Incidental Mutation 'R7915:Vars2'
| ID |
648047 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
045963-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7915 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35975731 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 229
(I229V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001565]
[ENSMUST00000043674]
[ENSMUST00000160734]
[ENSMUST00000160752]
[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 |
probably damaging
Transcript: ENSMUST00000043674
AA Change: I229V
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: I229V
| 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: 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: 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: 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 |
|
| Meta Mutation Damage Score |
0.6759 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
97% (66/68) |
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca17 |
T |
G |
17: 24,484,507 (GRCm39) |
H1585P |
probably damaging |
Het |
| Acaca |
A |
T |
11: 84,167,414 (GRCm39) |
T1063S |
probably benign |
Het |
| Actc1 |
T |
A |
2: 113,880,967 (GRCm39) |
K86M |
probably damaging |
Het |
| Amz1 |
A |
G |
5: 140,727,190 (GRCm39) |
N51S |
probably benign |
Het |
| Arhgap33 |
G |
A |
7: 30,222,648 (GRCm39) |
P1095S |
probably benign |
Het |
| Bicra |
T |
C |
7: 15,722,447 (GRCm39) |
T357A |
probably benign |
Het |
| C130032M10Rik |
A |
G |
9: 114,345,123 (GRCm39) |
R120G |
unknown |
Het |
| Cadps |
A |
G |
14: 12,705,544 (GRCm38) |
F284L |
possibly damaging |
Het |
| Ccdc83 |
G |
A |
7: 89,893,290 (GRCm39) |
Q156* |
probably null |
Het |
| Cdh20 |
T |
A |
1: 104,861,898 (GRCm39) |
M26K |
probably benign |
Het |
| Cdh23 |
A |
G |
10: 60,143,668 (GRCm39) |
L2979P |
probably damaging |
Het |
| Cdhr17 |
A |
G |
5: 17,032,012 (GRCm39) |
N556D |
probably benign |
Het |
| Crocc2 |
T |
C |
1: 93,141,363 (GRCm39) |
L1172P |
probably damaging |
Het |
| Cyp2d10 |
C |
T |
15: 82,288,628 (GRCm39) |
|
probably null |
Het |
| Cyp2j9 |
T |
A |
4: 96,479,621 (GRCm39) |
|
probably benign |
Het |
| Dgcr2 |
A |
G |
16: 17,677,266 (GRCm39) |
|
probably null |
Het |
| Dio3 |
A |
G |
12: 110,246,473 (GRCm39) |
M270V |
|
Het |
| Dll1 |
C |
A |
17: 15,588,690 (GRCm39) |
D662Y |
probably damaging |
Het |
| Drd1 |
G |
T |
13: 54,207,834 (GRCm39) |
P127T |
probably damaging |
Het |
| Evc2 |
T |
C |
5: 37,544,206 (GRCm39) |
S652P |
probably damaging |
Het |
| Fam149a |
C |
A |
8: 45,794,280 (GRCm39) |
M708I |
probably benign |
Het |
| Fam89a |
T |
C |
8: 125,467,895 (GRCm39) |
E139G |
probably damaging |
Het |
| Gpr141 |
T |
C |
13: 19,936,729 (GRCm39) |
I15M |
probably benign |
Het |
| Hcn4 |
G |
A |
9: 58,731,218 (GRCm39) |
E142K |
unknown |
Het |
| Hivep3 |
T |
A |
4: 119,954,962 (GRCm39) |
S1093T |
possibly damaging |
Het |
| Inpp5f |
C |
A |
7: 128,269,433 (GRCm39) |
T261K |
probably benign |
Het |
| Ints3 |
A |
T |
3: 90,340,132 (GRCm39) |
D42E |
probably benign |
Het |
| Krt90 |
A |
T |
15: 101,466,838 (GRCm39) |
|
probably null |
Het |
| Kti12 |
A |
C |
4: 108,705,443 (GRCm39) |
E119A |
probably benign |
Het |
| Kti12 |
G |
T |
4: 108,705,444 (GRCm39) |
E119D |
probably benign |
Het |
| Lrig1 |
C |
A |
6: 94,607,082 (GRCm39) |
|
probably null |
Het |
| Mapk14 |
A |
G |
17: 28,947,928 (GRCm39) |
T221A |
probably benign |
Het |
| Megf10 |
A |
T |
18: 57,373,807 (GRCm39) |
T202S |
probably benign |
Het |
| Neo1 |
A |
T |
9: 58,838,264 (GRCm39) |
F507I |
probably benign |
Het |
| Or7a35 |
A |
G |
10: 78,853,264 (GRCm39) |
Y36C |
probably damaging |
Het |
| Or8b48 |
A |
T |
9: 38,492,969 (GRCm39) |
Y132F |
probably damaging |
Het |
| Or8k37 |
T |
A |
2: 86,469,110 (GRCm39) |
*314L |
probably null |
Het |
| Peg10 |
T |
TCCA |
6: 4,756,451 (GRCm39) |
|
probably benign |
Het |
| Pkd1 |
T |
A |
17: 24,811,630 (GRCm39) |
Y3724* |
probably null |
Het |
| Plxnd1 |
T |
C |
6: 115,943,879 (GRCm39) |
D1140G |
probably benign |
Het |
| Pramel22 |
T |
C |
4: 143,382,315 (GRCm39) |
K127R |
possibly damaging |
Het |
| Prex1 |
A |
G |
2: 166,463,112 (GRCm39) |
S250P |
probably damaging |
Het |
| Prom1 |
A |
T |
5: 44,162,277 (GRCm39) |
M777K |
possibly damaging |
Het |
| Prrc2c |
A |
C |
1: 162,519,977 (GRCm39) |
S2125A |
probably benign |
Het |
| Ptpn12 |
A |
G |
5: 21,214,449 (GRCm39) |
I229T |
probably damaging |
Het |
| Ranbp6 |
A |
G |
19: 29,790,073 (GRCm39) |
V93A |
probably benign |
Het |
| Rtn3 |
A |
G |
19: 7,434,865 (GRCm39) |
C376R |
probably benign |
Het |
| Sis |
A |
C |
3: 72,828,471 (GRCm39) |
H1201Q |
probably damaging |
Het |
| Slc20a1 |
G |
A |
2: 129,049,757 (GRCm39) |
D340N |
probably benign |
Het |
| Slc3a2 |
G |
A |
19: 8,685,182 (GRCm39) |
R535W |
probably damaging |
Het |
| Slc5a2 |
T |
A |
7: 127,864,966 (GRCm39) |
L33Q |
probably damaging |
Het |
| Sltm |
G |
T |
9: 70,494,431 (GRCm39) |
R927L |
probably damaging |
Het |
| Spaca7b |
T |
C |
8: 11,728,645 (GRCm39) |
T9A |
possibly damaging |
Het |
| Stat1 |
A |
G |
1: 52,190,440 (GRCm39) |
D565G |
probably benign |
Het |
| Terb1 |
T |
C |
8: 105,173,848 (GRCm39) |
K745R |
possibly damaging |
Het |
| Tescl |
T |
C |
7: 24,033,113 (GRCm39) |
I71V |
probably damaging |
Het |
| Tgm1 |
T |
C |
14: 55,937,883 (GRCm39) |
D742G |
probably damaging |
Het |
| Tmem128 |
T |
A |
5: 38,423,875 (GRCm39) |
W30R |
probably benign |
Het |
| Tox |
T |
A |
4: 6,822,949 (GRCm39) |
M123L |
probably benign |
Het |
| Tsnaxip1 |
A |
G |
8: 106,569,413 (GRCm39) |
S547G |
possibly damaging |
Het |
| Ttn |
T |
A |
2: 76,567,539 (GRCm39) |
K27785* |
probably null |
Het |
| Tut7 |
T |
C |
13: 59,932,628 (GRCm39) |
I1345V |
probably benign |
Het |
| Usp38 |
A |
C |
8: 81,727,712 (GRCm39) |
S340R |
probably damaging |
Het |
| Utrn |
A |
T |
10: 12,340,956 (GRCm39) |
H2840Q |
probably damaging |
Het |
| Vmn1r16 |
A |
T |
6: 57,300,380 (GRCm39) |
Y81N |
probably damaging |
Het |
| Vmn2r98 |
A |
T |
17: 19,287,493 (GRCm39) |
D442V |
probably benign |
Het |
| Vps13d |
T |
C |
4: 144,813,389 (GRCm39) |
I3296V |
|
Het |
| Wwtr1 |
A |
G |
3: 57,483,020 (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 |
|
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 |
|
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'- ACGATCTGAATGTCCATACCTG -3'
(R):5'- TCTTTTAAAGCCATAGGACGCC -3'
Sequencing Primer
(F):5'- CTGCTGAACTCAGGGATTCC -3'
(R):5'- GCCATAGGACGCCCCACC -3'
|
| Posted On |
2020-09-15 |
Incidental Mutation