Incidental Mutation 'R0266:Vars1'
ID |
34958 |
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 |
038492-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.963)
|
Stock # |
R0266 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 35232845 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Arginine
at position 896
(S896R)
|
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: S896R
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: S896R
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 |
unknown
Transcript: ENSMUST00000173142
AA Change: S14R
|
SMART Domains |
Protein: ENSMUSP00000134669 Gene: ENSMUSG00000007029 AA Change: S14R
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: S896R
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: S896R
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: ENSMUST00000174084
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173302
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173336
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173911
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 98.3%
- 3x: 97.2%
- 10x: 94.9%
- 20x: 89.8%
|
Validation Efficiency |
100% (79/79) |
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: 77 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700001K19Rik |
A |
G |
12: 110,635,188 (GRCm39) |
S117P |
possibly damaging |
Het |
Aars2 |
T |
C |
17: 45,818,436 (GRCm39) |
|
probably benign |
Het |
Acot11 |
T |
C |
4: 106,607,185 (GRCm39) |
D466G |
probably damaging |
Het |
Adgrd1 |
G |
A |
5: 129,216,658 (GRCm39) |
A342T |
probably benign |
Het |
Apbb2 |
A |
T |
5: 66,459,954 (GRCm39) |
N714K |
probably benign |
Het |
Aqp12 |
C |
A |
1: 92,934,572 (GRCm39) |
H150N |
possibly damaging |
Het |
Brinp3 |
T |
A |
1: 146,558,418 (GRCm39) |
L114* |
probably null |
Het |
Ccng2 |
T |
C |
5: 93,419,148 (GRCm39) |
|
probably benign |
Het |
Cd36 |
T |
A |
5: 18,003,250 (GRCm39) |
R265S |
probably benign |
Het |
Ces4a |
T |
C |
8: 105,868,598 (GRCm39) |
L104S |
probably benign |
Het |
Clca4b |
T |
C |
3: 144,628,547 (GRCm39) |
I387V |
probably damaging |
Het |
Cul7 |
T |
A |
17: 46,965,521 (GRCm39) |
H566Q |
probably benign |
Het |
Ddx60 |
A |
T |
8: 62,486,527 (GRCm39) |
H1646L |
possibly damaging |
Het |
Dntt |
T |
C |
19: 41,047,566 (GRCm39) |
I503T |
probably damaging |
Het |
Dynlt1a |
T |
G |
17: 6,367,670 (GRCm39) |
E2D |
probably benign |
Het |
Efemp2 |
G |
T |
19: 5,528,027 (GRCm39) |
C78F |
probably damaging |
Het |
Esco1 |
T |
C |
18: 10,594,605 (GRCm39) |
E227G |
probably benign |
Het |
Fezf2 |
T |
A |
14: 12,342,607 (GRCm38) |
K419N |
probably damaging |
Het |
Gm17541 |
A |
T |
12: 4,739,487 (GRCm39) |
|
probably benign |
Het |
Gm2381 |
G |
A |
7: 42,469,372 (GRCm39) |
Q251* |
probably null |
Het |
Gm4782 |
T |
G |
6: 50,587,674 (GRCm39) |
S686R |
probably damaging |
Het |
Grin3a |
G |
A |
4: 49,665,501 (GRCm39) |
R1045* |
probably null |
Het |
Grm8 |
T |
C |
6: 27,285,895 (GRCm39) |
Y839C |
probably damaging |
Het |
Gtf3c1 |
G |
A |
7: 125,243,306 (GRCm39) |
P1766L |
possibly damaging |
Het |
Herc2 |
T |
A |
7: 55,856,326 (GRCm39) |
H3921Q |
probably damaging |
Het |
Hes6 |
A |
T |
1: 91,340,026 (GRCm39) |
D143E |
possibly damaging |
Het |
Hmcn2 |
A |
G |
2: 31,284,839 (GRCm39) |
E2055G |
probably benign |
Het |
Hmcn2 |
G |
A |
2: 31,335,365 (GRCm39) |
|
probably benign |
Het |
Ikzf3 |
A |
G |
11: 98,358,143 (GRCm39) |
L398P |
probably benign |
Het |
Il10ra |
A |
T |
9: 45,176,950 (GRCm39) |
I125N |
probably benign |
Het |
Kcnb2 |
G |
A |
1: 15,783,137 (GRCm39) |
|
probably benign |
Het |
Krt77 |
T |
C |
15: 101,777,813 (GRCm39) |
R81G |
possibly damaging |
Het |
Lrrc40 |
T |
A |
3: 157,747,298 (GRCm39) |
|
probably null |
Het |
Man1a2 |
C |
T |
3: 100,489,350 (GRCm39) |
R543Q |
probably damaging |
Het |
Mansc1 |
T |
C |
6: 134,587,670 (GRCm39) |
D169G |
probably benign |
Het |
Mdn1 |
T |
A |
4: 32,741,835 (GRCm39) |
S3869T |
probably damaging |
Het |
Mettl14 |
A |
T |
3: 123,176,475 (GRCm39) |
S58T |
probably benign |
Het |
Mrpl4 |
T |
C |
9: 20,914,610 (GRCm39) |
V62A |
probably benign |
Het |
Myh3 |
A |
G |
11: 66,984,498 (GRCm39) |
D1085G |
possibly damaging |
Het |
Myo5c |
C |
A |
9: 75,191,498 (GRCm39) |
|
probably benign |
Het |
Naalad2 |
G |
T |
9: 18,262,239 (GRCm39) |
|
probably benign |
Het |
Nat3 |
A |
G |
8: 68,000,432 (GRCm39) |
T104A |
probably benign |
Het |
Nek4 |
A |
G |
14: 30,679,253 (GRCm39) |
E198G |
probably damaging |
Het |
Olfm1 |
A |
G |
2: 28,119,619 (GRCm39) |
Y403C |
probably damaging |
Het |
Or5w11 |
C |
A |
2: 87,459,626 (GRCm39) |
T273K |
possibly damaging |
Het |
Or7e177 |
A |
T |
9: 20,212,454 (GRCm39) |
R320S |
probably benign |
Het |
Osbpl1a |
T |
A |
18: 13,004,220 (GRCm39) |
|
probably null |
Het |
Pax7 |
G |
A |
4: 139,507,047 (GRCm39) |
S330L |
possibly damaging |
Het |
Pcdhb15 |
C |
A |
18: 37,608,329 (GRCm39) |
D520E |
probably damaging |
Het |
Pgm3 |
T |
C |
9: 86,449,586 (GRCm39) |
T145A |
probably benign |
Het |
Phox2b |
G |
A |
5: 67,253,968 (GRCm39) |
|
probably null |
Het |
Pik3r6 |
A |
T |
11: 68,417,234 (GRCm39) |
R59* |
probably null |
Het |
Pold1 |
A |
G |
7: 44,190,449 (GRCm39) |
|
probably benign |
Het |
Ppp1r21 |
T |
C |
17: 88,876,500 (GRCm39) |
|
probably benign |
Het |
Prl5a1 |
A |
G |
13: 28,333,970 (GRCm39) |
K158E |
possibly damaging |
Het |
Rag2 |
T |
G |
2: 101,460,948 (GRCm39) |
C419W |
probably damaging |
Het |
Reln |
A |
G |
5: 22,193,774 (GRCm39) |
S1395P |
probably damaging |
Het |
Retnlb |
T |
G |
16: 48,639,022 (GRCm39) |
Y74* |
probably null |
Het |
Robo3 |
A |
G |
9: 37,333,936 (GRCm39) |
S633P |
probably damaging |
Het |
Ryr1 |
A |
G |
7: 28,740,104 (GRCm39) |
S3941P |
probably damaging |
Het |
Scnn1b |
A |
G |
7: 121,511,698 (GRCm39) |
N370S |
probably damaging |
Het |
Slc6a5 |
C |
A |
7: 49,588,156 (GRCm39) |
|
probably benign |
Het |
Sort1 |
T |
A |
3: 108,252,247 (GRCm39) |
N481K |
probably benign |
Het |
Sptlc3 |
T |
A |
2: 139,437,957 (GRCm39) |
I417K |
possibly damaging |
Het |
Svil |
T |
A |
18: 5,099,063 (GRCm39) |
|
probably benign |
Het |
Taf4b |
T |
C |
18: 14,946,134 (GRCm39) |
|
probably benign |
Het |
Tchp |
T |
C |
5: 114,847,394 (GRCm39) |
M71T |
possibly damaging |
Het |
Thsd4 |
T |
A |
9: 59,904,417 (GRCm39) |
H233L |
probably benign |
Het |
Tmem217 |
G |
T |
17: 29,745,573 (GRCm39) |
N52K |
possibly damaging |
Het |
Tmem38b |
T |
C |
4: 53,840,765 (GRCm39) |
L60S |
probably damaging |
Het |
Uqcrfs1 |
A |
C |
13: 30,725,146 (GRCm39) |
N131K |
probably benign |
Het |
Vmn1r170 |
A |
T |
7: 23,305,906 (GRCm39) |
M103L |
probably benign |
Het |
Vmn2r22 |
T |
C |
6: 123,614,363 (GRCm39) |
Y409C |
probably damaging |
Het |
Vmn2r92 |
C |
T |
17: 18,388,219 (GRCm39) |
A408V |
probably damaging |
Het |
Wdr49 |
A |
T |
3: 75,359,103 (GRCm39) |
I8N |
possibly damaging |
Het |
Zfp648 |
T |
A |
1: 154,080,632 (GRCm39) |
Y264N |
probably damaging |
Het |
Zmym1 |
A |
C |
4: 126,941,818 (GRCm39) |
F857V |
possibly 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 |
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 |
|
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'- AGCAAGTCTCTTGGCAATGTCATCG -3'
(R):5'- ACAGAGTCCAAAGCGTAGGGCATC -3'
Sequencing Primer
(F):5'- TGGCAATGTCATCGACCCC -3'
(R):5'- GGAATCCCTGCTGGAAAGTC -3'
|
Posted On |
2013-05-09 |