Incidental Mutation 'R1263:Vars2'
ID |
151688 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vars2
|
Ensembl Gene |
ENSMUSG00000038838 |
Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
Synonyms |
Vars2l, 1190004I24Rik |
MMRRC Submission |
039330-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R1263 (G1)
|
Quality Score |
170 |
Status
|
Not validated
|
Chromosome |
17 |
Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 35972501 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 39
(V39A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000126794
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000165144]
[ENSMUST00000169093]
|
AlphaFold |
Q3U2A8 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000043674
AA Change: V482A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000047917 Gene: ENSMUSG00000038838 AA Change: V482A
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 |
unknown
Transcript: ENSMUST00000164404
AA Change: V101A
|
SMART Domains |
Protein: ENSMUSP00000126084 Gene: ENSMUSG00000038838 AA Change: V101A
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: ENSMUST00000164978
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000165144
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165787
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168885
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000169093
AA Change: V39A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000126794 Gene: ENSMUSG00000038838 AA Change: V39A
Domain | Start | End | E-Value | Type |
Pfam:tRNA-synt_1
|
1 |
109 |
1.7e-29 |
PFAM |
|
Predicted Effect |
unknown
Transcript: ENSMUST00000168922
AA Change: V131A
|
SMART Domains |
Protein: ENSMUSP00000129196 Gene: ENSMUSG00000038838 AA Change: V131A
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 |
noncoding transcript
Transcript: ENSMUST00000171536
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170701
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174129
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 93.1%
|
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: 53 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca8b |
A |
C |
11: 109,832,433 (GRCm39) |
H1231Q |
possibly damaging |
Het |
Acbd4 |
T |
A |
11: 102,994,677 (GRCm39) |
|
probably null |
Het |
Atp13a4 |
T |
A |
16: 29,290,771 (GRCm39) |
Y226F |
possibly damaging |
Het |
Brd3 |
A |
C |
2: 27,352,534 (GRCm39) |
F132C |
probably damaging |
Het |
Btaf1 |
A |
T |
19: 36,933,924 (GRCm39) |
N184I |
probably benign |
Het |
Ccdc180 |
A |
G |
4: 45,903,887 (GRCm39) |
E351G |
possibly damaging |
Het |
Ccdc185 |
A |
T |
1: 182,574,918 (GRCm39) |
Y590* |
probably null |
Het |
Chi3l1 |
G |
A |
1: 134,116,980 (GRCm39) |
E315K |
probably benign |
Het |
Col6a6 |
T |
A |
9: 105,586,688 (GRCm39) |
M1778L |
probably benign |
Het |
Cyp3a59 |
A |
C |
5: 146,041,521 (GRCm39) |
Y355S |
probably damaging |
Het |
Cyp4a31 |
A |
G |
4: 115,431,908 (GRCm39) |
T396A |
probably benign |
Het |
Dnaaf6rt |
A |
T |
1: 31,262,296 (GRCm39) |
I93F |
probably damaging |
Het |
Dnah6 |
A |
T |
6: 73,121,948 (GRCm39) |
I1373N |
probably damaging |
Het |
Dop1b |
C |
A |
16: 93,574,274 (GRCm39) |
H1598N |
probably benign |
Het |
Erich4 |
T |
A |
7: 25,314,559 (GRCm39) |
K118M |
probably damaging |
Het |
Gkap1 |
A |
T |
13: 58,403,587 (GRCm39) |
V179E |
probably benign |
Het |
Gpr107 |
T |
G |
2: 31,068,267 (GRCm39) |
I243S |
possibly damaging |
Het |
Hs3st6 |
A |
G |
17: 24,977,504 (GRCm39) |
N328S |
probably damaging |
Het |
Kcnq5 |
A |
T |
1: 21,549,602 (GRCm39) |
I375N |
probably damaging |
Het |
Klhdc3 |
A |
T |
17: 46,987,892 (GRCm39) |
H266Q |
probably benign |
Het |
Krt71 |
C |
T |
15: 101,643,901 (GRCm39) |
G446R |
probably damaging |
Het |
L3mbtl2 |
A |
G |
15: 81,567,169 (GRCm39) |
T423A |
probably benign |
Het |
Mical3 |
T |
C |
6: 120,929,430 (GRCm39) |
E1812G |
probably damaging |
Het |
Nlrp1a |
A |
G |
11: 70,987,948 (GRCm39) |
I1174T |
probably benign |
Het |
Npas2 |
C |
A |
1: 39,373,849 (GRCm39) |
Q450K |
possibly damaging |
Het |
Nrp1 |
T |
A |
8: 129,194,870 (GRCm39) |
I442N |
probably damaging |
Het |
Or1j10 |
T |
A |
2: 36,267,006 (GRCm39) |
S73T |
probably damaging |
Het |
Or2y1 |
A |
T |
11: 49,385,848 (GRCm39) |
M163L |
probably benign |
Het |
Palld |
TGCGTAGCG |
TGCG |
8: 61,966,491 (GRCm39) |
|
probably null |
Het |
Pold3 |
T |
A |
7: 99,768,890 (GRCm39) |
Q36L |
possibly damaging |
Het |
Polg |
T |
C |
7: 79,109,534 (GRCm39) |
T428A |
probably benign |
Het |
Rfx7 |
T |
A |
9: 72,484,329 (GRCm39) |
V57E |
possibly damaging |
Het |
Rnf122 |
T |
G |
8: 31,602,177 (GRCm39) |
M1R |
probably null |
Het |
Sanbr |
A |
T |
11: 23,570,278 (GRCm39) |
Y207* |
probably null |
Het |
Scn10a |
T |
A |
9: 119,446,799 (GRCm39) |
T1410S |
probably damaging |
Het |
Serpinb13 |
T |
A |
1: 106,928,466 (GRCm39) |
V362E |
probably damaging |
Het |
Setdb1 |
T |
C |
3: 95,234,922 (GRCm39) |
N927S |
probably damaging |
Het |
Sft2d1 |
A |
G |
17: 8,539,470 (GRCm39) |
K91R |
probably benign |
Het |
Shprh |
A |
G |
10: 11,035,274 (GRCm39) |
H327R |
probably damaging |
Het |
Slc9b2 |
C |
A |
3: 135,042,156 (GRCm39) |
H478Q |
probably benign |
Het |
Styxl1 |
G |
T |
5: 135,782,737 (GRCm39) |
S117R |
probably damaging |
Het |
Synj2 |
T |
C |
17: 6,069,634 (GRCm39) |
F150L |
probably damaging |
Het |
Tep1 |
C |
A |
14: 51,082,970 (GRCm39) |
V1013L |
possibly damaging |
Het |
Tgfbi |
T |
A |
13: 56,778,468 (GRCm39) |
L413Q |
probably damaging |
Het |
Tmc5 |
G |
A |
7: 118,266,093 (GRCm39) |
R789Q |
probably damaging |
Het |
Tonsl |
T |
A |
15: 76,506,762 (GRCm39) |
I115F |
possibly damaging |
Het |
Trim38 |
A |
G |
13: 23,975,117 (GRCm39) |
Y352C |
probably damaging |
Het |
Txnl4a |
T |
A |
18: 80,250,536 (GRCm39) |
V44D |
probably benign |
Het |
Vmn2r105 |
A |
G |
17: 20,428,584 (GRCm39) |
C831R |
probably damaging |
Het |
Vmn2r26 |
T |
A |
6: 124,027,667 (GRCm39) |
I469N |
probably benign |
Het |
Vmn2r53 |
T |
C |
7: 12,315,533 (GRCm39) |
Y762C |
probably benign |
Het |
Vps13d |
T |
A |
4: 144,896,918 (GRCm39) |
Q334L |
probably benign |
Het |
Zfp277 |
A |
T |
12: 40,414,164 (GRCm39) |
I227N |
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 |
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'- TGCTGTGCAAGAAGATTCTGGGC -3'
(R):5'- TCATCCCAAGAGAAATGGACGAAGC -3'
Sequencing Primer
(F):5'- TGCAAGAAGATTCTGGGCTAGAAC -3'
(R):5'- TCAGTACCCTGACCAGAGTGTAG -3'
|
Posted On |
2014-01-29 |