Incidental Mutation 'R6957:Vars2'
| ID |
541553 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
045068-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6957 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 35977967 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamine
at position 67
(K67Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000132897
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001565]
[ENSMUST00000043674]
[ENSMUST00000159852]
[ENSMUST00000160039]
[ENSMUST00000160734]
[ENSMUST00000160752]
[ENSMUST00000162266]
[ENSMUST00000165144]
|
| 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: K67Q
PolyPhen 2
Score 0.197 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: K67Q
| 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: ENSMUST00000159852
|
| SMART Domains |
Protein: ENSMUSP00000124060
Gene: ENSMUSG00000001524
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Tfb2
|
22 |
61 |
1.6e-14 |
PFAM |
|
| 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
AA Change: K67Q
PolyPhen 2
Score 0.391 (Sensitivity: 0.90; Specificity: 0.89)
|
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 98.0%
|
| 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: 77 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310009B15Rik |
A |
G |
1: 138,779,857 (GRCm39) |
S132P |
probably damaging |
Het |
| Abcb5 |
A |
G |
12: 118,871,270 (GRCm39) |
F710L |
probably damaging |
Het |
| Acsm4 |
T |
G |
7: 119,310,622 (GRCm39) |
V503G |
probably damaging |
Het |
| Adam26a |
T |
A |
8: 44,021,940 (GRCm39) |
M517L |
probably benign |
Het |
| Adcy10 |
C |
A |
1: 165,391,854 (GRCm39) |
L1345I |
probably damaging |
Het |
| Adgrv1 |
T |
C |
13: 81,715,609 (GRCm39) |
I860V |
probably benign |
Het |
| Alcam |
T |
C |
16: 52,097,257 (GRCm39) |
D333G |
probably damaging |
Het |
| Amt |
C |
A |
9: 108,177,032 (GRCm39) |
F213L |
possibly damaging |
Het |
| Ascc3 |
A |
G |
10: 50,604,278 (GRCm39) |
T1333A |
probably damaging |
Het |
| Asxl3 |
C |
A |
18: 22,655,148 (GRCm39) |
L1053I |
probably damaging |
Het |
| Atxn10 |
T |
C |
15: 85,220,699 (GRCm39) |
S12P |
probably damaging |
Het |
| AU021092 |
T |
C |
16: 5,030,017 (GRCm39) |
I333V |
probably benign |
Het |
| Birc6 |
A |
G |
17: 74,886,486 (GRCm39) |
I577V |
probably benign |
Het |
| Cadm2 |
A |
T |
16: 66,609,726 (GRCm39) |
F132I |
probably benign |
Het |
| Casp3 |
T |
A |
8: 47,087,308 (GRCm39) |
V85D |
probably damaging |
Het |
| Ccdc168 |
C |
T |
1: 44,096,367 (GRCm39) |
C1577Y |
probably benign |
Het |
| Ccdc85a |
A |
T |
11: 28,342,944 (GRCm39) |
|
probably benign |
Het |
| Cd22 |
T |
C |
7: 30,566,999 (GRCm39) |
R760G |
possibly damaging |
Het |
| Cela3a |
A |
T |
4: 137,135,441 (GRCm39) |
W41R |
probably damaging |
Het |
| Cep164 |
A |
G |
9: 45,683,578 (GRCm39) |
|
probably null |
Het |
| Cntnap5b |
A |
G |
1: 100,202,197 (GRCm39) |
E348G |
probably benign |
Het |
| Ddx20 |
C |
A |
3: 105,591,626 (GRCm39) |
K181N |
probably benign |
Het |
| Dnah14 |
G |
C |
1: 181,612,740 (GRCm39) |
A3846P |
possibly damaging |
Het |
| Ern1 |
A |
C |
11: 106,294,365 (GRCm39) |
I813S |
probably damaging |
Het |
| Fam181a |
G |
A |
12: 103,282,773 (GRCm39) |
G226D |
probably damaging |
Het |
| Fam186a |
T |
A |
15: 99,844,357 (GRCm39) |
D629V |
unknown |
Het |
| Gipr |
T |
A |
7: 18,898,529 (GRCm39) |
T26S |
probably benign |
Het |
| Gm3159 |
A |
G |
14: 4,398,530 (GRCm38) |
R74G |
possibly damaging |
Het |
| Greb1l |
G |
A |
18: 10,558,786 (GRCm39) |
V1814I |
probably benign |
Het |
| Hacd1 |
A |
T |
2: 14,049,664 (GRCm39) |
V98E |
probably damaging |
Het |
| Iars1 |
T |
G |
13: 49,875,637 (GRCm39) |
F775V |
probably damaging |
Het |
| Il12rb2 |
G |
A |
6: 67,269,636 (GRCm39) |
L726F |
possibly damaging |
Het |
| Itih4 |
T |
C |
14: 30,614,560 (GRCm39) |
V474A |
probably damaging |
Het |
| Kmt2a |
A |
C |
9: 44,731,319 (GRCm39) |
|
probably benign |
Het |
| Ktn1 |
T |
A |
14: 47,904,810 (GRCm39) |
L196* |
probably null |
Het |
| Lipo4 |
A |
G |
19: 33,476,767 (GRCm39) |
V327A |
probably benign |
Het |
| Lratd2 |
T |
C |
15: 60,694,934 (GRCm39) |
T271A |
probably benign |
Het |
| Lrit1 |
G |
C |
14: 36,782,052 (GRCm39) |
V242L |
probably damaging |
Het |
| Lrp4 |
C |
A |
2: 91,317,387 (GRCm39) |
T837K |
probably damaging |
Het |
| Mad1l1 |
G |
T |
5: 140,051,572 (GRCm39) |
F664L |
probably damaging |
Het |
| Mecr |
A |
G |
4: 131,589,172 (GRCm39) |
T247A |
probably benign |
Het |
| Msi1 |
G |
A |
5: 115,583,483 (GRCm39) |
A228T |
probably benign |
Het |
| Mup5 |
T |
A |
4: 61,751,273 (GRCm39) |
N125I |
probably damaging |
Het |
| Mybl2 |
C |
T |
2: 162,914,728 (GRCm39) |
S282F |
possibly damaging |
Het |
| Myom2 |
G |
A |
8: 15,167,741 (GRCm39) |
A1109T |
probably null |
Het |
| Nalcn |
T |
C |
14: 123,744,966 (GRCm39) |
D354G |
probably damaging |
Het |
| Nckap1l |
T |
C |
15: 103,399,938 (GRCm39) |
V1040A |
possibly damaging |
Het |
| Nlrp12 |
T |
A |
7: 3,271,160 (GRCm39) |
D1051V |
probably damaging |
Het |
| Nudt7 |
A |
G |
8: 114,860,385 (GRCm39) |
K16R |
probably benign |
Het |
| Or4b1 |
G |
T |
2: 89,979,494 (GRCm39) |
Y285* |
probably null |
Het |
| Or8g29-ps1 |
A |
G |
9: 39,200,577 (GRCm39) |
V203A |
unknown |
Het |
| Paqr3 |
A |
T |
5: 97,256,110 (GRCm39) |
I88K |
possibly damaging |
Het |
| Parp9 |
A |
G |
16: 35,768,716 (GRCm39) |
M299V |
probably benign |
Het |
| Pde4dip |
A |
T |
3: 97,731,649 (GRCm39) |
|
probably null |
Het |
| Pex13 |
T |
G |
11: 23,605,628 (GRCm39) |
M201L |
probably benign |
Het |
| Pfas |
C |
A |
11: 68,884,709 (GRCm39) |
V498L |
probably benign |
Het |
| Phka2 |
G |
A |
X: 159,316,044 (GRCm39) |
V230I |
probably damaging |
Het |
| Plec |
T |
A |
15: 76,070,414 (GRCm39) |
D932V |
probably damaging |
Het |
| Qng1 |
C |
A |
13: 58,529,775 (GRCm39) |
C279F |
probably damaging |
Het |
| Qsox2 |
C |
T |
2: 26,107,654 (GRCm39) |
A445T |
probably benign |
Het |
| Rapgef1 |
C |
A |
2: 29,623,710 (GRCm39) |
Q820K |
possibly damaging |
Het |
| Samd13 |
A |
G |
3: 146,368,424 (GRCm39) |
|
probably null |
Het |
| Samm50 |
G |
T |
15: 84,082,850 (GRCm39) |
D104Y |
probably damaging |
Het |
| Sbk3 |
A |
T |
7: 4,970,522 (GRCm39) |
F282L |
probably benign |
Het |
| Sfmbt1 |
C |
T |
14: 30,509,546 (GRCm39) |
H342Y |
probably benign |
Het |
| Sgo2b |
CCATCATCATCATCATCATCAT |
CCATCATCATCATCATCAT |
8: 64,384,489 (GRCm39) |
|
probably benign |
Het |
| Slc12a2 |
T |
A |
18: 58,043,344 (GRCm39) |
L596* |
probably null |
Het |
| Spata31h1 |
A |
T |
10: 82,129,620 (GRCm39) |
I1130K |
probably benign |
Het |
| St8sia3 |
T |
C |
18: 64,404,853 (GRCm39) |
S377P |
probably benign |
Het |
| Stmnd1 |
T |
G |
13: 46,427,375 (GRCm39) |
S28A |
probably benign |
Het |
| Syne3 |
A |
T |
12: 104,920,561 (GRCm39) |
L458Q |
probably damaging |
Het |
| Synm |
C |
T |
7: 67,385,848 (GRCm39) |
V163I |
probably benign |
Het |
| Tbc1d23 |
A |
G |
16: 57,028,686 (GRCm39) |
C161R |
probably damaging |
Het |
| Tnfrsf4 |
G |
A |
4: 156,100,625 (GRCm39) |
V215I |
probably benign |
Het |
| Vmn2r13 |
A |
T |
5: 109,304,753 (GRCm39) |
Y559* |
probably null |
Het |
| Wdpcp |
T |
C |
11: 21,671,154 (GRCm39) |
I465T |
possibly damaging |
Het |
| Zwilch |
A |
C |
9: 64,069,844 (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 |
|
|
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 |
|
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'- TACCTCCTTGTGACTCCAGG -3'
(R):5'- AACACTCCCGATGCCTCATTTG -3'
Sequencing Primer
(F):5'- TGACTCCAGGCCTTAGTGG -3'
(R):5'- GATGCCTCATTTGCCTCTGG -3'
|
| Posted On |
2018-11-28 |
Incidental Mutation