Incidental Mutation 'R5907:Vars1'
ID |
460753 |
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 |
044104-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.963)
|
Stock # |
R5907 (G1)
|
Quality Score |
196 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 35231352 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Serine
at position 655
(N655S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000084572
(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: N655S
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: N655S
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 |
noncoding transcript
Transcript: ENSMUST00000173336
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000173584
AA Change: N655S
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: N655S
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: ENSMUST00000174084
|
Meta Mutation Damage Score |
0.7928 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.9%
- 20x: 93.7%
|
Validation Efficiency |
93% (92/99) |
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: 84 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4931429L15Rik |
A |
T |
9: 46,218,120 (GRCm39) |
I206N |
probably damaging |
Het |
Aadac |
T |
A |
3: 59,947,248 (GRCm39) |
D315E |
probably damaging |
Het |
Abcc8 |
A |
G |
7: 45,773,330 (GRCm39) |
F800L |
probably benign |
Het |
Adamts16 |
C |
A |
13: 70,877,029 (GRCm39) |
C1204F |
probably damaging |
Het |
Adcy7 |
A |
G |
8: 89,038,856 (GRCm39) |
T291A |
possibly damaging |
Het |
AI182371 |
G |
T |
2: 34,976,134 (GRCm39) |
Q255K |
possibly damaging |
Het |
Aig1 |
A |
T |
10: 13,677,528 (GRCm39) |
|
probably benign |
Het |
Ak5 |
T |
C |
3: 152,321,589 (GRCm39) |
D266G |
probably damaging |
Het |
Ank1 |
A |
T |
8: 23,630,220 (GRCm39) |
E93D |
probably damaging |
Het |
Bop1 |
T |
C |
15: 76,340,117 (GRCm39) |
D153G |
probably damaging |
Het |
Bub1 |
G |
T |
2: 127,661,142 (GRCm39) |
N316K |
probably benign |
Het |
Capn1 |
T |
C |
19: 6,047,827 (GRCm39) |
N412S |
probably benign |
Het |
Cdca4 |
A |
G |
12: 112,785,339 (GRCm39) |
S130P |
probably benign |
Het |
Cdh23 |
A |
T |
10: 60,264,158 (GRCm39) |
D663E |
probably damaging |
Het |
Clca3a1 |
T |
C |
3: 144,455,403 (GRCm39) |
|
probably benign |
Het |
Csmd2 |
C |
T |
4: 128,091,178 (GRCm39) |
P239L |
probably damaging |
Het |
Dlg2 |
A |
T |
7: 91,646,579 (GRCm39) |
|
probably benign |
Het |
Dnpep |
C |
T |
1: 75,288,635 (GRCm39) |
|
probably null |
Het |
Dop1b |
A |
T |
16: 93,598,469 (GRCm39) |
H1878L |
probably damaging |
Het |
Dscam |
C |
T |
16: 96,622,120 (GRCm39) |
D444N |
probably damaging |
Het |
Emc9 |
C |
T |
14: 55,819,569 (GRCm39) |
|
probably null |
Het |
Ero1b |
T |
A |
13: 12,615,207 (GRCm39) |
I346N |
probably damaging |
Het |
Etv3 |
A |
G |
3: 87,442,850 (GRCm39) |
T145A |
probably benign |
Het |
Fam170a |
T |
A |
18: 50,415,321 (GRCm39) |
|
probably null |
Het |
Fap |
A |
T |
2: 62,374,700 (GRCm39) |
I261N |
probably damaging |
Het |
Fbn2 |
T |
C |
18: 58,178,409 (GRCm39) |
N1943S |
probably damaging |
Het |
Glb1l3 |
A |
T |
9: 26,737,679 (GRCm39) |
V466E |
probably damaging |
Het |
Gm10521 |
A |
T |
1: 171,724,070 (GRCm39) |
H127L |
unknown |
Het |
Gm8186 |
G |
T |
17: 26,318,130 (GRCm39) |
N22K |
probably damaging |
Het |
Gpr132 |
A |
C |
12: 112,815,717 (GRCm39) |
L370V |
probably benign |
Het |
Hectd1 |
A |
T |
12: 51,845,537 (GRCm39) |
H449Q |
probably damaging |
Het |
Hook3 |
A |
G |
8: 26,534,306 (GRCm39) |
|
probably benign |
Het |
Ift140 |
A |
G |
17: 25,311,345 (GRCm39) |
D1180G |
probably benign |
Het |
Isoc2b |
A |
T |
7: 4,852,577 (GRCm39) |
|
probably null |
Het |
Itga4 |
C |
T |
2: 79,153,000 (GRCm39) |
H896Y |
probably benign |
Het |
Itga7 |
T |
C |
10: 128,778,850 (GRCm39) |
Y326H |
probably damaging |
Het |
Itpr3 |
A |
T |
17: 27,336,867 (GRCm39) |
E2397V |
probably damaging |
Het |
Jtb |
T |
G |
3: 90,142,884 (GRCm39) |
|
probably null |
Het |
Klk15 |
A |
G |
7: 43,588,183 (GRCm39) |
T164A |
probably benign |
Het |
Kmt2e |
C |
A |
5: 23,669,704 (GRCm39) |
H64N |
probably damaging |
Het |
Lamtor3 |
T |
A |
3: 137,633,054 (GRCm39) |
|
probably benign |
Het |
Laptm4b |
A |
G |
15: 34,258,830 (GRCm39) |
I35V |
possibly damaging |
Het |
Lrrc1 |
A |
C |
9: 77,341,379 (GRCm39) |
L393R |
probably damaging |
Het |
Ltn1 |
A |
G |
16: 87,178,391 (GRCm39) |
S1613P |
possibly damaging |
Het |
Mtmr4 |
T |
A |
11: 87,502,876 (GRCm39) |
W920R |
probably damaging |
Het |
Nbeal1 |
T |
C |
1: 60,267,950 (GRCm39) |
|
probably benign |
Het |
Nup133 |
A |
G |
8: 124,643,038 (GRCm39) |
Y761H |
possibly damaging |
Het |
Nwd2 |
T |
A |
5: 63,963,326 (GRCm39) |
V970D |
probably damaging |
Het |
Or4c126 |
A |
G |
2: 89,824,301 (GRCm39) |
H188R |
probably benign |
Het |
Or6n1 |
T |
C |
1: 173,916,785 (GRCm39) |
Y60H |
probably benign |
Het |
Or8k24 |
A |
T |
2: 86,216,218 (GRCm39) |
S181R |
probably damaging |
Het |
Osbp |
C |
T |
19: 11,951,240 (GRCm39) |
L262F |
probably damaging |
Het |
Phf8-ps |
G |
T |
17: 33,285,124 (GRCm39) |
D559E |
probably benign |
Het |
Phldb2 |
G |
T |
16: 45,645,551 (GRCm39) |
D343E |
probably damaging |
Het |
Phrf1 |
T |
A |
7: 140,840,453 (GRCm39) |
M1216K |
possibly damaging |
Het |
Phyh |
A |
T |
2: 4,935,462 (GRCm39) |
|
probably null |
Het |
Plekhf1 |
A |
T |
7: 37,921,594 (GRCm39) |
|
probably null |
Het |
Rars1 |
T |
C |
11: 35,719,475 (GRCm39) |
N116D |
probably damaging |
Het |
Rnf44 |
T |
A |
13: 54,830,621 (GRCm39) |
Q181L |
possibly damaging |
Het |
Rpe65 |
T |
C |
3: 159,321,319 (GRCm39) |
|
probably null |
Het |
Scaf1 |
A |
G |
7: 44,663,016 (GRCm39) |
|
probably benign |
Het |
Serpinb11 |
A |
T |
1: 107,299,919 (GRCm39) |
R88S |
probably benign |
Het |
Slc7a7 |
T |
C |
14: 54,616,560 (GRCm39) |
N174S |
probably damaging |
Het |
Slc9a5 |
T |
C |
8: 106,083,807 (GRCm39) |
|
probably null |
Het |
Slfn1 |
C |
A |
11: 83,012,002 (GRCm39) |
N39K |
possibly damaging |
Het |
Snx20 |
G |
A |
8: 89,353,923 (GRCm39) |
A269V |
possibly damaging |
Het |
Snx6 |
A |
G |
12: 54,801,104 (GRCm39) |
Y298H |
probably damaging |
Het |
Stk32c |
C |
T |
7: 138,700,590 (GRCm39) |
R213Q |
probably benign |
Het |
Tgfbr1 |
A |
T |
4: 47,396,555 (GRCm39) |
I190F |
probably damaging |
Het |
Ube2d2b |
T |
A |
5: 107,978,498 (GRCm39) |
F50I |
probably damaging |
Het |
Ubl5 |
G |
A |
9: 20,557,830 (GRCm39) |
|
probably benign |
Het |
Ubqln5 |
T |
G |
7: 103,777,781 (GRCm39) |
T348P |
possibly damaging |
Het |
Usp46 |
T |
C |
5: 74,197,746 (GRCm39) |
D22G |
probably benign |
Het |
Vmn2r103 |
A |
C |
17: 20,032,715 (GRCm39) |
I830L |
possibly damaging |
Het |
Vmn2r26 |
T |
A |
6: 124,016,830 (GRCm39) |
N431K |
probably benign |
Het |
Vmn2r4 |
G |
T |
3: 64,298,487 (GRCm39) |
P547Q |
probably damaging |
Het |
Yy1 |
T |
A |
12: 108,772,354 (GRCm39) |
|
probably benign |
Het |
Zbtb2 |
A |
T |
10: 4,318,592 (GRCm39) |
L478Q |
possibly damaging |
Het |
Zfp12 |
T |
C |
5: 143,225,743 (GRCm39) |
F17S |
probably damaging |
Het |
Zfp219 |
T |
A |
14: 52,244,606 (GRCm39) |
|
probably null |
Het |
Zfp629 |
G |
A |
7: 127,209,542 (GRCm39) |
H756Y |
probably damaging |
Het |
Zfp748 |
T |
C |
13: 67,689,292 (GRCm39) |
K656R |
possibly damaging |
Het |
Zfp958 |
T |
A |
8: 4,679,072 (GRCm39) |
Y366N |
probably benign |
Het |
Zp3 |
C |
T |
5: 136,017,377 (GRCm39) |
T396I |
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 |
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 |
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'- TGACTATGAGGTTGGGCAGC -3'
(R):5'- ACAGCGCACGTACCATTGTG -3'
Sequencing Primer
(F):5'- GGCCATTAGCATCATGGACTC -3'
(R):5'- CGTACCATTGTGGCCTTAACAGAG -3'
|
Posted On |
2017-02-28 |