Incidental Mutation 'R6273:Vars1'
| ID |
507496 |
| 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 |
044443-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R6273 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35232719 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Serine
at position 881
(L881S)
|
| 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: L881S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: L881S
| 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: L881S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: L881S
| 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: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 94.2%
|
| Validation Efficiency |
98% (78/80) |
| 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: 78 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 0610040J01Rik |
T |
A |
5: 64,055,561 (GRCm39) |
I99N |
probably damaging |
Het |
| Ank3 |
G |
A |
10: 69,838,395 (GRCm39) |
R1566K |
possibly damaging |
Het |
| Ankrd31 |
A |
G |
13: 96,988,181 (GRCm39) |
I1065V |
possibly damaging |
Het |
| Aox1 |
A |
G |
1: 58,378,831 (GRCm39) |
T1027A |
probably benign |
Het |
| Atm |
G |
A |
9: 53,399,222 (GRCm39) |
P1593L |
probably benign |
Het |
| Atp13a5 |
T |
G |
16: 29,167,555 (GRCm39) |
I132L |
probably benign |
Het |
| BC035044 |
A |
G |
6: 128,867,852 (GRCm39) |
|
probably benign |
Het |
| Cadm3 |
CT |
C |
1: 173,176,691 (GRCm39) |
|
probably benign |
Homo |
| Car3 |
C |
T |
3: 14,936,677 (GRCm39) |
P247S |
probably benign |
Het |
| Ccdc7a |
T |
C |
8: 129,513,819 (GRCm39) |
Y160C |
probably damaging |
Het |
| Cd1d1 |
A |
G |
3: 86,905,564 (GRCm39) |
V143A |
probably benign |
Het |
| Cemip2 |
T |
A |
19: 21,779,369 (GRCm39) |
V393E |
probably damaging |
Het |
| Cog6 |
A |
T |
3: 52,903,473 (GRCm39) |
F142I |
probably damaging |
Het |
| Cracd |
A |
T |
5: 77,005,568 (GRCm39) |
D643V |
unknown |
Het |
| Crhr1 |
T |
G |
11: 104,054,682 (GRCm39) |
N98K |
possibly damaging |
Het |
| Csf1 |
A |
G |
3: 107,656,479 (GRCm39) |
V72A |
probably damaging |
Het |
| Cwc15 |
T |
A |
9: 14,421,537 (GRCm39) |
I201K |
probably benign |
Het |
| Dgka |
T |
C |
10: 128,559,515 (GRCm39) |
K482R |
probably benign |
Het |
| Dnah7b |
T |
C |
1: 46,281,476 (GRCm39) |
S2846P |
possibly damaging |
Het |
| Dst |
T |
A |
1: 34,314,347 (GRCm39) |
I4199N |
probably damaging |
Het |
| Dusp7 |
A |
G |
9: 106,251,095 (GRCm39) |
T407A |
possibly damaging |
Het |
| Eml2 |
G |
A |
7: 18,935,088 (GRCm39) |
V432I |
probably damaging |
Het |
| Fem1a |
T |
C |
17: 56,564,083 (GRCm39) |
Y59H |
possibly damaging |
Het |
| Fetub |
C |
T |
16: 22,751,081 (GRCm39) |
R143C |
probably damaging |
Het |
| Filip1 |
A |
T |
9: 79,723,168 (GRCm39) |
D1150E |
probably benign |
Het |
| Gabra1 |
A |
G |
11: 42,031,138 (GRCm39) |
V264A |
probably damaging |
Het |
| Gm4131 |
T |
C |
14: 62,702,299 (GRCm39) |
E223G |
probably damaging |
Het |
| Gon4l |
T |
C |
3: 88,763,156 (GRCm39) |
V333A |
probably damaging |
Het |
| Gsk3b |
A |
G |
16: 38,028,408 (GRCm39) |
T289A |
probably benign |
Het |
| Hmcn2 |
T |
C |
2: 31,301,846 (GRCm39) |
S2912P |
probably damaging |
Het |
| Htr7 |
A |
T |
19: 36,018,969 (GRCm39) |
|
probably benign |
Het |
| Ibsp |
A |
G |
5: 104,458,167 (GRCm39) |
T235A |
probably benign |
Het |
| Ints13 |
A |
T |
6: 146,467,179 (GRCm39) |
D116E |
probably damaging |
Het |
| Irag1 |
G |
T |
7: 110,470,790 (GRCm39) |
H848N |
probably benign |
Het |
| Kctd19 |
T |
C |
8: 106,112,117 (GRCm39) |
N753S |
probably benign |
Het |
| Mdn1 |
A |
G |
4: 32,715,979 (GRCm39) |
N2054D |
probably benign |
Het |
| Mink1 |
A |
T |
11: 70,502,261 (GRCm39) |
K880* |
probably null |
Het |
| Myo15b |
T |
A |
11: 115,753,625 (GRCm39) |
L824Q |
possibly damaging |
Het |
| Napepld |
T |
C |
5: 21,870,320 (GRCm39) |
E366G |
probably benign |
Het |
| Obscn |
T |
A |
11: 58,967,819 (GRCm39) |
T2662S |
possibly damaging |
Het |
| Or2g7 |
T |
G |
17: 38,378,686 (GRCm39) |
L208R |
probably damaging |
Het |
| Or2n1b |
T |
A |
17: 38,459,833 (GRCm39) |
M118K |
possibly damaging |
Het |
| Or4k52 |
T |
C |
2: 111,611,567 (GRCm39) |
F301L |
probably benign |
Het |
| Or52p1 |
A |
G |
7: 104,267,102 (GRCm39) |
D72G |
probably damaging |
Het |
| Or5b12 |
A |
G |
19: 12,896,764 (GRCm39) |
V303A |
probably benign |
Het |
| Or6d13 |
A |
G |
6: 116,518,277 (GRCm39) |
T288A |
possibly damaging |
Het |
| Pah |
T |
C |
10: 87,412,077 (GRCm39) |
|
probably null |
Het |
| Panx3 |
T |
G |
9: 37,578,725 (GRCm39) |
I85L |
probably benign |
Het |
| Pate4 |
T |
C |
9: 35,519,086 (GRCm39) |
N94D |
probably benign |
Het |
| Pde4d |
A |
G |
13: 110,086,755 (GRCm39) |
M610V |
possibly damaging |
Het |
| Pik3c2b |
T |
C |
1: 132,994,449 (GRCm39) |
S138P |
probably benign |
Het |
| Pkn1 |
T |
C |
8: 84,398,899 (GRCm39) |
N696S |
probably damaging |
Het |
| Plppr2 |
A |
G |
9: 21,855,801 (GRCm39) |
E258G |
probably damaging |
Het |
| Plxnd1 |
A |
T |
6: 115,955,453 (GRCm39) |
M538K |
probably damaging |
Het |
| Prepl |
G |
T |
17: 85,390,696 (GRCm39) |
N87K |
probably benign |
Het |
| Prkag2 |
C |
A |
5: 25,152,534 (GRCm39) |
R190L |
probably damaging |
Het |
| Rara |
A |
G |
11: 98,861,048 (GRCm39) |
T179A |
probably benign |
Het |
| Rfx7 |
A |
G |
9: 72,524,279 (GRCm39) |
K490E |
possibly damaging |
Het |
| Rgsl1 |
C |
T |
1: 153,703,211 (GRCm39) |
V147M |
possibly damaging |
Het |
| Rph3a |
A |
G |
5: 121,083,485 (GRCm39) |
I595T |
possibly damaging |
Het |
| Rsf1 |
CG |
CGACGGCGGTG |
7: 97,229,115 (GRCm39) |
|
probably benign |
Homo |
| Slc35e2 |
C |
T |
4: 155,694,483 (GRCm39) |
P10L |
probably benign |
Het |
| Slc8a2 |
T |
C |
7: 15,879,259 (GRCm39) |
F582L |
possibly damaging |
Het |
| Sprr2e |
A |
G |
3: 92,260,171 (GRCm39) |
M1V |
probably null |
Het |
| Steap1 |
T |
A |
5: 5,790,827 (GRCm39) |
R40S |
possibly damaging |
Het |
| Tbc1d2 |
C |
T |
4: 46,629,912 (GRCm39) |
G252R |
probably benign |
Het |
| Thsd7a |
A |
T |
6: 12,408,835 (GRCm39) |
V729E |
probably damaging |
Het |
| Tmprss13 |
A |
G |
9: 45,256,630 (GRCm39) |
Y525C |
probably damaging |
Het |
| Tnik |
A |
T |
3: 28,631,649 (GRCm39) |
H383L |
possibly damaging |
Het |
| Vmn1r201 |
A |
C |
13: 22,659,385 (GRCm39) |
S200R |
probably damaging |
Het |
| Vmn2r130 |
A |
T |
17: 23,295,759 (GRCm39) |
H643L |
probably benign |
Het |
| Vmn2r14 |
A |
T |
5: 109,369,133 (GRCm39) |
W147R |
probably benign |
Het |
| Vps53 |
T |
C |
11: 75,992,844 (GRCm39) |
E367G |
probably benign |
Het |
| Xab2 |
C |
T |
8: 3,661,822 (GRCm39) |
G544S |
probably damaging |
Het |
| Ythdf3 |
T |
A |
3: 16,259,020 (GRCm39) |
V400E |
possibly damaging |
Het |
| Zfand5 |
C |
T |
19: 21,257,060 (GRCm39) |
P147S |
probably benign |
Het |
| Zfp768 |
A |
T |
7: 126,944,319 (GRCm39) |
|
probably null |
Het |
| Zswim8 |
A |
G |
14: 20,763,521 (GRCm39) |
M423V |
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 |
|
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 |
|
|
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'- ATTCCAAGTGGGCAGACTGG -3'
(R):5'- CTTCTACAGAGGATGCAGAGGAAC -3'
Sequencing Primer
(F):5'- GGGAGGGCCTTCAAGACTG -3'
(R):5'- TTGCCCACCTGCTGCAG -3'
|
| Posted On |
2018-03-15 |
Incidental Mutation