Incidental Mutation 'R0079:Vars2'
| ID |
19625 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
038366-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0079 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 35970048 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 780
(D780E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000169093]
|
| AlphaFold |
Q3U2A8 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000043674
AA Change: D780E
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: D780E
| 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 |
unknown
Transcript: ENSMUST00000168922
AA Change: D429E
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: D429E
| 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 |
0.6407 |
| Coding Region Coverage |
- 1x: 98.8%
- 3x: 97.8%
- 10x: 95.4%
- 20x: 90.7%
|
| Validation Efficiency |
78% (155/199) |
| 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 |
|---|
| 2410004P03Rik |
T |
A |
12: 17,057,183 (GRCm39) |
T105S |
possibly damaging |
Het |
| Abca13 |
G |
A |
11: 9,243,493 (GRCm39) |
M1785I |
probably benign |
Het |
| Adamts3 |
G |
C |
5: 89,840,912 (GRCm39) |
P804A |
probably benign |
Het |
| Ahrr |
G |
A |
13: 74,431,143 (GRCm39) |
|
probably benign |
Het |
| Ank2 |
G |
T |
3: 126,728,264 (GRCm39) |
D776E |
probably benign |
Het |
| Cep152 |
T |
A |
2: 125,460,373 (GRCm39) |
K193M |
possibly damaging |
Het |
| Cep55 |
C |
T |
19: 38,048,769 (GRCm39) |
L142F |
probably benign |
Het |
| Chd5 |
A |
G |
4: 152,470,206 (GRCm39) |
Y1884C |
probably damaging |
Het |
| Clasp1 |
T |
C |
1: 118,471,034 (GRCm39) |
L890P |
probably damaging |
Het |
| Cul9 |
C |
A |
17: 46,848,589 (GRCm39) |
E716* |
probably null |
Het |
| Cytip |
T |
A |
2: 58,050,006 (GRCm39) |
D21V |
probably benign |
Het |
| Denr |
T |
G |
5: 124,062,908 (GRCm39) |
F137C |
probably damaging |
Het |
| Dhrs3 |
A |
T |
4: 144,646,618 (GRCm39) |
S197C |
probably damaging |
Het |
| Egr4 |
A |
T |
6: 85,489,751 (GRCm39) |
M103K |
probably damaging |
Het |
| Eif4enif1 |
C |
T |
11: 3,192,676 (GRCm39) |
Q835* |
probably null |
Het |
| Gckr |
A |
G |
5: 31,463,883 (GRCm39) |
I268V |
probably benign |
Het |
| Glt6d1 |
C |
A |
2: 25,684,739 (GRCm39) |
|
probably null |
Het |
| Hpd |
T |
C |
5: 123,319,544 (GRCm39) |
Y8C |
probably damaging |
Het |
| Il12rb2 |
A |
T |
6: 67,338,889 (GRCm39) |
F16I |
probably benign |
Het |
| Ildr2 |
A |
T |
1: 166,135,289 (GRCm39) |
Y347F |
probably damaging |
Het |
| Kcnv1 |
T |
C |
15: 44,976,729 (GRCm39) |
D186G |
probably damaging |
Het |
| Khdrbs2 |
A |
G |
1: 32,558,996 (GRCm39) |
|
probably null |
Het |
| L1cam |
G |
T |
X: 72,913,364 (GRCm39) |
P16H |
probably damaging |
Het |
| Lyn |
A |
G |
4: 3,746,768 (GRCm39) |
H161R |
probably damaging |
Het |
| Mctp2 |
T |
A |
7: 71,863,864 (GRCm39) |
|
probably benign |
Het |
| Miox |
C |
T |
15: 89,220,477 (GRCm39) |
L189F |
possibly damaging |
Het |
| Mitf |
A |
C |
6: 97,973,401 (GRCm39) |
M220L |
probably benign |
Het |
| Mrpl21 |
T |
C |
19: 3,334,807 (GRCm39) |
Y50H |
possibly damaging |
Het |
| Myh1 |
T |
A |
11: 67,104,237 (GRCm39) |
L968Q |
probably damaging |
Het |
| Myo3b |
A |
G |
2: 69,925,502 (GRCm39) |
K18E |
possibly damaging |
Het |
| Ncoa6 |
TGC |
TGCGC |
2: 155,250,211 (GRCm39) |
|
probably null |
Het |
| Nlrp2 |
T |
A |
7: 5,330,729 (GRCm39) |
T556S |
possibly damaging |
Het |
| Nsmf |
T |
C |
2: 24,949,096 (GRCm39) |
|
probably benign |
Het |
| Nsun7 |
C |
T |
5: 66,452,856 (GRCm39) |
P558S |
probably benign |
Het |
| Or10h5 |
G |
A |
17: 33,435,079 (GRCm39) |
R80C |
probably benign |
Het |
| Or1e34 |
T |
G |
11: 73,778,563 (GRCm39) |
I212L |
probably benign |
Het |
| Or56a3 |
T |
C |
7: 104,735,135 (GRCm39) |
S71P |
probably damaging |
Het |
| Or5d40 |
A |
T |
2: 88,015,698 (GRCm39) |
Y159F |
possibly damaging |
Het |
| Phf19 |
T |
C |
2: 34,785,966 (GRCm39) |
N501S |
probably benign |
Het |
| Ranbp17 |
A |
C |
11: 33,450,682 (GRCm39) |
I85S |
probably damaging |
Het |
| Robo1 |
A |
G |
16: 72,730,230 (GRCm39) |
|
probably benign |
Het |
| Sntg1 |
A |
G |
1: 8,749,286 (GRCm39) |
|
probably benign |
Het |
| Snx15 |
A |
G |
19: 6,173,943 (GRCm39) |
L58P |
probably damaging |
Het |
| Spink5 |
G |
T |
18: 44,110,831 (GRCm39) |
C134F |
probably damaging |
Het |
| Strip2 |
T |
C |
6: 29,920,532 (GRCm39) |
|
probably null |
Het |
| Taf1d |
C |
T |
9: 15,221,240 (GRCm39) |
A182V |
probably benign |
Het |
| Tenm3 |
A |
G |
8: 48,796,380 (GRCm39) |
V475A |
possibly damaging |
Het |
| Tent4b |
T |
A |
8: 88,926,631 (GRCm39) |
Y14N |
possibly damaging |
Het |
| Tgds |
A |
T |
14: 118,353,647 (GRCm39) |
H223Q |
possibly damaging |
Het |
| Thoc2 |
G |
T |
X: 40,952,985 (GRCm39) |
S230Y |
probably benign |
Het |
| Tm9sf4 |
T |
A |
2: 153,033,065 (GRCm39) |
V290E |
probably damaging |
Het |
| Trak2 |
A |
T |
1: 58,965,883 (GRCm39) |
L97Q |
probably damaging |
Het |
| Trnau1ap |
A |
G |
4: 132,041,656 (GRCm39) |
Y145H |
probably damaging |
Het |
| Vmn1r170 |
T |
A |
7: 23,305,735 (GRCm39) |
S46T |
possibly damaging |
Het |
| Vmn1r20 |
A |
T |
6: 57,408,777 (GRCm39) |
R34S |
possibly damaging |
Het |
| Vmn1r28 |
G |
A |
6: 58,242,702 (GRCm39) |
A182T |
probably benign |
Het |
| Wdr64 |
T |
C |
1: 175,622,668 (GRCm39) |
M805T |
probably benign |
Het |
| Xdh |
G |
A |
17: 74,198,213 (GRCm39) |
R1225C |
probably damaging |
Het |
| Zfp341 |
T |
A |
2: 154,466,914 (GRCm39) |
Y94* |
probably null |
Het |
| Zfp641 |
T |
C |
15: 98,186,970 (GRCm39) |
N218D |
probably benign |
Het |
| Zscan22 |
T |
C |
7: 12,638,014 (GRCm39) |
|
probably null |
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 |
|
|
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 |
|
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'- CTGGCAACAGCTCTGGGCTATATAC -3'
(R):5'- CCTGAACTACCGCCATTTCTGCAAC -3'
Sequencing Primer
(F):5'- AGGAACATGCTTTCCCTGATGAG -3'
(R):5'- TCTGCAACAAGCTCTGGAATG -3'
|
| Posted On |
2013-04-11 |
Incidental Mutation