Incidental Mutation 'R0584:Vars2'
| ID |
56585 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
038774-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0584 (G1)
|
| Quality Score |
218 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 35977578 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 118
(V118A)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000043674
AA Change: V118A
PolyPhen 2
Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: V118A
| 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 |
noncoding transcript
Transcript: ENSMUST00000160535
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000162894
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165787
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162927
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164978
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171536
|
| 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: 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: 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 |
0.1226 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.2%
- 20x: 93.7%
|
| Validation Efficiency |
98% (47/48) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca7 |
T |
C |
10: 79,847,564 (GRCm39) |
S1745P |
probably damaging |
Het |
| Agfg2 |
G |
A |
5: 137,665,992 (GRCm39) |
T89I |
probably damaging |
Het |
| Agtr1a |
A |
G |
13: 30,565,017 (GRCm39) |
I27M |
probably damaging |
Het |
| Armh1 |
A |
T |
4: 117,087,047 (GRCm39) |
L206Q |
probably damaging |
Het |
| Asxl2 |
A |
T |
12: 3,546,632 (GRCm39) |
E472V |
probably damaging |
Het |
| Atp2c2 |
T |
A |
8: 120,465,157 (GRCm39) |
V313E |
probably benign |
Het |
| Casp12 |
A |
G |
9: 5,352,268 (GRCm39) |
I87V |
probably null |
Het |
| Ccl25 |
C |
T |
8: 4,404,085 (GRCm39) |
|
probably benign |
Het |
| Col9a1 |
T |
C |
1: 24,263,571 (GRCm39) |
|
probably benign |
Het |
| Cyth4 |
A |
G |
15: 78,494,078 (GRCm39) |
|
probably null |
Het |
| Dnah9 |
A |
G |
11: 65,881,315 (GRCm39) |
Y2587H |
probably damaging |
Het |
| Dppa3 |
T |
C |
6: 122,606,951 (GRCm39) |
I147T |
probably benign |
Het |
| Fam120b |
T |
C |
17: 15,622,384 (GRCm39) |
S121P |
probably damaging |
Het |
| Fam209 |
C |
T |
2: 172,316,081 (GRCm39) |
T152M |
probably benign |
Het |
| Fam98a |
A |
G |
17: 75,851,772 (GRCm39) |
L103P |
probably damaging |
Het |
| Fcho1 |
T |
C |
8: 72,168,369 (GRCm39) |
Y218C |
probably damaging |
Het |
| Fitm1 |
T |
C |
14: 55,814,113 (GRCm39) |
V203A |
probably benign |
Het |
| Gcn1 |
G |
A |
5: 115,733,074 (GRCm39) |
R1037Q |
probably damaging |
Het |
| Gm11563 |
A |
G |
11: 99,549,451 (GRCm39) |
I101T |
unknown |
Het |
| Gpd1l |
A |
G |
9: 114,743,412 (GRCm39) |
F163L |
probably damaging |
Het |
| Grp |
C |
A |
18: 66,006,766 (GRCm39) |
A30E |
possibly damaging |
Het |
| H1f7 |
C |
A |
15: 98,154,958 (GRCm39) |
E64* |
probably null |
Het |
| Icosl |
T |
C |
10: 77,907,709 (GRCm39) |
Y90H |
possibly damaging |
Het |
| Itsn2 |
A |
G |
12: 4,747,180 (GRCm39) |
T1194A |
probably benign |
Het |
| Lrp6 |
A |
G |
6: 134,433,039 (GRCm39) |
S1431P |
probably damaging |
Het |
| Ltbp1 |
T |
C |
17: 75,670,467 (GRCm39) |
S1503P |
probably damaging |
Het |
| Mef2a |
G |
T |
7: 66,884,896 (GRCm39) |
S406* |
probably null |
Het |
| Myh13 |
G |
T |
11: 67,251,200 (GRCm39) |
E1360* |
probably null |
Het |
| Nop58 |
A |
G |
1: 59,745,919 (GRCm39) |
D400G |
probably benign |
Het |
| Or5p79 |
T |
C |
7: 108,221,622 (GRCm39) |
L201P |
probably benign |
Het |
| Or6c205 |
T |
C |
10: 129,086,817 (GRCm39) |
V138A |
probably benign |
Het |
| Oscp1 |
A |
G |
4: 125,977,387 (GRCm39) |
|
probably null |
Het |
| Pde9a |
A |
T |
17: 31,678,951 (GRCm39) |
Y264F |
probably damaging |
Het |
| Pkhd1 |
T |
A |
1: 20,309,660 (GRCm39) |
K2763* |
probably null |
Het |
| Prkci |
T |
A |
3: 31,079,289 (GRCm39) |
C42* |
probably null |
Het |
| Ptprr |
T |
C |
10: 116,087,063 (GRCm39) |
V270A |
probably damaging |
Het |
| Rsf1 |
T |
A |
7: 97,311,335 (GRCm39) |
N688K |
possibly damaging |
Het |
| S1pr3 |
A |
T |
13: 51,573,697 (GRCm39) |
M293L |
probably benign |
Het |
| Scn10a |
A |
C |
9: 119,499,597 (GRCm39) |
L232R |
probably damaging |
Het |
| Sirt5 |
T |
A |
13: 43,548,204 (GRCm39) |
|
probably null |
Het |
| Sp6 |
C |
T |
11: 96,913,091 (GRCm39) |
T268M |
probably damaging |
Het |
| Spag5 |
A |
G |
11: 78,194,921 (GRCm39) |
N76S |
possibly damaging |
Het |
| Tecta |
T |
C |
9: 42,259,204 (GRCm39) |
N1560D |
possibly damaging |
Het |
| Togaram1 |
T |
C |
12: 65,014,279 (GRCm39) |
L510P |
probably damaging |
Het |
| Umps |
A |
G |
16: 33,779,494 (GRCm39) |
I401T |
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 |
|
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 |
|
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'- CTTGCCTGGAAGGAATGAGGAAGTC -3'
(R):5'- TGTATTGGGGATTGCAGCCTCCAC -3'
Sequencing Primer
(F):5'- tgtgaaaaggcagaggaagg -3'
(R):5'- GTATTGTATGAAATCCCCACCG -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation