Incidental Mutation 'R0882:Vars2'
| ID |
80681 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
039049-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0882 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35968191 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 899
(E899G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000169093]
|
| AlphaFold |
Q3U2A8 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000043674
AA Change: E899G
PolyPhen 2
Score 0.408 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: E899G
| 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 |
noncoding transcript
Transcript: ENSMUST00000164295
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000165787
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168885
|
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174129
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170701
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
| Meta Mutation Damage Score |
0.0951 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 99.0%
- 10x: 97.8%
- 20x: 96.0%
|
| Validation Efficiency |
100% (49/49) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aasdh |
G |
A |
5: 77,024,130 (GRCm39) |
T174M |
probably damaging |
Het |
| Adh1 |
A |
T |
3: 137,992,558 (GRCm39) |
I225F |
possibly damaging |
Het |
| Agap2 |
A |
G |
10: 126,923,319 (GRCm39) |
K691E |
unknown |
Het |
| Alcam |
T |
C |
16: 52,073,573 (GRCm39) |
D564G |
possibly damaging |
Het |
| Apbb2 |
T |
A |
5: 66,557,598 (GRCm39) |
T289S |
probably damaging |
Het |
| Cacna1c |
C |
T |
6: 118,589,586 (GRCm39) |
R1446H |
probably damaging |
Het |
| Cep68 |
T |
C |
11: 20,189,393 (GRCm39) |
I540V |
probably benign |
Het |
| Ctla4 |
T |
C |
1: 60,948,397 (GRCm39) |
V23A |
probably benign |
Het |
| Dnah7b |
T |
A |
1: 46,379,292 (GRCm39) |
D3675E |
probably benign |
Het |
| Fam209 |
G |
T |
2: 172,314,555 (GRCm39) |
V15F |
probably benign |
Het |
| Fat3 |
A |
G |
9: 15,942,664 (GRCm39) |
V1236A |
possibly damaging |
Het |
| Gabbr2 |
A |
G |
4: 46,718,904 (GRCm39) |
I38T |
probably damaging |
Het |
| Gdpd4 |
T |
C |
7: 97,615,505 (GRCm39) |
I110T |
probably damaging |
Het |
| Gm4841 |
C |
T |
18: 60,402,852 (GRCm39) |
A414T |
possibly damaging |
Het |
| Gtf3c4 |
A |
T |
2: 28,724,782 (GRCm39) |
Y176N |
probably damaging |
Het |
| H2bc18 |
G |
A |
3: 96,177,060 (GRCm39) |
|
probably null |
Het |
| Igsf9b |
T |
C |
9: 27,230,612 (GRCm39) |
Y264H |
probably damaging |
Het |
| Itih4 |
A |
T |
14: 30,614,231 (GRCm39) |
N394Y |
probably damaging |
Het |
| Kmt2c |
T |
C |
5: 25,500,605 (GRCm39) |
T3815A |
possibly damaging |
Het |
| Lrwd1 |
T |
C |
5: 136,152,254 (GRCm39) |
|
probably null |
Het |
| Mc3r |
A |
G |
2: 172,091,711 (GRCm39) |
K311R |
probably benign |
Het |
| Myb |
T |
C |
10: 21,032,259 (GRCm39) |
T41A |
possibly damaging |
Het |
| Nfix |
T |
C |
8: 85,454,554 (GRCm39) |
D201G |
probably damaging |
Het |
| Nos1 |
T |
C |
5: 118,085,512 (GRCm39) |
V1280A |
probably damaging |
Het |
| Or51a5 |
A |
C |
7: 102,771,782 (GRCm39) |
S66A |
probably benign |
Het |
| Or8a1b |
T |
C |
9: 37,623,168 (GRCm39) |
M136V |
probably benign |
Het |
| Pcdh15 |
A |
G |
10: 74,178,488 (GRCm39) |
T582A |
probably damaging |
Het |
| Pcdhb12 |
C |
A |
18: 37,570,375 (GRCm39) |
A507E |
probably damaging |
Het |
| Pdia3 |
G |
A |
2: 121,262,858 (GRCm39) |
G275S |
probably damaging |
Het |
| Pkp2 |
C |
A |
16: 16,087,575 (GRCm39) |
A753E |
probably damaging |
Het |
| Plekha3 |
G |
A |
2: 76,513,142 (GRCm39) |
V76I |
possibly damaging |
Het |
| Pnpla6 |
T |
C |
8: 3,567,081 (GRCm39) |
L33P |
probably damaging |
Het |
| Pot1b |
C |
T |
17: 55,973,400 (GRCm39) |
|
probably benign |
Het |
| Prr5l |
T |
C |
2: 101,588,886 (GRCm39) |
E88G |
possibly damaging |
Het |
| Prss57 |
G |
A |
10: 79,621,699 (GRCm39) |
H97Y |
probably damaging |
Het |
| Rttn |
C |
T |
18: 88,991,813 (GRCm39) |
Q131* |
probably null |
Het |
| Scaf11 |
G |
T |
15: 96,316,176 (GRCm39) |
S1129R |
possibly damaging |
Het |
| Slc25a20 |
T |
A |
9: 108,559,189 (GRCm39) |
M185K |
possibly damaging |
Het |
| Sorbs3 |
T |
A |
14: 70,445,021 (GRCm39) |
E19V |
probably damaging |
Het |
| Srgap2 |
A |
T |
1: 131,217,253 (GRCm39) |
C1020S |
probably benign |
Het |
| Thoc2l |
T |
C |
5: 104,666,875 (GRCm39) |
S466P |
probably benign |
Het |
| Tmem109 |
T |
C |
19: 10,849,205 (GRCm39) |
R217G |
possibly damaging |
Het |
| Trio |
A |
T |
15: 27,732,980 (GRCm39) |
I2967N |
probably damaging |
Het |
| Vmn2r109 |
A |
G |
17: 20,774,842 (GRCm39) |
|
probably benign |
Het |
| Vps53 |
A |
G |
11: 75,973,485 (GRCm39) |
F170L |
probably damaging |
Het |
| Zc2hc1a |
G |
A |
3: 7,591,422 (GRCm39) |
S149N |
possibly damaging |
Het |
| Zfp820 |
A |
G |
17: 22,042,817 (GRCm39) |
|
probably benign |
Het |
| Zhx3 |
A |
C |
2: 160,622,629 (GRCm39) |
F513V |
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 |
|
|
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 |
|
R7428:Vars2
|
UTSW |
17 |
35,977,578 (GRCm39) |
missense |
probably benign |
0.00 |
|
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'- AGGTCATCAAGCTGCTTCTGTAACTTC -3'
(R):5'- TGGTTGTATAAACCCTTAGGCAACACC -3'
Sequencing Primer
(F):5'- GTAGATCTTCATGGTGTCACCCAG -3'
(R):5'- TTAGGCAACACCTCCCATGC -3'
|
| Posted On |
2013-11-07 |
Incidental Mutation