Incidental Mutation 'R9450:Vars2'
| ID |
714222 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R9450 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
35655634-35667592 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35662135 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 421
(T421A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000165144]
[ENSMUST00000169093]
|
| AlphaFold |
Q3U2A8 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000043674
AA Change: T421A
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: T421A
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838
AA Change: T40A
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: T70A
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 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 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700007K13Rik |
TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC |
TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC |
2: 28,466,110 (GRCm38) |
|
probably benign |
Het |
| 2200002D01Rik |
CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
7: 29,247,623 (GRCm38) |
|
probably benign |
Het |
| 2810004N23Rik |
T |
C |
8: 124,840,476 (GRCm38) |
K229E |
probably damaging |
Het |
| 4931409K22Rik |
T |
A |
5: 24,549,449 (GRCm38) |
I395F |
probably benign |
Het |
| 9030624J02Rik |
T |
C |
7: 118,752,895 (GRCm38) |
|
probably null |
Het |
| Abca8b |
T |
C |
11: 109,969,104 (GRCm38) |
T523A |
probably damaging |
Het |
| Adamts18 |
G |
T |
8: 113,764,310 (GRCm38) |
D508E |
probably benign |
Het |
| Arap2 |
T |
C |
5: 62,698,419 (GRCm38) |
E558G |
probably benign |
Het |
| Arid4a |
A |
T |
12: 71,072,600 (GRCm38) |
D331V |
|
Het |
| Ash1l |
A |
T |
3: 89,007,832 (GRCm38) |
K1923M |
possibly damaging |
Het |
| Atad2b |
T |
A |
12: 5,013,859 (GRCm38) |
S947T |
probably benign |
Het |
| B4galt1 |
A |
T |
4: 40,853,804 (GRCm38) |
M1K |
probably null |
Het |
| BC025446 |
T |
A |
15: 75,220,725 (GRCm38) |
C98S |
probably damaging |
Het |
| Ccpg1 |
G |
A |
9: 72,997,421 (GRCm38) |
S4N |
unknown |
Het |
| Cfap43 |
A |
T |
19: 47,897,871 (GRCm38) |
L102M |
probably benign |
Het |
| Clic6 |
T |
C |
16: 92,530,756 (GRCm38) |
I483T |
possibly damaging |
Het |
| Col6a6 |
A |
T |
9: 105,784,174 (GRCm38) |
D245E |
probably benign |
Het |
| Cpsf7 |
G |
A |
19: 10,540,849 (GRCm38) |
|
probably null |
Het |
| Depdc5 |
A |
G |
5: 32,934,010 (GRCm38) |
D721G |
probably benign |
Het |
| Dhx29 |
C |
T |
13: 112,947,328 (GRCm38) |
T639I |
possibly damaging |
Het |
| Dock7 |
T |
C |
4: 98,973,189 (GRCm38) |
E1397G |
unknown |
Het |
| Dsp |
C |
T |
13: 38,192,403 (GRCm38) |
T1388M |
probably damaging |
Het |
| Fam186b |
C |
T |
15: 99,285,544 (GRCm38) |
G73D |
probably damaging |
Het |
| Ganab |
A |
G |
19: 8,915,712 (GRCm38) |
D960G |
probably damaging |
Het |
| Gm12394 |
G |
T |
4: 42,793,833 (GRCm38) |
Q100K |
probably benign |
Het |
| Gria1 |
T |
C |
11: 57,309,789 (GRCm38) |
V764A |
probably damaging |
Het |
| Grk3 |
T |
C |
5: 112,915,047 (GRCm38) |
K645E |
probably benign |
Het |
| Hecw2 |
A |
T |
1: 53,839,029 (GRCm38) |
Y1339* |
probably null |
Het |
| Hmcn2 |
C |
A |
2: 31,426,833 (GRCm38) |
T3808N |
probably damaging |
Het |
| Il20rb |
A |
T |
9: 100,473,002 (GRCm38) |
N129K |
possibly damaging |
Het |
| Itgb4 |
T |
C |
11: 115,983,271 (GRCm38) |
Y340H |
probably damaging |
Het |
| Itgb6 |
T |
C |
2: 60,628,028 (GRCm38) |
I460M |
probably benign |
Het |
| Kat14 |
T |
C |
2: 144,400,819 (GRCm38) |
I599T |
possibly damaging |
Het |
| Kif1b |
A |
C |
4: 149,238,010 (GRCm38) |
D817E |
probably benign |
Het |
| Lamb2 |
T |
A |
9: 108,480,561 (GRCm38) |
C94* |
probably null |
Het |
| Larp1 |
T |
C |
11: 58,051,064 (GRCm38) |
S743P |
probably damaging |
Het |
| Ldlrap1 |
T |
C |
4: 134,747,179 (GRCm38) |
N267S |
probably damaging |
Het |
| Ltbp2 |
G |
A |
12: 84,791,090 (GRCm38) |
P1192L |
probably benign |
Het |
| Ltf |
T |
C |
9: 111,021,996 (GRCm38) |
L92P |
probably damaging |
Het |
| Mns1 |
C |
A |
9: 72,452,608 (GRCm38) |
Q347K |
probably benign |
Het |
| Myof |
A |
T |
19: 37,960,926 (GRCm38) |
F611I |
probably damaging |
Het |
| Nop56 |
T |
C |
2: 130,275,681 (GRCm38) |
L76P |
probably damaging |
Het |
| Nphp1 |
T |
C |
2: 127,774,088 (GRCm38) |
H114R |
|
Het |
| Olfr1280 |
T |
A |
2: 111,316,053 (GRCm38) |
N191K |
probably benign |
Het |
| Olfr1512 |
G |
C |
14: 52,372,653 (GRCm38) |
Y133* |
probably null |
Het |
| Olfr390 |
C |
A |
11: 73,787,275 (GRCm38) |
N112K |
possibly damaging |
Het |
| Park2 |
C |
A |
17: 11,838,634 (GRCm38) |
H301N |
possibly damaging |
Het |
| Pcdha12 |
A |
G |
18: 37,020,939 (GRCm38) |
D237G |
probably damaging |
Het |
| Pitpnm3 |
A |
T |
11: 72,061,586 (GRCm38) |
M593K |
possibly damaging |
Het |
| Plxdc1 |
C |
T |
11: 97,954,855 (GRCm38) |
V211I |
probably damaging |
Het |
| Prpf38a |
A |
T |
4: 108,572,875 (GRCm38) |
H143Q |
probably damaging |
Het |
| Sdk2 |
T |
C |
11: 113,806,279 (GRCm38) |
T1769A |
probably benign |
Het |
| Stab1 |
T |
C |
14: 31,162,939 (GRCm38) |
D153G |
possibly damaging |
Het |
| Tm7sf3 |
C |
T |
6: 146,623,681 (GRCm38) |
D89N |
possibly damaging |
Het |
| Tnrc6b |
T |
A |
15: 80,880,436 (GRCm38) |
M713K |
probably benign |
Het |
| Top2a |
T |
C |
11: 99,003,608 (GRCm38) |
K966E |
possibly damaging |
Het |
| Vmn1r1 |
A |
T |
1: 182,157,205 (GRCm38) |
C298* |
probably null |
Het |
| Vwa3a |
T |
C |
7: 120,804,030 (GRCm38) |
|
probably null |
Het |
| Vwa5b1 |
G |
T |
4: 138,588,629 (GRCm38) |
Q601K |
possibly damaging |
Het |
| Zbtb46 |
T |
C |
2: 181,395,488 (GRCm38) |
K454E |
probably damaging |
Het |
| Zfp426 |
T |
C |
9: 20,470,281 (GRCm38) |
H470R |
probably benign |
Het |
|
| Other mutations in Vars2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02106:Vars2
|
APN |
17 |
35,664,621 (GRCm38) |
unclassified |
probably benign |
|
|
IGL02320:Vars2
|
APN |
17 |
35,660,454 (GRCm38) |
missense |
probably benign |
0.07 |
|
IGL02580:Vars2
|
APN |
17 |
35,660,885 (GRCm38) |
missense |
possibly damaging |
0.50 |
|
IGL02691:Vars2
|
APN |
17 |
35,660,248 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03039:Vars2
|
APN |
17 |
35,664,121 (GRCm38) |
missense |
probably damaging |
1.00 |
|
PIT4445001:Vars2
|
UTSW |
17 |
35,666,211 (GRCm38) |
nonsense |
probably null |
|
|
R0079:Vars2
|
UTSW |
17 |
35,659,156 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R0152:Vars2
|
UTSW |
17 |
35,660,027 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0346:Vars2
|
UTSW |
17 |
35,664,864 (GRCm38) |
unclassified |
probably benign |
|
|
R0426:Vars2
|
UTSW |
17 |
35,664,584 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0584:Vars2
|
UTSW |
17 |
35,666,686 (GRCm38) |
missense |
possibly damaging |
0.82 |
|
R0589:Vars2
|
UTSW |
17 |
35,659,176 (GRCm38) |
missense |
probably benign |
|
|
R0882:Vars2
|
UTSW |
17 |
35,657,299 (GRCm38) |
missense |
probably benign |
0.41 |
|
R1234:Vars2
|
UTSW |
17 |
35,667,146 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1263:Vars2
|
UTSW |
17 |
35,661,609 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1559:Vars2
|
UTSW |
17 |
35,666,258 (GRCm38) |
unclassified |
probably benign |
|
|
R1772:Vars2
|
UTSW |
17 |
35,660,084 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1809:Vars2
|
UTSW |
17 |
35,662,216 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1913:Vars2
|
UTSW |
17 |
35,666,922 (GRCm38) |
missense |
probably benign |
0.02 |
|
R1986:Vars2
|
UTSW |
17 |
35,660,061 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2504:Vars2
|
UTSW |
17 |
35,664,793 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3426:Vars2
|
UTSW |
17 |
35,661,974 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4539:Vars2
|
UTSW |
17 |
35,666,888 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R4751:Vars2
|
UTSW |
17 |
35,659,343 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
R4861:Vars2
|
UTSW |
17 |
35,661,933 (GRCm38) |
missense |
probably benign |
0.00 |
|
R4861:Vars2
|
UTSW |
17 |
35,661,933 (GRCm38) |
missense |
probably benign |
0.00 |
|
R5028:Vars2
|
UTSW |
17 |
35,659,473 (GRCm38) |
critical splice donor site |
probably null |
|
|
R5217:Vars2
|
UTSW |
17 |
35,658,149 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5292:Vars2
|
UTSW |
17 |
35,660,786 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6056:Vars2
|
UTSW |
17 |
35,665,788 (GRCm38) |
missense |
probably benign |
0.01 |
|
R6211:Vars2
|
UTSW |
17 |
35,665,662 (GRCm38) |
splice site |
probably null |
|
|
R6213:Vars2
|
UTSW |
17 |
35,660,440 (GRCm38) |
missense |
probably benign |
0.27 |
|
R6374:Vars2
|
UTSW |
17 |
35,660,045 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6746:Vars2
|
UTSW |
17 |
35,660,402 (GRCm38) |
critical splice donor site |
probably null |
|
|
R6749:Vars2
|
UTSW |
17 |
35,666,713 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6957:Vars2
|
UTSW |
17 |
35,667,075 (GRCm38) |
missense |
probably benign |
0.39 |
|
R7107:Vars2
|
UTSW |
17 |
35,658,250 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7428:Vars2
|
UTSW |
17 |
35,666,686 (GRCm38) |
missense |
probably benign |
0.00 |
|
R7538:Vars2
|
UTSW |
17 |
35,660,780 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7553:Vars2
|
UTSW |
17 |
35,664,788 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R7741:Vars2
|
UTSW |
17 |
35,660,943 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7784:Vars2
|
UTSW |
17 |
35,658,158 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
R7823:Vars2
|
UTSW |
17 |
35,659,136 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7915:Vars2
|
UTSW |
17 |
35,664,839 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8201:Vars2
|
UTSW |
17 |
35,658,310 (GRCm38) |
missense |
probably benign |
|
|
R8955:Vars2
|
UTSW |
17 |
35,661,649 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8964:Vars2
|
UTSW |
17 |
35,659,807 (GRCm38) |
missense |
possibly damaging |
0.46 |
|
R9101:Vars2
|
UTSW |
17 |
35,659,088 (GRCm38) |
missense |
possibly damaging |
0.51 |
|
R9202:Vars2
|
UTSW |
17 |
35,666,659 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9202:Vars2
|
UTSW |
17 |
35,663,552 (GRCm38) |
critical splice acceptor site |
probably null |
|
|
X0021:Vars2
|
UTSW |
17 |
35,659,034 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
Z1176:Vars2
|
UTSW |
17 |
35,664,791 (GRCm38) |
missense |
possibly damaging |
0.55 |
|
Z1177:Vars2
|
UTSW |
17 |
35,663,472 (GRCm38) |
missense |
probably benign |
0.17 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGATACCTGCAGATGGGCA -3'
(R):5'- AGATGAGGCATGAGATGTAGTGT -3'
Sequencing Primer
(F):5'- TCCTGTAGGCCCCGGAATAG -3'
(R):5'- GTGTTTCTTAAATCCCAAAGCCAAGG -3'
|
| Posted On |
2022-06-15 |
Incidental Mutation