Incidental Mutation 'R0445:Vars1'
ID |
39341 |
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 |
038646-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.963)
|
Stock # |
R0445 (G1)
|
Quality Score |
160 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 35230785 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Histidine to Arginine
at position 557
(H557R)
|
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: H557R
PolyPhen 2
Score 0.110 (Sensitivity: 0.93; Specificity: 0.86)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: H557R
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 |
probably benign
Transcript: ENSMUST00000173584
AA Change: H557R
PolyPhen 2
Score 0.309 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: H557R
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: ENSMUST00000173302
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174084
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173911
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173336
|
Meta Mutation Damage Score |
0.5321 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 95.9%
- 20x: 91.3%
|
Validation Efficiency |
100% (77/77) |
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: 61 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700067P10Rik |
A |
C |
17: 48,400,542 (GRCm39) |
|
probably null |
Het |
A2m |
C |
T |
6: 121,634,914 (GRCm39) |
T687I |
probably damaging |
Het |
Acsbg1 |
A |
G |
9: 54,523,179 (GRCm39) |
S483P |
probably damaging |
Het |
Adam22 |
T |
A |
5: 8,230,591 (GRCm39) |
|
probably benign |
Het |
Aggf1 |
A |
G |
13: 95,490,509 (GRCm39) |
V595A |
possibly damaging |
Het |
Aplf |
A |
T |
6: 87,640,734 (GRCm39) |
L71I |
probably damaging |
Het |
Arid3c |
G |
T |
4: 41,725,172 (GRCm39) |
P292T |
probably benign |
Het |
Bltp1 |
T |
C |
3: 37,054,214 (GRCm39) |
V3111A |
probably damaging |
Het |
Brms1l |
T |
A |
12: 55,908,191 (GRCm39) |
Y213* |
probably null |
Het |
C87436 |
T |
A |
6: 86,426,832 (GRCm39) |
S332T |
possibly damaging |
Het |
Cad |
G |
A |
5: 31,230,053 (GRCm39) |
A1454T |
probably benign |
Het |
Cdkn3 |
T |
C |
14: 47,004,857 (GRCm39) |
|
probably null |
Het |
Cnot1 |
A |
G |
8: 96,486,836 (GRCm39) |
C624R |
probably damaging |
Het |
Cntnap5c |
A |
T |
17: 58,411,738 (GRCm39) |
I541F |
probably benign |
Het |
Dennd1b |
A |
G |
1: 139,095,503 (GRCm39) |
|
probably benign |
Het |
Dscam |
A |
T |
16: 96,573,703 (GRCm39) |
I753N |
probably damaging |
Het |
Eef2 |
C |
CN |
10: 81,014,604 (GRCm39) |
|
probably null |
Het |
Epg5 |
T |
A |
18: 78,057,399 (GRCm39) |
V1826D |
possibly damaging |
Het |
Epha8 |
T |
C |
4: 136,659,711 (GRCm39) |
Y755C |
probably damaging |
Het |
Esco1 |
A |
T |
18: 10,574,989 (GRCm39) |
N694K |
probably damaging |
Het |
Fermt3 |
T |
C |
19: 6,980,667 (GRCm39) |
H300R |
probably benign |
Het |
Galnt5 |
C |
A |
2: 57,888,962 (GRCm39) |
F187L |
probably benign |
Het |
Gm17067 |
A |
G |
7: 42,358,046 (GRCm39) |
I152T |
probably benign |
Het |
Gnb3 |
T |
C |
6: 124,814,218 (GRCm39) |
D154G |
possibly damaging |
Het |
Gpr155 |
G |
A |
2: 73,200,488 (GRCm39) |
|
probably benign |
Het |
Hdac3 |
A |
G |
18: 38,076,777 (GRCm39) |
I240T |
probably damaging |
Het |
Ifitm1 |
A |
T |
7: 140,548,354 (GRCm39) |
|
probably null |
Het |
Kif1b |
A |
T |
4: 149,272,466 (GRCm39) |
L1455Q |
probably benign |
Het |
Krt1 |
A |
C |
15: 101,756,056 (GRCm39) |
L388R |
probably damaging |
Het |
Lrp1 |
T |
A |
10: 127,426,505 (GRCm39) |
K635* |
probably null |
Het |
Map3k2 |
A |
G |
18: 32,350,263 (GRCm39) |
Y371C |
probably damaging |
Het |
Mcu |
T |
C |
10: 59,292,467 (GRCm39) |
|
probably benign |
Het |
Mkrn1 |
C |
T |
6: 39,381,788 (GRCm39) |
V167I |
probably benign |
Het |
Mrpl9 |
T |
A |
3: 94,352,198 (GRCm39) |
|
probably benign |
Het |
Naip2 |
T |
C |
13: 100,298,395 (GRCm39) |
Y547C |
possibly damaging |
Het |
Nup88 |
G |
A |
11: 70,838,555 (GRCm39) |
T487I |
probably benign |
Het |
Oas3 |
G |
A |
5: 120,894,210 (GRCm39) |
R39C |
probably damaging |
Het |
Obscn |
C |
T |
11: 58,890,161 (GRCm39) |
R7457H |
unknown |
Het |
Or13c25 |
G |
A |
4: 52,910,849 (GRCm39) |
T315M |
probably benign |
Het |
Or2y13 |
T |
A |
11: 49,414,784 (GRCm39) |
V78E |
probably damaging |
Het |
Paf1 |
T |
C |
7: 28,095,113 (GRCm39) |
S118P |
probably damaging |
Het |
Parp4 |
T |
A |
14: 56,840,205 (GRCm39) |
|
probably null |
Het |
Pcdh15 |
A |
T |
10: 74,178,381 (GRCm39) |
Y157F |
probably damaging |
Het |
Pex10 |
G |
A |
4: 155,153,531 (GRCm39) |
|
probably null |
Het |
Phrf1 |
C |
T |
7: 140,827,244 (GRCm39) |
|
probably benign |
Het |
Polr3a |
G |
T |
14: 24,504,989 (GRCm39) |
D1090E |
probably benign |
Het |
Ppfia4 |
A |
C |
1: 134,255,027 (GRCm39) |
L276R |
probably benign |
Het |
Rdh16f1 |
T |
C |
10: 127,626,736 (GRCm39) |
L263S |
probably benign |
Het |
Ryr3 |
T |
C |
2: 112,696,399 (GRCm39) |
D967G |
probably benign |
Het |
Shc1 |
G |
T |
3: 89,333,844 (GRCm39) |
A226S |
probably damaging |
Het |
Slc4a1 |
A |
G |
11: 102,245,192 (GRCm39) |
V585A |
probably benign |
Het |
Stk38l |
T |
A |
6: 146,677,184 (GRCm39) |
S461T |
probably benign |
Het |
Tbkbp1 |
A |
T |
11: 97,040,295 (GRCm39) |
S40T |
probably damaging |
Het |
Tet1 |
A |
G |
10: 62,715,720 (GRCm39) |
M25T |
probably benign |
Het |
Themis |
A |
G |
10: 28,658,007 (GRCm39) |
R192G |
probably damaging |
Het |
Tmem144 |
T |
C |
3: 79,732,661 (GRCm39) |
T206A |
probably benign |
Het |
Tmem74b |
G |
A |
2: 151,548,879 (GRCm39) |
R202H |
probably damaging |
Het |
Trpm1 |
T |
C |
7: 63,894,590 (GRCm39) |
|
probably benign |
Het |
Zbtb12 |
C |
A |
17: 35,115,277 (GRCm39) |
A354E |
possibly damaging |
Het |
Zfp143 |
A |
T |
7: 109,660,324 (GRCm39) |
|
probably benign |
Het |
Zftraf1 |
T |
C |
15: 76,532,457 (GRCm39) |
H217R |
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 |
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 |
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'- TCAGACACAGAGCCTTCTGTCACC -3'
(R):5'- GTCCGAACAGTTCTCATATCCAGCC -3'
Sequencing Primer
(F):5'- TGGCAACAACCCGGATTG -3'
(R):5'- ATATCCAGCCCCAGTCCTG -3'
|
Posted On |
2013-05-23 |