Incidental Mutation 'R5488:Vim'
| ID |
430441 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vim
|
| Ensembl Gene |
ENSMUSG00000026728 |
| Gene Name |
vimentin |
| Synonyms |
|
| MMRRC Submission |
043049-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.635)
|
| Stock # |
R5488 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
13579122-13587637 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 13580392 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 202
(T202S)
|
| 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: T202S
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000028062
Gene: ENSMUSG00000026728
AA Change: T202S
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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: T202S
PolyPhen 2
Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
|
| SMART Domains |
Protein: ENSMUSP00000141494
Gene: ENSMUSG00000026728
AA Change: T202S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Filament_head
|
6 |
101 |
3.8e-19 |
PFAM |
|
Pfam:Filament
|
102 |
410 |
3.6e-116 |
PFAM |
|
| Meta Mutation Damage Score |
0.0583 |
| Coding Region Coverage |
- 1x: 98.2%
- 3x: 97.2%
- 10x: 95.1%
- 20x: 90.5%
|
| Validation Efficiency |
97% (58/60) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca14 |
T |
A |
7: 119,851,473 (GRCm39) |
V817D |
probably damaging |
Het |
| Abca5 |
A |
G |
11: 110,183,009 (GRCm39) |
V1016A |
probably benign |
Het |
| Ano2 |
G |
T |
6: 126,016,216 (GRCm39) |
M916I |
possibly damaging |
Het |
| Aqr |
T |
C |
2: 113,963,554 (GRCm39) |
N632S |
probably damaging |
Het |
| Cd48 |
G |
A |
1: 171,523,273 (GRCm39) |
V39I |
possibly damaging |
Het |
| Cdcp3 |
A |
G |
7: 130,848,324 (GRCm39) |
D710G |
probably damaging |
Het |
| Cdk17 |
A |
G |
10: 93,068,274 (GRCm39) |
T344A |
probably damaging |
Het |
| Chd8 |
A |
T |
14: 52,450,505 (GRCm39) |
|
probably benign |
Het |
| Col4a1 |
A |
T |
8: 11,362,550 (GRCm39) |
|
probably benign |
Het |
| Col9a3 |
G |
A |
2: 180,258,318 (GRCm39) |
R579H |
probably damaging |
Het |
| Cripto |
G |
A |
9: 110,772,265 (GRCm39) |
R44C |
probably benign |
Het |
| Cyp2c69 |
T |
G |
19: 39,839,603 (GRCm39) |
Q340P |
probably null |
Het |
| D630003M21Rik |
T |
A |
2: 158,058,941 (GRCm39) |
T320S |
probably benign |
Het |
| D630045J12Rik |
A |
T |
6: 38,173,782 (GRCm39) |
S129T |
possibly damaging |
Het |
| Eif4a3l1 |
C |
G |
6: 136,306,555 (GRCm39) |
R339G |
probably damaging |
Het |
| Fam13a |
A |
T |
6: 59,001,303 (GRCm39) |
L8Q |
probably null |
Het |
| Fam83b |
T |
C |
9: 76,452,881 (GRCm39) |
N62S |
probably benign |
Het |
| Foxred1 |
A |
T |
9: 35,121,266 (GRCm39) |
V94E |
probably damaging |
Het |
| Gprc5a |
T |
C |
6: 135,055,868 (GRCm39) |
V105A |
probably damaging |
Het |
| Gvin3 |
T |
A |
7: 106,200,797 (GRCm39) |
|
noncoding transcript |
Het |
| Itga2 |
A |
T |
13: 114,979,971 (GRCm39) |
W1077R |
probably damaging |
Het |
| Kat6b |
A |
G |
14: 21,719,332 (GRCm39) |
D1228G |
probably damaging |
Het |
| Kctd3 |
A |
G |
1: 188,713,563 (GRCm39) |
Y391H |
probably damaging |
Het |
| Kdelr2 |
T |
A |
5: 143,389,784 (GRCm39) |
I23N |
probably damaging |
Het |
| Kmt2a |
A |
T |
9: 44,752,335 (GRCm39) |
|
probably benign |
Het |
| Lao1 |
A |
G |
4: 118,824,566 (GRCm39) |
E216G |
probably damaging |
Het |
| Mark4 |
G |
T |
7: 19,163,532 (GRCm39) |
|
probably null |
Het |
| Mcm10 |
A |
G |
2: 4,996,929 (GRCm39) |
W851R |
probably damaging |
Het |
| Mettl21e |
T |
C |
1: 44,257,276 (GRCm39) |
Y14C |
probably benign |
Het |
| Miga1 |
CACAACAACAACAACAACA |
CACAACAACAACAACA |
3: 152,039,083 (GRCm39) |
|
probably benign |
Het |
| Mmp20 |
A |
G |
9: 7,643,958 (GRCm39) |
|
probably null |
Het |
| Nlrp5 |
A |
T |
7: 23,117,359 (GRCm39) |
D361V |
probably benign |
Het |
| Nrip3 |
T |
C |
7: 109,361,045 (GRCm39) |
T210A |
probably damaging |
Het |
| Or12d2 |
T |
C |
17: 37,624,559 (GRCm39) |
T239A |
probably damaging |
Het |
| Or52s1b |
T |
C |
7: 102,822,658 (GRCm39) |
Y62C |
probably damaging |
Het |
| Pcdh10 |
G |
A |
3: 45,335,803 (GRCm39) |
G706S |
probably damaging |
Het |
| Pdzd2 |
G |
A |
15: 12,382,762 (GRCm39) |
P1197L |
probably benign |
Het |
| Pfkfb3 |
T |
C |
2: 11,489,480 (GRCm39) |
S273G |
probably benign |
Het |
| Pkn3 |
T |
C |
2: 29,978,596 (GRCm39) |
|
probably null |
Het |
| Rab40c |
G |
A |
17: 26,109,643 (GRCm39) |
T78I |
probably damaging |
Het |
| Rec8 |
A |
T |
14: 55,860,283 (GRCm39) |
Q291L |
probably benign |
Het |
| Robo4 |
CGG |
CG |
9: 37,322,786 (GRCm39) |
|
probably null |
Het |
| Sart3 |
A |
G |
5: 113,909,441 (GRCm39) |
W86R |
probably damaging |
Het |
| Slc6a11 |
A |
G |
6: 114,220,855 (GRCm39) |
D462G |
probably damaging |
Het |
| Syne2 |
A |
G |
12: 75,934,946 (GRCm39) |
T143A |
probably benign |
Het |
| Tardbp |
A |
G |
4: 148,703,097 (GRCm39) |
F289S |
probably benign |
Het |
| Tdpoz1 |
T |
A |
3: 93,577,974 (GRCm39) |
Y270F |
possibly damaging |
Het |
| Tmem117 |
ACCC |
ACC |
15: 94,992,698 (GRCm39) |
|
probably null |
Het |
| Trim43a |
A |
T |
9: 88,464,229 (GRCm39) |
I47F |
probably damaging |
Het |
| Vps13b |
A |
T |
15: 35,770,688 (GRCm39) |
I2044L |
probably benign |
Het |
| Wdr5 |
T |
G |
2: 27,415,165 (GRCm39) |
D192E |
probably damaging |
Het |
| Zmym2 |
A |
G |
14: 57,193,712 (GRCm39) |
K1176E |
possibly damaging |
Het |
|
| Other mutations in Vim |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
|
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'- TCCAGCTAACACCTGCAGAG -3'
(R):5'- CCAAAGACTGCCCTAAATAGTGG -3'
Sequencing Primer
(F):5'- TGCCACCTCGACAAGTTG -3'
(R):5'- GACTGCCCTAAATAGTGGAGTTTTTC -3'
|
| Posted On |
2016-10-05 |
Incidental Mutation