Incidental Mutation 'R1712:Vars1'
ID |
190717 |
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 |
039745-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.964)
|
Stock # |
R1712 (G1)
|
Quality Score |
202 |
Status
|
Not validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 35233728 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Proline
at position 1018
(L1018P)
|
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 damaging
Transcript: ENSMUST00000087315
AA Change: L1018P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: L1018P
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 damaging
Transcript: ENSMUST00000173584
AA Change: L1018P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: L1018P
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: ENSMUST00000173911
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173336
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174084
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.2%
|
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: 83 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Accs |
T |
A |
2: 93,678,448 (GRCm39) |
E12D |
probably damaging |
Het |
Ahnak2 |
C |
A |
12: 112,748,998 (GRCm39) |
R283L |
probably benign |
Het |
BC005624 |
T |
C |
2: 30,864,020 (GRCm39) |
E191G |
probably damaging |
Het |
C1galt1 |
A |
G |
6: 7,871,217 (GRCm39) |
N351S |
probably benign |
Het |
Ccdc162 |
T |
C |
10: 41,415,427 (GRCm39) |
R2179G |
probably benign |
Het |
Ccdc88c |
G |
A |
12: 100,905,284 (GRCm39) |
T1108M |
probably benign |
Het |
Cd47 |
T |
C |
16: 49,714,543 (GRCm39) |
L184P |
probably damaging |
Het |
Cdc40 |
T |
C |
10: 40,717,372 (GRCm39) |
K440E |
probably damaging |
Het |
Cenpe |
G |
A |
3: 134,971,694 (GRCm39) |
V2262I |
probably damaging |
Het |
Cep290 |
A |
G |
10: 100,390,361 (GRCm39) |
K2035E |
probably benign |
Het |
Cks1brt |
G |
T |
8: 85,898,172 (GRCm39) |
L8F |
probably benign |
Het |
Col17a1 |
T |
C |
19: 47,637,442 (GRCm39) |
|
probably benign |
Het |
Coro6 |
A |
T |
11: 77,360,293 (GRCm39) |
N421I |
probably benign |
Het |
Cps1 |
T |
C |
1: 67,269,440 (GRCm39) |
S1480P |
probably damaging |
Het |
Csrnp3 |
G |
T |
2: 65,832,826 (GRCm39) |
A110S |
probably damaging |
Het |
Cyp2d10 |
G |
T |
15: 82,287,240 (GRCm39) |
T461K |
probably damaging |
Het |
Dmxl2 |
A |
G |
9: 54,308,769 (GRCm39) |
V1994A |
probably benign |
Het |
Dnah11 |
T |
A |
12: 118,160,379 (GRCm39) |
N117I |
probably benign |
Het |
Dnajc3 |
A |
G |
14: 119,195,307 (GRCm39) |
Y74C |
probably damaging |
Het |
Fam13c |
T |
A |
10: 70,390,403 (GRCm39) |
F555I |
possibly damaging |
Het |
Fbn1 |
T |
A |
2: 125,188,354 (GRCm39) |
D1495V |
probably damaging |
Het |
Fbrsl1 |
T |
C |
5: 110,595,862 (GRCm39) |
T58A |
probably benign |
Het |
Gjd3 |
A |
G |
11: 102,691,706 (GRCm39) |
I99T |
possibly damaging |
Het |
Glce |
T |
C |
9: 61,977,857 (GRCm39) |
N9S |
probably damaging |
Het |
Gosr1 |
T |
C |
11: 76,641,704 (GRCm39) |
T125A |
possibly damaging |
Het |
Ifi27l2a |
T |
A |
12: 103,406,202 (GRCm39) |
|
probably null |
Het |
Jph1 |
C |
T |
1: 17,167,456 (GRCm39) |
D125N |
possibly damaging |
Het |
Kbtbd12 |
A |
T |
6: 88,595,676 (GRCm39) |
S51R |
probably damaging |
Het |
Klra9 |
A |
T |
6: 130,166,659 (GRCm39) |
|
probably null |
Het |
Kmo |
A |
T |
1: 175,484,289 (GRCm39) |
M340L |
probably benign |
Het |
Lama1 |
T |
C |
17: 68,024,181 (GRCm39) |
I93T |
possibly damaging |
Het |
Limk2 |
A |
T |
11: 3,308,104 (GRCm39) |
|
probably null |
Het |
Mgat5 |
C |
A |
1: 127,248,375 (GRCm39) |
N92K |
probably benign |
Het |
Mib2 |
T |
A |
4: 155,739,256 (GRCm39) |
I908F |
probably damaging |
Het |
Mical1 |
T |
G |
10: 41,356,359 (GRCm39) |
L304R |
probably damaging |
Het |
Mtbp |
G |
T |
15: 55,434,690 (GRCm39) |
|
probably null |
Het |
Myo3a |
T |
C |
2: 22,455,004 (GRCm39) |
Y70H |
probably damaging |
Het |
Neb |
T |
C |
2: 52,133,401 (GRCm39) |
Y3379C |
probably damaging |
Het |
Neurod2 |
G |
T |
11: 98,218,029 (GRCm39) |
N378K |
probably damaging |
Het |
Oog4 |
G |
A |
4: 143,166,484 (GRCm39) |
L107F |
probably damaging |
Het |
Or2g25 |
A |
G |
17: 37,970,799 (GRCm39) |
S142P |
probably benign |
Het |
Or4k40 |
T |
A |
2: 111,251,003 (GRCm39) |
M98L |
probably benign |
Het |
Or6x1 |
A |
G |
9: 40,099,161 (GRCm39) |
Y250C |
probably damaging |
Het |
Or8k20 |
T |
A |
2: 86,106,337 (GRCm39) |
T165S |
probably damaging |
Het |
Pfdn6 |
T |
C |
17: 34,158,528 (GRCm39) |
Y82C |
probably damaging |
Het |
Pla2g4d |
C |
A |
2: 120,107,971 (GRCm39) |
A313S |
possibly damaging |
Het |
Ptcd3 |
C |
A |
6: 71,885,637 (GRCm39) |
E30* |
probably null |
Het |
Rai1 |
A |
G |
11: 60,078,428 (GRCm39) |
T831A |
probably benign |
Het |
Rims1 |
G |
A |
1: 22,367,172 (GRCm39) |
T1176M |
probably damaging |
Het |
Rin1 |
A |
C |
19: 5,105,171 (GRCm39) |
I744L |
probably benign |
Het |
Rora |
T |
A |
9: 69,282,771 (GRCm39) |
S430T |
probably benign |
Het |
Rsph10b |
T |
A |
5: 143,873,967 (GRCm39) |
S23T |
probably damaging |
Het |
Ryr1 |
T |
C |
7: 28,746,928 (GRCm39) |
N3773S |
probably benign |
Het |
Scn4a |
A |
G |
11: 106,230,180 (GRCm39) |
Y543H |
probably damaging |
Het |
Scn4a |
C |
A |
11: 106,236,373 (GRCm39) |
G296C |
probably benign |
Het |
Scn7a |
T |
C |
2: 66,535,447 (GRCm39) |
T435A |
probably benign |
Het |
Shank2 |
G |
T |
7: 143,964,890 (GRCm39) |
D833Y |
probably damaging |
Het |
Slc9a2 |
T |
C |
1: 40,802,770 (GRCm39) |
S607P |
possibly damaging |
Het |
Slx4 |
G |
A |
16: 3,809,458 (GRCm39) |
R346W |
probably damaging |
Het |
Spata20 |
A |
T |
11: 94,371,340 (GRCm39) |
C675S |
probably benign |
Het |
Suclg2 |
A |
T |
6: 95,563,997 (GRCm39) |
I196N |
probably damaging |
Het |
Sv2b |
G |
A |
7: 74,798,807 (GRCm39) |
H272Y |
possibly damaging |
Het |
Svep1 |
T |
C |
4: 58,070,629 (GRCm39) |
I2386V |
probably benign |
Het |
Taf13 |
A |
T |
3: 108,488,445 (GRCm39) |
E109D |
possibly damaging |
Het |
Tanc2 |
A |
G |
11: 105,790,606 (GRCm39) |
T976A |
probably benign |
Het |
Tax1bp1 |
A |
G |
6: 52,706,311 (GRCm39) |
Y104C |
probably damaging |
Het |
Tfeb |
T |
C |
17: 48,099,911 (GRCm39) |
|
probably null |
Het |
Tlr9 |
T |
C |
9: 106,101,248 (GRCm39) |
Y180H |
probably damaging |
Het |
Trappc9 |
G |
A |
15: 72,897,816 (GRCm39) |
R377W |
probably damaging |
Het |
Ttc12 |
T |
A |
9: 49,356,499 (GRCm39) |
T510S |
probably benign |
Het |
Ubqln1 |
T |
C |
13: 58,339,895 (GRCm39) |
E280G |
probably damaging |
Het |
Urm1 |
T |
C |
2: 29,731,437 (GRCm39) |
W44R |
probably damaging |
Het |
Usp32 |
A |
T |
11: 84,933,406 (GRCm39) |
I34N |
probably benign |
Het |
Vcan |
A |
T |
13: 89,869,894 (GRCm39) |
V206D |
probably damaging |
Het |
Vim |
T |
C |
2: 13,583,270 (GRCm39) |
V224A |
probably damaging |
Het |
Vmn2r106 |
G |
T |
17: 20,498,997 (GRCm39) |
H305N |
probably benign |
Het |
Vmn2r78 |
A |
G |
7: 86,604,132 (GRCm39) |
N770S |
probably damaging |
Het |
Wdr33 |
T |
A |
18: 32,029,684 (GRCm39) |
L961Q |
unknown |
Het |
Xylt2 |
A |
G |
11: 94,559,575 (GRCm39) |
S356P |
possibly damaging |
Het |
Zbtb14 |
A |
G |
17: 69,694,575 (GRCm39) |
N91S |
probably damaging |
Het |
Zc3h6 |
T |
C |
2: 128,858,654 (GRCm39) |
L895S |
probably damaging |
Het |
Zc3h7b |
C |
T |
15: 81,661,289 (GRCm39) |
P376L |
probably benign |
Het |
Zfp131 |
T |
C |
13: 120,228,079 (GRCm39) |
T523A |
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 |
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 |
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'- TAGTGTGATGGCCTACTGCCTGAC -3'
(R):5'- CTCCTCTGTGACAAAGGGCATGAAG -3'
Sequencing Primer
(F):5'- GCCTACTGCCTGACGTTTC -3'
(R):5'- CAGGTTTTAGACACTCCTAGAGATGG -3'
|
Posted On |
2014-05-14 |