Incidental Mutation 'R7428:Vars2'
ID |
576281 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vars2
|
Ensembl Gene |
ENSMUSG00000038838 |
Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
Synonyms |
Vars2l, 1190004I24Rik |
MMRRC Submission |
045506-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R7428 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 35977578 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glutamic Acid
at position 118
(V118E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001565]
[ENSMUST00000043674]
[ENSMUST00000160039]
[ENSMUST00000160734]
[ENSMUST00000160752]
[ENSMUST00000162266]
[ENSMUST00000165144]
[ENSMUST00000169093]
|
AlphaFold |
Q3U2A8 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000001565
|
SMART Domains |
Protein: ENSMUSP00000001565 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
375 |
6.4e-141 |
PFAM |
PDB:3DOM|C
|
383 |
459 |
7e-13 |
PDB |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000043674
AA Change: V118E
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000047917 Gene: ENSMUSG00000038838 AA Change: V118E
Domain | Start | End | E-Value | Type |
Pfam:tRNA-synt_1
|
112 |
736 |
3.3e-179 |
PFAM |
Pfam:tRNA-synt_1g
|
141 |
221 |
2e-8 |
PFAM |
Pfam:Anticodon_1
|
780 |
932 |
3.6e-32 |
PFAM |
low complexity region
|
1005 |
1015 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160039
|
SMART Domains |
Protein: ENSMUSP00000124683 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
164 |
2.9e-44 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160734
|
SMART Domains |
Protein: ENSMUSP00000124335 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
375 |
1.9e-137 |
PFAM |
PDB:3DOM|C
|
383 |
459 |
7e-13 |
PDB |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160752
|
SMART Domains |
Protein: ENSMUSP00000124458 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
160 |
6.4e-32 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000162266
|
SMART Domains |
Protein: ENSMUSP00000124103 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
91 |
1.8e-22 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000164404
|
SMART Domains |
Protein: ENSMUSP00000126084 Gene: ENSMUSG00000038838
Domain | Start | End | E-Value | Type |
Pfam:tRNA-synt_1
|
1 |
201 |
1e-49 |
PFAM |
Pfam:tRNA-synt_1g
|
68 |
172 |
4e-7 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000165144
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000168922
|
SMART Domains |
Protein: ENSMUSP00000129196 Gene: ENSMUSG00000038838
Domain | Start | End | E-Value | Type |
Pfam:tRNA-synt_1
|
2 |
386 |
3e-105 |
PFAM |
Pfam:Anticodon_1
|
430 |
566 |
8.2e-29 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000169093
|
SMART Domains |
Protein: ENSMUSP00000126794 Gene: ENSMUSG00000038838
Domain | Start | End | E-Value | Type |
Pfam:tRNA-synt_1
|
1 |
109 |
1.7e-29 |
PFAM |
|
Meta Mutation Damage Score |
0.0967 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
Validation Efficiency |
100% (71/71) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 70 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Anxa10 |
T |
A |
8: 62,545,543 (GRCm39) |
Y63F |
probably benign |
Het |
Atl2 |
T |
C |
17: 80,183,227 (GRCm39) |
|
probably null |
Het |
B3gnt4 |
A |
G |
5: 123,648,794 (GRCm39) |
N53S |
probably damaging |
Het |
Bpifb5 |
G |
A |
2: 154,067,042 (GRCm39) |
M98I |
probably benign |
Het |
Cacna2d3 |
A |
G |
14: 28,786,232 (GRCm39) |
M585T |
probably damaging |
Het |
Cbarp |
T |
C |
10: 79,967,138 (GRCm39) |
D701G |
probably damaging |
Het |
Cep295 |
A |
G |
9: 15,244,794 (GRCm39) |
S1221P |
possibly damaging |
Het |
Cep350 |
T |
C |
1: 155,770,365 (GRCm39) |
S1842G |
probably benign |
Het |
Cntrl |
T |
A |
2: 35,060,546 (GRCm39) |
W1913R |
probably benign |
Het |
Creb5 |
C |
A |
6: 53,658,143 (GRCm39) |
Q158K |
unknown |
Het |
Crtam |
G |
C |
9: 40,892,478 (GRCm39) |
A266G |
probably benign |
Het |
Cry2 |
T |
C |
2: 92,243,392 (GRCm39) |
D483G |
possibly damaging |
Het |
Csmd1 |
A |
G |
8: 16,073,864 (GRCm39) |
F2044L |
possibly damaging |
Het |
Cxcr6 |
A |
T |
9: 123,639,305 (GRCm39) |
Y109F |
probably benign |
Het |
Cyb5b |
A |
G |
8: 107,897,048 (GRCm39) |
D106G |
probably benign |
Het |
D630036H23Rik |
T |
C |
12: 36,431,537 (GRCm39) |
R154G |
unknown |
Het |
Ddit4l |
A |
G |
3: 137,331,931 (GRCm39) |
E99G |
probably damaging |
Het |
Dmbt1 |
A |
T |
7: 130,710,192 (GRCm39) |
T1495S |
possibly damaging |
Het |
Gm21886 |
A |
T |
18: 80,132,867 (GRCm39) |
L97Q |
probably damaging |
Het |
Hlcs |
A |
G |
16: 94,068,758 (GRCm39) |
V154A |
probably benign |
Het |
Hpdl |
A |
T |
4: 116,678,062 (GRCm39) |
L133Q |
probably damaging |
Het |
Inpp5f |
A |
G |
7: 128,281,529 (GRCm39) |
D510G |
probably damaging |
Het |
Ism2 |
G |
T |
12: 87,333,769 (GRCm39) |
T92K |
possibly damaging |
Het |
Kif13b |
T |
C |
14: 65,025,909 (GRCm39) |
I1422T |
probably benign |
Het |
Leng8 |
C |
T |
7: 4,146,572 (GRCm39) |
R395W |
probably damaging |
Het |
Mocs2 |
A |
G |
13: 114,957,400 (GRCm39) |
I6V |
probably benign |
Het |
Mthfr |
A |
G |
4: 148,136,060 (GRCm39) |
M378V |
probably benign |
Het |
Myh13 |
A |
G |
11: 67,223,390 (GRCm39) |
T237A |
probably damaging |
Het |
Nr1h4 |
T |
C |
10: 89,334,267 (GRCm39) |
E41G |
probably benign |
Het |
Nup205 |
T |
A |
6: 35,204,494 (GRCm39) |
I1460N |
probably damaging |
Het |
Nup98 |
A |
T |
7: 101,784,208 (GRCm39) |
|
probably null |
Het |
Nxpe5 |
A |
C |
5: 138,238,022 (GRCm39) |
Y194S |
probably damaging |
Het |
Or12e9 |
G |
T |
2: 87,202,034 (GRCm39) |
V53L |
probably benign |
Het |
Or52m1 |
A |
G |
7: 102,289,533 (GRCm39) |
I27V |
probably benign |
Het |
Or5m12 |
T |
A |
2: 85,734,475 (GRCm39) |
R308* |
probably null |
Het |
Or5m3 |
A |
T |
2: 85,838,563 (GRCm39) |
I148L |
probably benign |
Het |
Or9s18 |
A |
G |
13: 65,300,866 (GRCm39) |
Y276C |
probably damaging |
Het |
Otof |
G |
T |
5: 30,547,169 (GRCm39) |
D383E |
probably damaging |
Het |
Pcdh9 |
G |
T |
14: 94,124,547 (GRCm39) |
T541K |
probably damaging |
Het |
Pclo |
A |
T |
5: 14,800,531 (GRCm39) |
I1179F |
|
Het |
Pde6c |
T |
C |
19: 38,145,984 (GRCm39) |
|
probably null |
Het |
Pdia6 |
T |
C |
12: 17,328,546 (GRCm39) |
V167A |
probably damaging |
Het |
Phf7 |
C |
T |
14: 30,962,370 (GRCm39) |
R145Q |
possibly damaging |
Het |
Plxnb1 |
T |
C |
9: 108,937,236 (GRCm39) |
V1139A |
probably benign |
Het |
Prkg1 |
T |
C |
19: 30,556,235 (GRCm39) |
I585M |
probably damaging |
Het |
Prom2 |
A |
G |
2: 127,381,731 (GRCm39) |
L195P |
probably damaging |
Het |
Ptprd |
G |
A |
4: 76,004,705 (GRCm39) |
P17S |
probably benign |
Het |
Rfx4 |
C |
A |
10: 84,731,876 (GRCm39) |
Q618K |
probably benign |
Het |
Rhobtb1 |
T |
A |
10: 69,084,654 (GRCm39) |
I15N |
probably damaging |
Het |
Sap30 |
C |
T |
8: 57,940,546 (GRCm39) |
V19M |
possibly damaging |
Het |
Scrib |
G |
A |
15: 75,933,047 (GRCm39) |
T721M |
probably damaging |
Het |
Slc12a1 |
C |
A |
2: 125,056,052 (GRCm39) |
T861N |
probably benign |
Het |
Slc35f1 |
T |
A |
10: 52,965,510 (GRCm39) |
S308R |
probably damaging |
Het |
Slc35f4 |
T |
A |
14: 49,536,355 (GRCm39) |
I427F |
probably damaging |
Het |
Slco4c1 |
T |
C |
1: 96,765,245 (GRCm39) |
T402A |
possibly damaging |
Het |
Sprr2f |
G |
A |
3: 92,273,251 (GRCm39) |
V17M |
unknown |
Het |
Stab1 |
T |
C |
14: 30,881,216 (GRCm39) |
T605A |
probably benign |
Het |
Taar8c |
A |
C |
10: 23,977,446 (GRCm39) |
L122R |
probably damaging |
Het |
Tbc1d2 |
G |
A |
4: 46,649,965 (GRCm39) |
P24S |
probably benign |
Het |
Tex36 |
T |
C |
7: 133,196,866 (GRCm39) |
|
probably null |
Het |
Tmem145 |
T |
C |
7: 25,006,590 (GRCm39) |
|
probably null |
Het |
Ttn |
T |
G |
2: 76,550,698 (GRCm39) |
D31528A |
probably damaging |
Het |
Vmn1r195 |
T |
C |
13: 22,463,022 (GRCm39) |
V164A |
probably benign |
Het |
Vmn2r69 |
T |
C |
7: 85,060,467 (GRCm39) |
I372M |
probably benign |
Het |
Vmn2r93 |
A |
T |
17: 18,546,672 (GRCm39) |
H848L |
probably benign |
Het |
Wnt9b |
T |
C |
11: 103,621,643 (GRCm39) |
Q338R |
probably benign |
Het |
Zfp128 |
A |
G |
7: 12,624,289 (GRCm39) |
D219G |
probably benign |
Het |
Zfp541 |
A |
T |
7: 15,826,793 (GRCm39) |
R1181W |
probably damaging |
Het |
Zfp867 |
C |
T |
11: 59,354,760 (GRCm39) |
G190S |
probably benign |
Het |
Zfp971 |
T |
A |
2: 177,674,967 (GRCm39) |
C189S |
probably damaging |
Het |
|
Other mutations in Vars2 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL02106:Vars2
|
APN |
17 |
35,975,513 (GRCm39) |
unclassified |
probably benign |
|
IGL02320:Vars2
|
APN |
17 |
35,971,346 (GRCm39) |
missense |
probably benign |
0.07 |
IGL02580:Vars2
|
APN |
17 |
35,971,777 (GRCm39) |
missense |
possibly damaging |
0.50 |
IGL02691:Vars2
|
APN |
17 |
35,971,140 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03039:Vars2
|
APN |
17 |
35,975,013 (GRCm39) |
missense |
probably damaging |
1.00 |
PIT4445001:Vars2
|
UTSW |
17 |
35,977,103 (GRCm39) |
nonsense |
probably null |
|
R0079:Vars2
|
UTSW |
17 |
35,970,048 (GRCm39) |
missense |
probably damaging |
0.99 |
R0152:Vars2
|
UTSW |
17 |
35,970,919 (GRCm39) |
missense |
probably damaging |
1.00 |
R0346:Vars2
|
UTSW |
17 |
35,975,756 (GRCm39) |
unclassified |
probably benign |
|
R0426:Vars2
|
UTSW |
17 |
35,975,476 (GRCm39) |
missense |
probably damaging |
1.00 |
R0584:Vars2
|
UTSW |
17 |
35,977,578 (GRCm39) |
missense |
possibly damaging |
0.82 |
R0589:Vars2
|
UTSW |
17 |
35,970,068 (GRCm39) |
missense |
probably benign |
|
R0882:Vars2
|
UTSW |
17 |
35,968,191 (GRCm39) |
missense |
probably benign |
0.41 |
R1234:Vars2
|
UTSW |
17 |
35,978,038 (GRCm39) |
missense |
probably damaging |
1.00 |
R1263:Vars2
|
UTSW |
17 |
35,972,501 (GRCm39) |
missense |
probably damaging |
1.00 |
R1559:Vars2
|
UTSW |
17 |
35,977,150 (GRCm39) |
unclassified |
probably benign |
|
R1772:Vars2
|
UTSW |
17 |
35,970,976 (GRCm39) |
missense |
probably damaging |
1.00 |
R1809:Vars2
|
UTSW |
17 |
35,973,108 (GRCm39) |
missense |
probably damaging |
1.00 |
R1913:Vars2
|
UTSW |
17 |
35,977,814 (GRCm39) |
missense |
probably benign |
0.02 |
R1986:Vars2
|
UTSW |
17 |
35,970,953 (GRCm39) |
missense |
probably damaging |
1.00 |
R2504:Vars2
|
UTSW |
17 |
35,975,685 (GRCm39) |
missense |
probably damaging |
1.00 |
R3426:Vars2
|
UTSW |
17 |
35,972,866 (GRCm39) |
missense |
probably damaging |
1.00 |
R4539:Vars2
|
UTSW |
17 |
35,977,780 (GRCm39) |
missense |
probably damaging |
0.99 |
R4751:Vars2
|
UTSW |
17 |
35,970,235 (GRCm39) |
missense |
possibly damaging |
0.89 |
R4861:Vars2
|
UTSW |
17 |
35,972,825 (GRCm39) |
missense |
probably benign |
0.00 |
R4861:Vars2
|
UTSW |
17 |
35,972,825 (GRCm39) |
missense |
probably benign |
0.00 |
R5028:Vars2
|
UTSW |
17 |
35,970,365 (GRCm39) |
critical splice donor site |
probably null |
|
R5217:Vars2
|
UTSW |
17 |
35,969,041 (GRCm39) |
missense |
probably damaging |
1.00 |
R5292:Vars2
|
UTSW |
17 |
35,971,678 (GRCm39) |
missense |
probably damaging |
1.00 |
R6056:Vars2
|
UTSW |
17 |
35,976,680 (GRCm39) |
missense |
probably benign |
0.01 |
R6211:Vars2
|
UTSW |
17 |
35,976,554 (GRCm39) |
splice site |
probably null |
|
R6213:Vars2
|
UTSW |
17 |
35,971,332 (GRCm39) |
missense |
probably benign |
0.27 |
R6374:Vars2
|
UTSW |
17 |
35,970,937 (GRCm39) |
missense |
probably damaging |
1.00 |
R6746:Vars2
|
UTSW |
17 |
35,971,294 (GRCm39) |
critical splice donor site |
probably null |
|
R6749:Vars2
|
UTSW |
17 |
35,977,605 (GRCm39) |
missense |
probably damaging |
1.00 |
R6957:Vars2
|
UTSW |
17 |
35,977,967 (GRCm39) |
missense |
probably benign |
0.39 |
R7107:Vars2
|
UTSW |
17 |
35,969,142 (GRCm39) |
missense |
probably damaging |
1.00 |
R7538:Vars2
|
UTSW |
17 |
35,971,672 (GRCm39) |
missense |
probably damaging |
1.00 |
R7553:Vars2
|
UTSW |
17 |
35,975,680 (GRCm39) |
missense |
possibly damaging |
0.93 |
R7741:Vars2
|
UTSW |
17 |
35,971,835 (GRCm39) |
missense |
probably damaging |
1.00 |
R7784:Vars2
|
UTSW |
17 |
35,969,050 (GRCm39) |
missense |
possibly damaging |
0.95 |
R7823:Vars2
|
UTSW |
17 |
35,970,028 (GRCm39) |
missense |
probably damaging |
1.00 |
R7915:Vars2
|
UTSW |
17 |
35,975,731 (GRCm39) |
missense |
probably damaging |
1.00 |
R8201:Vars2
|
UTSW |
17 |
35,969,202 (GRCm39) |
missense |
probably benign |
|
R8955:Vars2
|
UTSW |
17 |
35,972,541 (GRCm39) |
missense |
probably damaging |
1.00 |
R8964:Vars2
|
UTSW |
17 |
35,970,699 (GRCm39) |
missense |
possibly damaging |
0.46 |
R9101:Vars2
|
UTSW |
17 |
35,969,980 (GRCm39) |
missense |
possibly damaging |
0.51 |
R9202:Vars2
|
UTSW |
17 |
35,977,551 (GRCm39) |
missense |
probably damaging |
1.00 |
R9202:Vars2
|
UTSW |
17 |
35,974,444 (GRCm39) |
critical splice acceptor site |
probably null |
|
R9450:Vars2
|
UTSW |
17 |
35,973,027 (GRCm39) |
missense |
probably damaging |
0.98 |
X0021:Vars2
|
UTSW |
17 |
35,969,926 (GRCm39) |
missense |
possibly damaging |
0.93 |
Z1176:Vars2
|
UTSW |
17 |
35,975,683 (GRCm39) |
missense |
possibly damaging |
0.55 |
Z1177:Vars2
|
UTSW |
17 |
35,974,364 (GRCm39) |
missense |
probably benign |
0.17 |
|
Predicted Primers |
PCR Primer
(F):5'- AGAACTAGTTGTTGCTGTTGCC -3'
(R):5'- ATTGTATGAAATCCCCACCGG -3'
Sequencing Primer
(F):5'- TCGTCTACAGAGTTCCAGGAC -3'
(R):5'- CCGGGCCAGGTGAAAAG -3'
|
Posted On |
2019-10-07 |