y152F possibly damaging Het
Hdac7 T C 15: 97,698,671 (GRCm39) T629A possibly damaging Het
Hmcn1 G A 1: 150,608,689 (GRCm39) P1498S possibly damaging Het
Iqcf3 T A 9: 106,434,714 (GRCm39) K41N probably benign Het
Kif26a C T 12: 112,142,887 (GRCm39) A1047V probably damaging Het
Lrriq3 T C 3: 154,893,313 (GRCm39) M338T probably benign Het
Map1a T C 2: 121,121,304 (GRCm39) probably null Het
Ncoa2 G T 1: 13,260,355 (GRCm39) Q107K possibly damaging Het
Nsd2 A G 5: 34,003,489 (GRCm39) D213G possibly damaging Het
Nuggc T C 14: 65,847,345 (GRCm39) S131P probably damaging Het
Nwd2 A G 5: 63,964,232 (GRCm39) E1272G probably damaging Het
Or2y1 A T 11: 49,385,882 (GRCm39) N174I probably damaging Het
Or4a78 T C 2: 89,497,811 (GRCm39) I140V probably benign Het
Or4f14c T C 2: 111,941,330 (GRCm39) H89R probably benign Het
Or52m1 G A 7: 102,289,788 (GRCm39) V112I probably benign Het
Or5b113 A T 19: 13,342,514 (GRCm39) H174L probably damaging Het
Or8h9 T A 2: 86,789,119 (GRCm39) I228F probably damaging Het
Otud7a C T 7: 63,378,845 (GRCm39) R232W probably damaging Het
Pacsin3 C A 2: 91,094,160 (GRCm39) A363D probably benign Het
Pcdh17 C T 14: 84,770,350 (GRCm39) R943* probably null Het
Pkd1 A G 17: 24,800,172 (GRCm39) T2978A probably benign Het
Pkhd1l1 T C 15: 44,406,983 (GRCm39) S2407P probably benign Het
Ppip5k2 A T 1: 97,671,822 (GRCm39) Y489* probably null Het
Rasgrp1 T C 2: 117,118,429 (GRCm39) D520G probably benign Het
Rbm20 C A 19: 53,852,551 (GRCm39) T1177K probably benign Het
Rex2 A C 4: 147,142,039 (GRCm39) N176H probably damaging Het
Rsl1d1 T C 16: 11,017,300 (GRCm39) N194S possibly damaging Het
Sel1l3 C A 5: 53,329,924 (GRCm39) R477L probably benign Het
Sidt2 A G 9: 45,850,563 (GRCm39) Y851H probably damaging Het
Sirpb1b G A 3: 15,640,074 (GRCm39) probably benign Het
Slc6a7 C A 18: 61,138,866 (GRCm39) R214L probably benign Het
Srrt G C 5: 137,294,835 (GRCm39) I739M probably benign Het
Tbc1d22a T C 15: 86,119,839 (GRCm39) L81P probably damaging Het
Trim42 A G 9: 97,245,429 (GRCm39) I457T probably damaging Het
Ttc23l T A 15: 10,537,731 (GRCm39) I180F probably benign Het
Usp9y T C Y: 1,364,679 (GRCm39) M1045V probably benign Het
Vmn2r118 T C 17: 55,899,496 (GRCm39) T803A probably damaging Het
Vwa3a C A 7: 120,383,307 (GRCm39) A636D probably damaging Het
Wdr26 A G 1: 181,036,812 (GRCm39) F143S probably damaging Het
Other mutations in Vim
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00786:Vim APN 2 13,583,321 (GRCm39) critical splice donor site probably null
IGL01660:Vim APN 2 13,579,624 (GRCm39) missense probably damaging 1.00
IGL01868:Vim APN 2 13,583,249 (GRCm39) missense possibly damaging 0.69
IGL02166:Vim APN 2 13,579,405 (GRCm39) missense probably damaging 1.00
IGL02867:Vim APN 2 13,585,491 (GRCm39) missense probably damaging 1.00
IGL02889:Vim APN 2 13,585,491 (GRCm39) missense probably damaging 1.00
R0276:Vim UTSW 2 13,579,670 (GRCm39) missense probably benign 0.01
R0626:Vim UTSW 2 13,579,463 (GRCm39) missense probably benign 0.00
R1695:Vim UTSW 2 13,584,921 (GRCm39) missense probably benign 0.00
R1712:Vim UTSW 2 13,583,270 (GRCm39) missense probably damaging 0.98
R3609:Vim UTSW 2 13,583,437 (GRCm39) missense possibly damaging 0.67
R3610:Vim UTSW 2 13,583,437 (GRCm39) missense possibly damaging 0.67
R3810:Vim UTSW 2 13,583,563 (GRCm39) critical splice donor site probably null
R4063:Vim UTSW 2 13,584,827 (GRCm39) critical splice acceptor site probably null
R4347:Vim UTSW 2 13,580,329 (GRCm39) intron probably benign
R4647:Vim UTSW 2 13,587,306 (GRCm39) missense probably benign 0.18
R4678:Vim UTSW 2 13,579,775 (GRCm39) missense probably damaging 1.00
R5261:Vim UTSW 2 13,579,643 (GRCm39) missense probably null 1.00
R5342:Vim UTSW 2 13,584,824 (GRCm39) splice site probably null
R5488:Vim UTSW 2 13,580,392 (GRCm39) missense probably benign 0.01
R5838:Vim UTSW 2 13,585,001 (GRCm39) missense probably damaging 1.00
R5988:Vim UTSW 2 13,587,296 (GRCm39) missense probably benign 0.01
R7513:Vim UTSW 2 13,583,443 (GRCm39) missense possibly damaging 0.94
R8490:Vim UTSW 2 13,584,265 (GRCm39) missense probably damaging 1.00
R9043:Vim UTSW 2 13,579,249 (GRCm39) missense unknown
R9166:Vim UTSW 2 13,579,556 (GRCm39) missense probably benign 0.00
R9603:Vim UTSW 2 13,579,148 (GRCm39) start gained probably benign
R9649:Vim UTSW 2 13,579,703 (GRCm39) missense probably damaging 0.98
R9792:Vim UTSW 2 13,579,598 (GRCm39) missense probably benign 0.21
X0018:Vim UTSW 2 13,579,559 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCTATGTGACCACGTCCAC -3'
(R):5'- AGGCCTTACTTCTCTCGCAG -3'

Sequencing Primer
(F):5'- ACACGCACCTACAGTCTGGG -3'
(R):5'- ATGTCCTCGGCCAGGTTGTC -3'
Posted On 2022-11-14