Incidental Mutation 'R0276:Vim'
ID 35345
Institutional Source Beutler Lab
Gene Symbol Vim
Ensembl Gene ENSMUSG00000026728
Gene Name vimentin
Synonyms
MMRRC Submission 038498-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.635) question?
Stock # R0276 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 13579122-13587637 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 13579670 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 143 (K143R)
Ref Sequence ENSEMBL: ENSMUSP00000141494 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028062] [ENSMUST00000141365] [ENSMUST00000193675]
AlphaFold P20152
Predicted Effect probably benign
Transcript: ENSMUST00000028062
AA Change: K143R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000028062
Gene: ENSMUSG00000026728
AA Change: K143R

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 7.8e-23 PFAM
Filament 102 410 6.65e-150 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000141365
SMART Domains Protein: ENSMUSP00000114742
Gene: ENSMUSG00000026728

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 1.8e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148248
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155605
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191615
Predicted Effect probably benign
Transcript: ENSMUST00000193675
AA Change: K143R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000141494
Gene: ENSMUSG00000026728
AA Change: K143R

DomainStartEndE-ValueType
Pfam:Filament_head 6 101 3.8e-19 PFAM
Pfam:Filament 102 410 3.6e-116 PFAM
Meta Mutation Damage Score 0.0870 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.8%
  • 10x: 96.2%
  • 20x: 93.8%
Validation Efficiency 98% (101/103)
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: 100 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts13 A G 2: 26,865,772 (GRCm39) N109S possibly damaging Het
Adcy10 T A 1: 165,400,160 (GRCm39) M1523K possibly damaging Het
Agtpbp1 C T 13: 59,609,845 (GRCm39) S1095N possibly damaging Het
Ang2 C T 14: 51,432,975 (GRCm39) V136I probably damaging Het
Arhgap10 A T 8: 78,140,210 (GRCm39) M250K probably benign Het
Arhgap33 A T 7: 30,222,669 (GRCm39) W1088R probably benign Het
Arhgef15 T C 11: 68,844,298 (GRCm39) probably benign Het
Aspm T C 1: 139,406,209 (GRCm39) S1699P possibly damaging Het
Atp12a C A 14: 56,625,151 (GRCm39) D1014E probably damaging Het
Atp1a4 T A 1: 172,085,468 (GRCm39) K45M probably damaging Het
Atp8a1 A T 5: 67,944,016 (GRCm39) probably benign Het
Baiap3 A C 17: 25,462,661 (GRCm39) F1099C probably damaging Het
Bcas3 T A 11: 85,361,663 (GRCm39) probably null Het
Bms1 G A 6: 118,385,095 (GRCm39) T371M possibly damaging Het
Camta1 C A 4: 151,159,597 (GRCm39) R1614L probably damaging Het
Capn3 T C 2: 120,318,546 (GRCm39) probably benign Het
Ccdc180 A G 4: 45,923,534 (GRCm39) D1105G probably damaging Het
Ccdc33 G T 9: 57,965,675 (GRCm39) P364Q probably damaging Het
Clstn3 A G 6: 124,408,699 (GRCm39) probably benign Het
Cntrl A T 2: 35,041,744 (GRCm39) Y619F possibly damaging Het
Col12a1 A T 9: 79,538,023 (GRCm39) Y2514* probably null Het
Cpt1b T C 15: 89,304,162 (GRCm39) H503R probably benign Het
Crb1 T A 1: 139,251,073 (GRCm39) T293S possibly damaging Het
D130043K22Rik C T 13: 25,042,028 (GRCm39) T319I possibly damaging Het
Dnaaf10 T C 11: 17,179,821 (GRCm39) I274T probably benign Het
Dzip1l G A 9: 99,543,051 (GRCm39) R502Q probably benign Het
Efcab5 A G 11: 77,020,702 (GRCm39) M673T probably damaging Het
Efcab5 G A 11: 77,031,749 (GRCm39) R42W probably damaging Het
F2rl3 A G 8: 73,489,426 (GRCm39) T218A probably benign Het
Fam135a C T 1: 24,107,045 (GRCm39) R31H probably damaging Het
Fcer2a A T 8: 3,739,811 (GRCm39) N53K possibly damaging Het
Golgb1 A C 16: 36,734,238 (GRCm39) K1162Q probably damaging Het
Gpr137b A T 13: 13,542,160 (GRCm39) probably benign Het
Haspin A T 11: 73,027,313 (GRCm39) L592Q probably damaging Het
Helq A G 5: 100,938,013 (GRCm39) F478L probably damaging Het
Iho1 A T 9: 108,305,639 (GRCm39) M11K possibly damaging Het
Il17rb T A 14: 29,726,337 (GRCm39) T84S probably damaging Het
Itga4 T C 2: 79,151,837 (GRCm39) L880P probably damaging Het
Itih5 A G 2: 10,190,375 (GRCm39) I61V possibly damaging Het
Ivl G A 3: 92,478,821 (GRCm39) L415F unknown Het
Kif2a A G 13: 107,113,158 (GRCm39) probably benign Het
Kmt2d T C 15: 98,748,192 (GRCm39) probably benign Het
Lars2 A G 9: 123,267,186 (GRCm39) probably benign Het
Lilrb4a T C 10: 51,367,677 (GRCm39) V73A probably benign Het
Lratd2 G T 15: 60,695,523 (GRCm39) Y74* probably null Het
Lrrc8a A G 2: 30,146,800 (GRCm39) D538G possibly damaging Het
Lrrk1 G A 7: 65,946,011 (GRCm39) probably benign Het
Mc2r A T 18: 68,541,203 (GRCm39) I30K possibly damaging Het
Mybbp1a C A 11: 72,340,933 (GRCm39) probably null Het
Napg C T 18: 63,120,034 (GRCm39) R149C probably damaging Het
Ncam2 A G 16: 81,314,517 (GRCm39) probably benign Het
Nlk T C 11: 78,462,301 (GRCm39) I509V probably benign Het
Nlrp2 A T 7: 5,331,108 (GRCm39) N429K probably benign Het
Nlrp9b A G 7: 19,762,423 (GRCm39) T247A probably benign Het
Noxo1 A T 17: 24,919,136 (GRCm39) probably null Het
Or1n1b A T 2: 36,780,035 (GRCm39) M275K probably benign Het
Or2ag2b A T 7: 106,417,904 (GRCm39) I205L probably benign Het
Or3a10 A G 11: 73,935,944 (GRCm39) I52T probably damaging Het
Or4c107 T A 2: 88,789,099 (GRCm39) C96* probably null Het
Or4m1 C A 14: 50,557,636 (GRCm39) A219S probably benign Het
Oxr1 T C 15: 41,683,458 (GRCm39) S294P probably damaging Het
Pfpl A G 19: 12,406,601 (GRCm39) Y284C probably damaging Het
Pi16 A T 17: 29,545,917 (GRCm39) T232S probably benign Het
Plcxd2 A T 16: 45,830,070 (GRCm39) N50K probably benign Het
Plekhn1 T A 4: 156,312,703 (GRCm39) N52Y probably damaging Het
Prl2c5 T C 13: 13,357,634 (GRCm39) probably benign Het
Prrc2b G A 2: 32,109,666 (GRCm39) V1080I probably damaging Het
Psg28 A T 7: 18,164,321 (GRCm39) N130K probably benign Het
Psme4 C A 11: 30,761,980 (GRCm39) T440K probably damaging Het
Ptcd2 T C 13: 99,458,104 (GRCm39) K296E probably benign Het
Ptprq T C 10: 107,378,596 (GRCm39) probably null Het
Rab5b A C 10: 128,522,615 (GRCm39) probably null Het
Rft1 T A 14: 30,412,540 (GRCm39) S534T probably benign Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Rsu1 A T 2: 13,174,946 (GRCm39) probably benign Het
Senp6 A G 9: 80,044,029 (GRCm39) M887V probably benign Het
Sgcz T A 8: 38,420,073 (GRCm39) M60L probably benign Het
Siglec1 G A 2: 130,925,861 (GRCm39) Q282* probably null Het
Sipa1l2 T C 8: 126,148,679 (GRCm39) T1655A probably damaging Het
Slc28a2b T A 2: 122,352,409 (GRCm39) S389T probably damaging Het
Slc43a3 G A 2: 84,768,007 (GRCm39) probably benign Het
Snx29 T C 16: 11,556,237 (GRCm39) V756A probably benign Het
Spta1 T A 1: 174,045,460 (GRCm39) H1539Q probably damaging Het
Stk3 A C 15: 35,099,615 (GRCm39) S104A probably damaging Het
Stk38 C A 17: 29,211,390 (GRCm39) probably null Het
Stx6 T C 1: 155,049,909 (GRCm39) probably benign Het
Thbs4 G A 13: 92,912,040 (GRCm39) T230I probably benign Het
Thrsp A G 7: 97,066,709 (GRCm39) M1T probably null Het
Tmem63b A T 17: 45,986,299 (GRCm39) probably benign Het
Top2a A G 11: 98,900,733 (GRCm39) probably benign Het
Tpd52l2 T C 2: 181,143,852 (GRCm39) probably null Het
Trak1 A G 9: 121,283,404 (GRCm39) E390G probably damaging Het
Trappc3 T A 4: 126,167,745 (GRCm39) D101E possibly damaging Het
Trhr A G 15: 44,060,482 (GRCm39) M1V probably null Het
Triobp T A 15: 78,857,876 (GRCm39) I1159K probably benign Het
Unc45a A G 7: 79,976,045 (GRCm39) probably benign Het
Usb1 A G 8: 96,060,085 (GRCm39) D12G probably damaging Het
Ushbp1 C T 8: 71,847,293 (GRCm39) C113Y possibly damaging Het
Vmn2r75 T C 7: 85,797,515 (GRCm39) K766R probably benign Het
Xpo5 T G 17: 46,552,433 (GRCm39) C1089G 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
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
R9793: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'- GCTTCAAGACTCGGTGGACTTCTC -3'
(R):5'- TCCTCCTGTCTGGTAACTGTAAGCC -3'

Sequencing Primer
(F):5'- ACTTCTCGCTGGCCGAC -3'
(R):5'- CACTGCAAAGTTTAGGTTCAGG -3'
Posted On 2013-05-09