Incidental Mutation 'R1697:Vars1'
| ID |
192363 |
| 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 |
039730-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.963)
|
| Stock # |
R1697 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 35217198 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 419
(A419T)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000087315]
[ENSMUST00000172570]
[ENSMUST00000173584]
[ENSMUST00000174260]
|
| AlphaFold |
Q9Z1Q9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000087315
|
| SMART Domains |
Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
| 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: ENSMUST00000166828
AA Change: A419T
PolyPhen 2
Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000133003
Gene: ENSMUSG00000091747
AA Change: A419T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TLV_coat
|
37 |
582 |
2.4e-96 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172570
|
| SMART Domains |
Protein: ENSMUSP00000134245
Gene: ENSMUSG00000007029
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GST_C
|
2 |
76 |
1.2e-13 |
PFAM |
|
low complexity region
|
112 |
124 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172637
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173584
|
| SMART Domains |
Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
| 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 |
probably benign
Transcript: ENSMUST00000174260
|
| SMART Domains |
Protein: ENSMUSP00000134313
Gene: ENSMUSG00000007029
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GST_N
|
2 |
81 |
2.2e-16 |
PFAM |
|
Pfam:GST_C
|
96 |
198 |
2.1e-13 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.6%
- 20x: 93.3%
|
| Validation Efficiency |
99% (67/68) |
| 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: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930486L24Rik |
A |
T |
13: 60,992,928 (GRCm39) |
D250E |
probably damaging |
Het |
| 4930571K23Rik |
A |
G |
7: 124,968,201 (GRCm39) |
|
noncoding transcript |
Het |
| Acsl3 |
T |
C |
1: 78,683,114 (GRCm39) |
|
probably benign |
Het |
| Acsl6 |
C |
A |
11: 54,220,792 (GRCm39) |
T244K |
probably damaging |
Het |
| Adam26b |
T |
A |
8: 43,974,000 (GRCm39) |
N334I |
probably damaging |
Het |
| Adgrl4 |
C |
T |
3: 151,223,248 (GRCm39) |
T608M |
probably damaging |
Het |
| Aldh2 |
A |
G |
5: 121,716,404 (GRCm39) |
|
probably null |
Het |
| Alms1 |
A |
G |
6: 85,599,436 (GRCm39) |
T1890A |
possibly damaging |
Het |
| Capn7 |
C |
T |
14: 31,082,117 (GRCm39) |
T441M |
probably damaging |
Het |
| Cd9 |
A |
T |
6: 125,441,367 (GRCm39) |
C85S |
probably damaging |
Het |
| Chrm3 |
T |
C |
13: 9,928,794 (GRCm39) |
T81A |
probably damaging |
Het |
| Ctif |
A |
G |
18: 75,757,376 (GRCm39) |
|
probably benign |
Het |
| Dcc |
T |
A |
18: 71,503,808 (GRCm39) |
D950V |
probably damaging |
Het |
| Eif4g1 |
T |
C |
16: 20,498,530 (GRCm39) |
V422A |
probably damaging |
Het |
| Enthd1 |
A |
G |
15: 80,337,124 (GRCm39) |
S437P |
probably damaging |
Het |
| Fads1 |
A |
G |
19: 10,171,464 (GRCm39) |
|
probably benign |
Het |
| Fat3 |
T |
A |
9: 15,856,176 (GRCm39) |
I3869L |
probably benign |
Het |
| Fbxw5 |
T |
A |
2: 25,392,473 (GRCm39) |
V85E |
possibly damaging |
Het |
| Fcgbpl1 |
T |
A |
7: 27,853,772 (GRCm39) |
C1579S |
probably damaging |
Het |
| Fem1b |
T |
C |
9: 62,704,456 (GRCm39) |
D268G |
possibly damaging |
Het |
| Focad |
T |
C |
4: 88,327,225 (GRCm39) |
L1772P |
probably damaging |
Het |
| Gtf3a |
C |
A |
5: 146,888,723 (GRCm39) |
Q145K |
possibly damaging |
Het |
| Hacl1 |
T |
C |
14: 31,342,957 (GRCm39) |
|
probably null |
Het |
| Herc2 |
T |
A |
7: 55,803,653 (GRCm39) |
F2229L |
probably benign |
Het |
| Hs3st4 |
A |
T |
7: 123,996,080 (GRCm39) |
I249L |
probably benign |
Het |
| Iqsec1 |
A |
T |
6: 90,786,752 (GRCm39) |
Y7* |
probably null |
Het |
| Irag2 |
A |
G |
6: 145,083,341 (GRCm39) |
|
probably benign |
Het |
| Klk1b1 |
T |
A |
7: 43,619,750 (GRCm39) |
M103K |
probably benign |
Het |
| Krt5 |
A |
G |
15: 101,619,020 (GRCm39) |
V287A |
probably benign |
Het |
| Lgals12 |
T |
A |
19: 7,581,530 (GRCm39) |
Q59L |
possibly damaging |
Het |
| Loxl4 |
A |
G |
19: 42,593,379 (GRCm39) |
V264A |
possibly damaging |
Het |
| Lrp1b |
T |
C |
2: 40,712,695 (GRCm39) |
D3099G |
probably damaging |
Het |
| Mical3 |
G |
A |
6: 120,984,369 (GRCm39) |
T169I |
possibly damaging |
Het |
| Muc21 |
A |
C |
17: 35,931,540 (GRCm39) |
|
probably benign |
Het |
| Myef2l |
G |
A |
3: 10,154,613 (GRCm39) |
V461I |
possibly damaging |
Het |
| Myh7b |
A |
C |
2: 155,462,054 (GRCm39) |
S317R |
probably damaging |
Het |
| Nrbp1 |
T |
A |
5: 31,403,157 (GRCm39) |
I210N |
probably damaging |
Het |
| Nsd1 |
A |
T |
13: 55,361,872 (GRCm39) |
|
probably null |
Het |
| Nup58 |
A |
T |
14: 60,482,119 (GRCm39) |
|
probably benign |
Het |
| Or1j17 |
C |
T |
2: 36,578,259 (GRCm39) |
L82F |
probably damaging |
Het |
| Or2t49 |
A |
T |
11: 58,392,502 (GRCm39) |
S293R |
probably damaging |
Het |
| Or5h22 |
A |
G |
16: 58,895,270 (GRCm39) |
Y58H |
probably damaging |
Het |
| Or5i1 |
T |
A |
2: 87,612,929 (GRCm39) |
I15N |
possibly damaging |
Het |
| Or6c2b |
T |
C |
10: 128,947,737 (GRCm39) |
T186A |
probably benign |
Het |
| Pcnx2 |
A |
G |
8: 126,577,087 (GRCm39) |
Y982H |
probably damaging |
Het |
| Pias3 |
T |
C |
3: 96,609,541 (GRCm39) |
L312P |
probably damaging |
Het |
| Plekhm1 |
G |
A |
11: 103,267,710 (GRCm39) |
P754S |
probably damaging |
Het |
| Ppp2r5c |
T |
A |
12: 110,512,057 (GRCm39) |
L145* |
probably null |
Het |
| Ppp2r5c |
T |
A |
12: 110,527,906 (GRCm39) |
|
probably benign |
Het |
| Pramel29 |
A |
C |
4: 143,935,162 (GRCm39) |
I193S |
probably damaging |
Het |
| Proser3 |
T |
C |
7: 30,239,446 (GRCm39) |
M553V |
probably benign |
Het |
| Shf |
G |
A |
2: 122,199,163 (GRCm39) |
P51S |
probably damaging |
Het |
| Smurf2 |
A |
T |
11: 106,715,514 (GRCm39) |
D664E |
possibly damaging |
Het |
| Spag9 |
G |
A |
11: 93,887,391 (GRCm39) |
A99T |
probably benign |
Het |
| Stim1 |
T |
G |
7: 102,003,713 (GRCm39) |
C49G |
probably damaging |
Het |
| Stk32c |
T |
C |
7: 138,701,740 (GRCm39) |
I238V |
probably benign |
Het |
| Tenm2 |
C |
T |
11: 35,954,004 (GRCm39) |
G1236R |
possibly damaging |
Het |
| Tfb2m |
T |
A |
1: 179,372,464 (GRCm39) |
E133V |
probably null |
Het |
| Tmem209 |
A |
T |
6: 30,497,867 (GRCm39) |
C143S |
probably benign |
Het |
| Tnr |
T |
G |
1: 159,679,600 (GRCm39) |
N191K |
probably benign |
Het |
| Vmn2r111 |
T |
C |
17: 22,767,041 (GRCm39) |
S819G |
probably benign |
Het |
| Wls |
T |
C |
3: 159,602,995 (GRCm39) |
V136A |
probably benign |
Het |
| Ybx2 |
C |
T |
11: 69,830,887 (GRCm39) |
S217L |
probably benign |
Het |
| Zfp82 |
T |
C |
7: 29,756,779 (GRCm39) |
D37G |
probably benign |
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 |
|
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 |
|
R4856:Vars1
|
UTSW |
17 |
35,234,702 (GRCm39) |
missense |
probably benign |
0.37 |
|
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'- GGAAGTCTTGTTCCCGCTGATTTCG -3'
(R):5'- GGACTTGCTTAAGGCCACTTACCTG -3'
Sequencing Primer
(F):5'- GGCCTCCCTTAGAGAAGTTAATG -3'
(R):5'- ggactctgctttgggacaatac -3'
|
| Posted On |
2014-05-14 |
Incidental Mutation