Incidental Mutation 'R7823:Vars2'
| ID |
602034 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
045877-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7823 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 35970028 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Arginine
at position 787
(L787R)
|
| 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: L787R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: L787R
| 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: 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 |
possibly damaging
Transcript: ENSMUST00000168922
AA Change: L436R
PolyPhen 2
Score 0.552 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: L436R
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
| Validation Efficiency |
99% (68/69) |
| 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: 73 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc4 |
A |
G |
14: 118,771,484 (GRCm39) |
V869A |
probably benign |
Het |
| Alox15 |
C |
A |
11: 70,235,494 (GRCm39) |
V623L |
possibly damaging |
Het |
| Angpt4 |
T |
G |
2: 151,753,286 (GRCm39) |
L12R |
unknown |
Het |
| Cdh24 |
C |
T |
14: 54,874,875 (GRCm39) |
A42T |
probably damaging |
Het |
| Cep250 |
T |
A |
2: 155,807,336 (GRCm39) |
S234T |
possibly damaging |
Het |
| Clnk |
T |
A |
5: 38,907,694 (GRCm39) |
Y188F |
probably benign |
Het |
| Csmd2 |
A |
T |
4: 128,103,698 (GRCm39) |
T306S |
|
Het |
| Cyp2f2 |
G |
A |
7: 26,828,678 (GRCm39) |
V183I |
probably benign |
Het |
| Dgka |
T |
A |
10: 128,572,135 (GRCm39) |
Y50F |
probably benign |
Het |
| Dgkh |
C |
T |
14: 78,841,921 (GRCm39) |
V434I |
probably benign |
Het |
| Epb41 |
A |
G |
4: 131,701,993 (GRCm39) |
|
probably null |
Het |
| Fam220a |
A |
G |
5: 143,549,011 (GRCm39) |
D141G |
probably damaging |
Het |
| Fbxo11 |
A |
G |
17: 88,300,610 (GRCm39) |
L807S |
probably damaging |
Het |
| G530012D18Rik |
G |
C |
1: 85,504,923 (GRCm39) |
|
probably benign |
Het |
| Ggt1 |
G |
A |
10: 75,410,175 (GRCm39) |
V36M |
possibly damaging |
Het |
| Gjb2 |
T |
C |
14: 57,337,963 (GRCm39) |
I82V |
probably benign |
Het |
| Gm7579 |
T |
A |
7: 141,766,307 (GRCm39) |
C238S |
unknown |
Het |
| Hps1 |
G |
A |
19: 42,744,146 (GRCm39) |
T681M |
possibly damaging |
Het |
| Iqck |
T |
C |
7: 118,472,046 (GRCm39) |
Y64H |
probably damaging |
Het |
| Ldlr |
G |
A |
9: 21,653,602 (GRCm39) |
|
probably null |
Het |
| Macc1 |
A |
C |
12: 119,410,800 (GRCm39) |
K523Q |
probably damaging |
Het |
| Mon2 |
A |
T |
10: 122,868,559 (GRCm39) |
I498N |
probably damaging |
Het |
| Mphosph9 |
T |
C |
5: 124,442,319 (GRCm39) |
E373G |
probably damaging |
Het |
| Mthfr |
T |
C |
4: 148,135,944 (GRCm39) |
I314T |
probably benign |
Het |
| Mtmr4 |
T |
G |
11: 87,503,015 (GRCm39) |
I1023S |
probably damaging |
Het |
| Myo9a |
T |
A |
9: 59,719,233 (GRCm39) |
F507I |
probably damaging |
Het |
| Nlrp10 |
T |
A |
7: 108,523,468 (GRCm39) |
M671L |
probably benign |
Het |
| Nt5c1a |
T |
C |
4: 123,102,365 (GRCm39) |
V97A |
probably damaging |
Het |
| Nxpe5 |
A |
G |
5: 138,237,844 (GRCm39) |
R123G |
possibly damaging |
Het |
| Obscn |
T |
C |
11: 58,998,766 (GRCm39) |
S1369G |
probably damaging |
Het |
| Oga |
A |
G |
19: 45,765,354 (GRCm39) |
V151A |
possibly damaging |
Het |
| Or4a75 |
A |
G |
2: 89,447,613 (GRCm39) |
*308Q |
probably null |
Het |
| Or52m2 |
A |
G |
7: 102,264,164 (GRCm39) |
S11P |
probably benign |
Het |
| Or5b99 |
A |
T |
19: 12,976,781 (GRCm39) |
I144F |
probably damaging |
Het |
| Or6c33 |
T |
A |
10: 129,854,136 (GRCm39) |
M302K |
probably benign |
Het |
| Or6k2 |
A |
G |
1: 173,987,254 (GRCm39) |
K305R |
probably benign |
Het |
| Or8b57 |
A |
T |
9: 40,003,644 (GRCm39) |
V202E |
probably damaging |
Het |
| Pak6 |
G |
A |
2: 118,525,793 (GRCm39) |
A618T |
probably benign |
Het |
| Pax7 |
T |
A |
4: 139,468,150 (GRCm39) |
E489V |
probably benign |
Het |
| Phactr4 |
G |
A |
4: 132,088,930 (GRCm39) |
R651* |
probably null |
Het |
| Pik3c2b |
C |
T |
1: 133,030,043 (GRCm39) |
R1435C |
probably damaging |
Het |
| Pla2g4c |
A |
T |
7: 13,063,944 (GRCm39) |
I68F |
probably damaging |
Het |
| Plppr1 |
A |
G |
4: 49,325,703 (GRCm39) |
M300V |
probably benign |
Het |
| Ptgfrn |
C |
T |
3: 100,950,725 (GRCm39) |
V863I |
probably damaging |
Het |
| Rabep2 |
T |
C |
7: 126,037,893 (GRCm39) |
S222P |
probably damaging |
Het |
| Ramacl |
A |
G |
13: 67,055,351 (GRCm39) |
|
probably benign |
Het |
| Rbm20 |
A |
T |
19: 53,831,785 (GRCm39) |
D673V |
probably benign |
Het |
| Rsf1 |
GCG |
GCGACGGCGACG |
7: 97,229,114 (GRCm39) |
|
probably benign |
Het |
| Scn4a |
C |
A |
11: 106,233,334 (GRCm39) |
A413S |
probably damaging |
Het |
| Scn9a |
A |
T |
2: 66,314,135 (GRCm39) |
M1850K |
probably damaging |
Het |
| Sh3tc2 |
T |
A |
18: 62,086,188 (GRCm39) |
M1K |
probably null |
Het |
| Slc22a28 |
G |
A |
19: 8,041,890 (GRCm39) |
T439I |
probably benign |
Het |
| Slc25a36 |
A |
G |
9: 96,966,444 (GRCm39) |
|
probably null |
Het |
| Smpd3 |
A |
C |
8: 106,982,254 (GRCm39) |
C617G |
probably benign |
Het |
| Spata3 |
T |
C |
1: 85,949,781 (GRCm39) |
|
probably benign |
Het |
| Srp68 |
C |
T |
11: 116,156,265 (GRCm39) |
R159Q |
probably damaging |
Het |
| Ssbp2 |
C |
A |
13: 91,790,448 (GRCm39) |
L104I |
possibly damaging |
Het |
| St8sia3 |
T |
A |
18: 64,400,027 (GRCm39) |
F7L |
probably benign |
Het |
| Stard9 |
T |
C |
2: 120,532,587 (GRCm39) |
V2948A |
probably damaging |
Het |
| Syne4 |
A |
G |
7: 30,018,280 (GRCm39) |
T341A |
probably benign |
Het |
| Tcf7l2 |
T |
A |
19: 55,731,521 (GRCm39) |
D91E |
possibly damaging |
Het |
| Tekt5 |
T |
A |
16: 10,203,943 (GRCm39) |
I236F |
probably damaging |
Het |
| Tlk2 |
T |
C |
11: 105,144,133 (GRCm39) |
Y316H |
probably damaging |
Het |
| Tmem184b |
C |
T |
15: 79,249,491 (GRCm39) |
A326T |
probably benign |
Het |
| Tnks2 |
G |
A |
19: 36,829,954 (GRCm39) |
|
probably null |
Het |
| Trpc4 |
C |
A |
3: 54,209,640 (GRCm39) |
Y668* |
probably null |
Het |
| Ttc9c |
A |
T |
19: 8,793,286 (GRCm39) |
F118Y |
probably benign |
Het |
| Ulk1 |
C |
T |
5: 110,946,780 (GRCm39) |
C95Y |
probably damaging |
Het |
| Vwa3a |
T |
C |
7: 120,372,185 (GRCm39) |
S254P |
probably damaging |
Het |
| Wdr81 |
T |
C |
11: 75,340,627 (GRCm39) |
Y1250C |
probably damaging |
Het |
| Xirp2 |
A |
T |
2: 67,342,118 (GRCm39) |
D1453V |
probably damaging |
Het |
| Zbtb38 |
A |
T |
9: 96,568,029 (GRCm39) |
C1018* |
probably null |
Het |
| Zfp622 |
C |
T |
15: 25,984,709 (GRCm39) |
T25M |
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 |
|
|
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 |
|
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'- ACATGCTTTCCCTGATGAGG -3'
(R):5'- TGCAACAAGCTCTGGAATGCC -3'
Sequencing Primer
(F):5'- CTGATGAGGGGGCACTGG -3'
(R):5'- GAATGCCCTGCGCTTTG -3'
|
| Posted On |
2019-12-03 |
Incidental Mutation