Incidental Mutation 'R4856:Vars1'
ID |
374003 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vars1
|
Ensembl Gene |
ENSMUSG00000007029 |
Gene Name |
valyl-tRNA synthetase 1 |
Synonyms |
Bat6, Vars2, G7a, Bat-6, D17H6S56E, Vars |
MMRRC Submission |
042467-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.963)
|
Stock # |
R4856 (G1)
|
Quality Score |
152 |
Status
|
Not validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 35234702 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glutamic Acid
at position 1177
(V1177E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000133994
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000007245]
[ENSMUST00000087315]
[ENSMUST00000172499]
[ENSMUST00000173584]
|
AlphaFold |
Q9Z1Q9 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000007245
|
SMART Domains |
Protein: ENSMUSP00000007245 Gene: ENSMUSG00000007030
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
VWA
|
314 |
499 |
2.59e0 |
SMART |
low complexity region
|
683 |
701 |
N/A |
INTRINSIC |
low complexity region
|
840 |
861 |
N/A |
INTRINSIC |
low complexity region
|
864 |
877 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000087315
AA Change: V1177E
PolyPhen 2
Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: V1177E
Domain | Start | End | E-Value | Type |
Pfam:GST_N
|
2 |
81 |
5.7e-16 |
PFAM |
Pfam:GST_C
|
107 |
198 |
7.3e-13 |
PFAM |
low complexity region
|
234 |
256 |
N/A |
INTRINSIC |
low complexity region
|
261 |
271 |
N/A |
INTRINSIC |
Pfam:tRNA-synt_1
|
307 |
938 |
2e-197 |
PFAM |
Pfam:tRNA-synt_1g
|
336 |
496 |
6e-6 |
PFAM |
Pfam:tRNA-synt_1_2
|
555 |
623 |
1.9e-11 |
PFAM |
Pfam:Anticodon_1
|
983 |
1138 |
2.6e-34 |
PFAM |
low complexity region
|
1153 |
1174 |
N/A |
INTRINSIC |
low complexity region
|
1207 |
1225 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000172499
|
SMART Domains |
Protein: ENSMUSP00000133418 Gene: ENSMUSG00000007030
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
VWA
|
314 |
478 |
7.28e0 |
SMART |
low complexity region
|
662 |
680 |
N/A |
INTRINSIC |
low complexity region
|
819 |
840 |
N/A |
INTRINSIC |
low complexity region
|
843 |
856 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172637
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172999
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000173142
|
SMART Domains |
Protein: ENSMUSP00000134669 Gene: ENSMUSG00000007029
Domain | Start | End | E-Value | Type |
SCOP:d1gaxa3
|
32 |
67 |
3e-7 |
SMART |
PDB:1IYW|B
|
36 |
122 |
4e-6 |
PDB |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173302
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000173584
AA Change: V1177E
PolyPhen 2
Score 0.374 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: V1177E
Domain | Start | End | E-Value | Type |
low complexity region
|
25 |
38 |
N/A |
INTRINSIC |
low complexity region
|
44 |
58 |
N/A |
INTRINSIC |
low complexity region
|
78 |
89 |
N/A |
INTRINSIC |
Pfam:GST_C
|
96 |
198 |
7.8e-14 |
PFAM |
low complexity region
|
234 |
256 |
N/A |
INTRINSIC |
low complexity region
|
261 |
271 |
N/A |
INTRINSIC |
Pfam:tRNA-synt_1
|
307 |
938 |
1.9e-200 |
PFAM |
Pfam:tRNA-synt_1g
|
336 |
493 |
2.1e-7 |
PFAM |
Pfam:tRNA-synt_1_2
|
555 |
623 |
1.1e-12 |
PFAM |
Pfam:Anticodon_1
|
983 |
1138 |
7.2e-36 |
PFAM |
low complexity region
|
1153 |
1174 |
N/A |
INTRINSIC |
coiled coil region
|
1197 |
1225 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174084
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173336
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173911
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.4%
- 20x: 92.8%
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this gene belongs to class-I aminoacyl-tRNA synthetase family and is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 85 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aebp2 |
G |
A |
6: 140,589,799 (GRCm39) |
|
probably null |
Het |
Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
Atp2b4 |
T |
A |
1: 133,634,518 (GRCm39) |
I1177L |
probably benign |
Het |
Bub3 |
A |
T |
7: 131,163,297 (GRCm39) |
D76V |
probably damaging |
Het |
Cacna2d4 |
G |
A |
6: 119,255,217 (GRCm39) |
R578Q |
possibly damaging |
Het |
Caprin2 |
A |
C |
6: 148,774,509 (GRCm39) |
S268A |
probably benign |
Het |
Card6 |
T |
C |
15: 5,134,623 (GRCm39) |
|
probably null |
Het |
Cdk13 |
A |
G |
13: 17,894,319 (GRCm39) |
S1103P |
probably benign |
Het |
Cfap221 |
T |
C |
1: 119,861,934 (GRCm39) |
T614A |
probably damaging |
Het |
Cfap221 |
T |
A |
1: 119,912,488 (GRCm39) |
Y133F |
probably damaging |
Het |
Clcc1 |
A |
G |
3: 108,584,154 (GRCm39) |
T513A |
probably benign |
Het |
Clec4g |
T |
A |
8: 3,766,419 (GRCm39) |
|
probably benign |
Het |
Cntln |
A |
C |
4: 84,889,466 (GRCm39) |
E316D |
probably benign |
Het |
Cpne2 |
T |
A |
8: 95,290,592 (GRCm39) |
D392E |
probably benign |
Het |
Cry1 |
G |
T |
10: 84,984,634 (GRCm39) |
P147T |
probably damaging |
Het |
Cyp4a29 |
T |
C |
4: 115,110,078 (GRCm39) |
V440A |
probably benign |
Het |
Ddx46 |
A |
G |
13: 55,786,012 (GRCm39) |
D64G |
unknown |
Het |
Dhx34 |
A |
G |
7: 15,949,367 (GRCm39) |
S354P |
possibly damaging |
Het |
Ecm2 |
A |
T |
13: 49,676,263 (GRCm39) |
I327F |
possibly damaging |
Het |
Elavl3 |
T |
C |
9: 21,937,614 (GRCm39) |
K189E |
possibly damaging |
Het |
Enam |
A |
T |
5: 88,636,593 (GRCm39) |
R82* |
probably null |
Het |
Erf |
A |
G |
7: 24,945,636 (GRCm39) |
V45A |
probably damaging |
Het |
Fat3 |
T |
A |
9: 15,932,626 (GRCm39) |
I1436F |
probably benign |
Het |
Flnc |
T |
C |
6: 29,447,889 (GRCm39) |
Y1231H |
probably damaging |
Het |
Ggta1 |
T |
A |
2: 35,292,803 (GRCm39) |
H180L |
possibly damaging |
Het |
Grin2c |
T |
C |
11: 115,151,616 (GRCm39) |
T115A |
probably damaging |
Het |
H6pd |
C |
T |
4: 150,067,235 (GRCm39) |
V384M |
possibly damaging |
Het |
Hba-x |
A |
G |
11: 32,227,008 (GRCm39) |
E39G |
probably benign |
Het |
Hnrnpul2 |
C |
T |
19: 8,807,191 (GRCm39) |
P618S |
probably benign |
Het |
Hpse2 |
C |
T |
19: 42,777,396 (GRCm39) |
R590H |
probably damaging |
Het |
Ighv1-54 |
C |
A |
12: 115,157,423 (GRCm39) |
G75C |
probably damaging |
Het |
Ighv8-11 |
C |
A |
12: 115,530,774 (GRCm39) |
R118L |
possibly damaging |
Het |
Iqcm |
A |
T |
8: 76,615,228 (GRCm39) |
R436S |
possibly damaging |
Het |
Islr |
T |
C |
9: 58,064,889 (GRCm39) |
D206G |
probably damaging |
Het |
Itih1 |
A |
G |
14: 30,658,658 (GRCm39) |
|
probably null |
Het |
Jam2 |
G |
A |
16: 84,598,490 (GRCm39) |
D34N |
probably benign |
Het |
Klhl14 |
A |
T |
18: 21,691,029 (GRCm39) |
|
probably null |
Het |
Lama2 |
TTTGCGCATT |
TTT |
10: 26,919,639 (GRCm39) |
|
probably null |
Het |
Lrrc66 |
A |
G |
5: 73,765,910 (GRCm39) |
F378L |
probably benign |
Het |
Map10 |
T |
A |
8: 126,397,431 (GRCm39) |
Y275N |
probably damaging |
Het |
Mpi |
T |
C |
9: 57,452,590 (GRCm39) |
Y314C |
probably damaging |
Het |
Mpp3 |
A |
G |
11: 101,915,962 (GRCm39) |
Y55H |
probably benign |
Het |
Nectin4 |
T |
C |
1: 171,212,383 (GRCm39) |
V327A |
possibly damaging |
Het |
Nlrp12 |
T |
A |
7: 3,289,072 (GRCm39) |
D480V |
probably damaging |
Het |
Nolc1 |
GAGCAGCAGCAGCAGCAGCAGCAGCAGC |
GAGCAGCAGCAGCAGCAGCAGCAGC |
19: 46,071,594 (GRCm39) |
|
probably benign |
Het |
Notch2 |
A |
T |
3: 98,009,735 (GRCm39) |
Y554F |
probably damaging |
Het |
Nrsn2 |
T |
C |
2: 152,211,531 (GRCm39) |
K167E |
probably benign |
Het |
Olr1 |
T |
A |
6: 129,470,559 (GRCm39) |
K203* |
probably null |
Het |
Or14j8 |
A |
T |
17: 38,262,962 (GRCm39) |
S318T |
probably benign |
Het |
Or2ag13 |
T |
A |
7: 106,473,177 (GRCm39) |
I92F |
probably damaging |
Het |
Or5b117 |
T |
C |
19: 13,431,885 (GRCm39) |
|
probably null |
Het |
Or8b3 |
A |
T |
9: 38,314,764 (GRCm39) |
N195I |
probably damaging |
Het |
Or9i2 |
T |
A |
19: 13,815,643 (GRCm39) |
E298V |
probably damaging |
Het |
Osbpl9 |
T |
C |
4: 108,925,564 (GRCm39) |
N485S |
probably benign |
Het |
Pbk |
T |
A |
14: 66,052,650 (GRCm39) |
H164Q |
probably damaging |
Het |
Pfn2 |
G |
T |
3: 57,754,874 (GRCm39) |
N10K |
probably damaging |
Het |
Pik3ca |
A |
G |
3: 32,491,312 (GRCm39) |
D133G |
probably damaging |
Het |
Pramel27 |
G |
T |
4: 143,579,873 (GRCm39) |
R486L |
probably benign |
Het |
Prl6a1 |
A |
T |
13: 27,502,983 (GRCm39) |
D193V |
probably damaging |
Het |
Rad21 |
G |
T |
15: 51,831,896 (GRCm39) |
P395Q |
probably damaging |
Het |
Reps1 |
T |
A |
10: 17,999,373 (GRCm39) |
I720N |
probably damaging |
Het |
Rpn2 |
T |
C |
2: 157,159,964 (GRCm39) |
|
probably null |
Het |
Rreb1 |
G |
A |
13: 38,115,034 (GRCm39) |
V798M |
possibly damaging |
Het |
Sardh |
C |
T |
2: 27,134,489 (GRCm39) |
R9H |
probably benign |
Het |
Scgb3a2 |
C |
T |
18: 43,899,819 (GRCm39) |
P36S |
probably damaging |
Het |
Scn10a |
C |
A |
9: 119,523,375 (GRCm39) |
G6V |
possibly damaging |
Het |
Scn10a |
C |
T |
9: 119,523,376 (GRCm39) |
G6R |
possibly damaging |
Het |
Scn3a |
T |
C |
2: 65,291,376 (GRCm39) |
D1790G |
probably damaging |
Het |
Sec24b |
A |
T |
3: 129,777,619 (GRCm39) |
H1226Q |
probably benign |
Het |
Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
Slc12a3 |
G |
A |
8: 95,078,438 (GRCm39) |
|
probably null |
Het |
Slitrk6 |
T |
C |
14: 110,989,315 (GRCm39) |
T131A |
probably damaging |
Het |
Spata1 |
C |
G |
3: 146,175,529 (GRCm39) |
D326H |
probably damaging |
Het |
Tex52 |
A |
T |
6: 128,361,951 (GRCm39) |
|
probably null |
Het |
Tma16 |
A |
C |
8: 66,934,129 (GRCm39) |
C75W |
probably damaging |
Het |
Tmem67 |
G |
A |
4: 12,089,416 (GRCm39) |
|
probably benign |
Het |
Trgv4 |
T |
C |
13: 19,369,236 (GRCm39) |
V29A |
probably benign |
Het |
Trmt10a |
A |
T |
3: 137,854,146 (GRCm39) |
K75* |
probably null |
Het |
Ttc3 |
T |
C |
16: 94,191,142 (GRCm39) |
V228A |
probably benign |
Het |
Ttn |
T |
C |
2: 76,561,644 (GRCm39) |
D28954G |
probably damaging |
Het |
Uggt2 |
A |
G |
14: 119,273,376 (GRCm39) |
|
probably null |
Het |
Vmn1r59 |
T |
C |
7: 5,457,532 (GRCm39) |
D76G |
possibly damaging |
Het |
Vmn2r114 |
G |
T |
17: 23,527,008 (GRCm39) |
A508E |
probably benign |
Het |
Vps41 |
G |
A |
13: 19,013,425 (GRCm39) |
V348M |
probably damaging |
Het |
Zbtb43 |
T |
C |
2: 33,343,944 (GRCm39) |
H427R |
probably damaging |
Het |
|
Other mutations in Vars1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01520:Vars1
|
APN |
17 |
35,232,849 (GRCm39) |
missense |
probably benign |
0.00 |
IGL02160:Vars1
|
APN |
17 |
35,220,478 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02303:Vars1
|
APN |
17 |
35,234,460 (GRCm39) |
splice site |
probably benign |
|
IGL03027:Vars1
|
APN |
17 |
35,232,663 (GRCm39) |
missense |
probably damaging |
1.00 |
Maladroit
|
UTSW |
17 |
35,224,451 (GRCm39) |
missense |
probably benign |
0.30 |
Whoops
|
UTSW |
17 |
35,232,620 (GRCm39) |
missense |
probably damaging |
1.00 |
FR4304:Vars1
|
UTSW |
17 |
35,234,965 (GRCm39) |
small insertion |
probably benign |
|
FR4548:Vars1
|
UTSW |
17 |
35,234,967 (GRCm39) |
small insertion |
probably benign |
|
FR4548:Vars1
|
UTSW |
17 |
35,234,965 (GRCm39) |
small insertion |
probably benign |
|
FR4589:Vars1
|
UTSW |
17 |
35,234,964 (GRCm39) |
small insertion |
probably benign |
|
R0045:Vars1
|
UTSW |
17 |
35,229,595 (GRCm39) |
missense |
probably damaging |
1.00 |
R0045:Vars1
|
UTSW |
17 |
35,229,595 (GRCm39) |
missense |
probably damaging |
1.00 |
R0045:Vars1
|
UTSW |
17 |
35,217,042 (GRCm39) |
missense |
probably benign |
0.13 |
R0266:Vars1
|
UTSW |
17 |
35,232,845 (GRCm39) |
missense |
probably benign |
0.00 |
R0267:Vars1
|
UTSW |
17 |
35,230,572 (GRCm39) |
splice site |
probably benign |
|
R0391:Vars1
|
UTSW |
17 |
35,230,462 (GRCm39) |
missense |
possibly damaging |
0.79 |
R0445:Vars1
|
UTSW |
17 |
35,230,785 (GRCm39) |
missense |
probably benign |
0.31 |
R0449:Vars1
|
UTSW |
17 |
35,231,703 (GRCm39) |
splice site |
probably null |
|
R0557:Vars1
|
UTSW |
17 |
35,223,960 (GRCm39) |
missense |
possibly damaging |
0.90 |
R0559:Vars1
|
UTSW |
17 |
35,233,034 (GRCm39) |
nonsense |
probably null |
|
R0730:Vars1
|
UTSW |
17 |
35,233,276 (GRCm39) |
missense |
probably damaging |
1.00 |
R0748:Vars1
|
UTSW |
17 |
35,216,988 (GRCm39) |
missense |
probably damaging |
1.00 |
R1692:Vars1
|
UTSW |
17 |
35,232,701 (GRCm39) |
missense |
probably damaging |
1.00 |
R1693:Vars1
|
UTSW |
17 |
35,217,172 (GRCm39) |
missense |
probably benign |
0.31 |
R1697:Vars1
|
UTSW |
17 |
35,217,198 (GRCm39) |
missense |
probably benign |
0.43 |
R1699:Vars1
|
UTSW |
17 |
35,233,734 (GRCm39) |
missense |
possibly damaging |
0.93 |
R1712:Vars1
|
UTSW |
17 |
35,233,728 (GRCm39) |
missense |
probably damaging |
1.00 |
R1989:Vars1
|
UTSW |
17 |
35,230,814 (GRCm39) |
missense |
possibly damaging |
0.94 |
R2349:Vars1
|
UTSW |
17 |
35,234,728 (GRCm39) |
missense |
probably benign |
|
R2365:Vars1
|
UTSW |
17 |
35,234,428 (GRCm39) |
missense |
probably benign |
0.01 |
R3790:Vars1
|
UTSW |
17 |
35,218,310 (GRCm39) |
missense |
probably benign |
0.34 |
R4615:Vars1
|
UTSW |
17 |
35,232,857 (GRCm39) |
missense |
probably damaging |
0.97 |
R4844:Vars1
|
UTSW |
17 |
35,230,588 (GRCm39) |
missense |
probably damaging |
1.00 |
R4886:Vars1
|
UTSW |
17 |
35,234,702 (GRCm39) |
missense |
probably benign |
0.37 |
R5570:Vars1
|
UTSW |
17 |
35,235,214 (GRCm39) |
missense |
probably benign |
0.04 |
R5706:Vars1
|
UTSW |
17 |
35,224,457 (GRCm39) |
splice site |
probably null |
|
R5858:Vars1
|
UTSW |
17 |
35,224,451 (GRCm39) |
missense |
probably benign |
0.30 |
R5907:Vars1
|
UTSW |
17 |
35,231,352 (GRCm39) |
missense |
probably damaging |
1.00 |
R5917:Vars1
|
UTSW |
17 |
35,231,491 (GRCm39) |
missense |
probably damaging |
0.99 |
R5944:Vars1
|
UTSW |
17 |
35,232,620 (GRCm39) |
missense |
probably damaging |
1.00 |
R6023:Vars1
|
UTSW |
17 |
35,220,585 (GRCm39) |
missense |
probably damaging |
1.00 |
R6073:Vars1
|
UTSW |
17 |
35,220,505 (GRCm39) |
missense |
probably benign |
|
R6273:Vars1
|
UTSW |
17 |
35,232,719 (GRCm39) |
missense |
probably damaging |
1.00 |
R6390:Vars1
|
UTSW |
17 |
35,234,615 (GRCm39) |
missense |
probably benign |
0.00 |
R6658:Vars1
|
UTSW |
17 |
35,234,717 (GRCm39) |
missense |
probably benign |
0.03 |
R7067:Vars1
|
UTSW |
17 |
35,230,455 (GRCm39) |
missense |
probably damaging |
0.98 |
R7387:Vars1
|
UTSW |
17 |
35,223,768 (GRCm39) |
nonsense |
probably null |
|
R7954:Vars1
|
UTSW |
17 |
35,234,960 (GRCm39) |
missense |
probably benign |
0.01 |
R8139:Vars1
|
UTSW |
17 |
35,230,480 (GRCm39) |
missense |
probably benign |
0.16 |
R8347:Vars1
|
UTSW |
17 |
35,234,953 (GRCm39) |
missense |
possibly damaging |
0.92 |
R8387:Vars1
|
UTSW |
17 |
35,229,490 (GRCm39) |
missense |
probably damaging |
0.99 |
R8855:Vars1
|
UTSW |
17 |
35,234,620 (GRCm39) |
missense |
probably benign |
0.00 |
R8866:Vars1
|
UTSW |
17 |
35,234,620 (GRCm39) |
missense |
probably benign |
0.00 |
R9131:Vars1
|
UTSW |
17 |
35,223,773 (GRCm39) |
missense |
possibly damaging |
0.77 |
R9620:Vars1
|
UTSW |
17 |
35,235,001 (GRCm39) |
missense |
unknown |
|
R9695:Vars1
|
UTSW |
17 |
35,231,564 (GRCm39) |
missense |
possibly damaging |
0.82 |
Z1177:Vars1
|
UTSW |
17 |
35,230,453 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TGCGTGCTGACTACAACCTG -3'
(R):5'- AGTACAGTGACAAAGGGCCC -3'
Sequencing Primer
(F):5'- ACCAGGCCCGACTGTAAG -3'
(R):5'- TGTGCAGGAGTCCACAGG -3'
|
Posted On |
2016-03-01 |