Incidental Mutation 'R1989:Vars1'
ID |
223108 |
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 |
040001-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.963)
|
Stock # |
R1989 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
17 |
Chromosomal Location |
35219963-35235298 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 35230814 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Phenylalanine to Leucine
at position 567
(F567L)
|
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 |
possibly damaging
Transcript: ENSMUST00000087315
AA Change: F567L
PolyPhen 2
Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000084572 Gene: ENSMUSG00000007029 AA Change: F567L
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 |
possibly damaging
Transcript: ENSMUST00000173584
AA Change: F567L
PolyPhen 2
Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000133994 Gene: ENSMUSG00000007029 AA Change: F567L
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: ENSMUST00000173336
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174084
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173911
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.3%
|
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 |
1700034J05Rik |
T |
A |
6: 146,854,394 (GRCm39) |
D216V |
possibly damaging |
Het |
Acaca |
T |
C |
11: 84,153,355 (GRCm39) |
M921T |
probably damaging |
Het |
Actn2 |
A |
T |
13: 12,355,276 (GRCm39) |
W36R |
probably benign |
Het |
Adcy9 |
A |
T |
16: 4,116,591 (GRCm39) |
V643D |
probably damaging |
Het |
Agbl4 |
A |
T |
4: 111,423,879 (GRCm39) |
T302S |
possibly damaging |
Het |
Akap13 |
A |
G |
7: 75,354,264 (GRCm39) |
N1795S |
probably benign |
Het |
Ang |
T |
A |
14: 51,339,008 (GRCm39) |
C50S |
probably damaging |
Het |
Anxa13 |
T |
A |
15: 58,205,344 (GRCm39) |
|
noncoding transcript |
Het |
Asxl3 |
T |
C |
18: 22,585,420 (GRCm39) |
V115A |
probably damaging |
Het |
B4galt5 |
A |
T |
2: 167,146,923 (GRCm39) |
W304R |
probably damaging |
Het |
Bptf |
T |
C |
11: 106,965,652 (GRCm39) |
K1118E |
probably damaging |
Het |
Cacna1b |
T |
C |
2: 24,611,386 (GRCm39) |
Y335C |
probably damaging |
Het |
Catsperb |
A |
T |
12: 101,568,970 (GRCm39) |
I881F |
probably damaging |
Het |
Ccn1 |
A |
T |
3: 145,353,498 (GRCm39) |
Y355N |
probably benign |
Het |
Chrm5 |
A |
G |
2: 112,310,597 (GRCm39) |
V173A |
probably damaging |
Het |
Cyfip2 |
A |
T |
11: 46,144,825 (GRCm39) |
Y676* |
probably null |
Het |
Cyp2f2 |
A |
G |
7: 26,828,628 (GRCm39) |
D90G |
probably damaging |
Het |
Dnah5 |
T |
C |
15: 28,343,737 (GRCm39) |
I2379T |
probably damaging |
Het |
E2f8 |
T |
C |
7: 48,523,028 (GRCm39) |
E349G |
probably benign |
Het |
Ebf1 |
T |
C |
11: 44,512,793 (GRCm39) |
M134T |
probably damaging |
Het |
Fn1 |
T |
C |
1: 71,690,784 (GRCm39) |
H59R |
probably damaging |
Het |
Focad |
T |
C |
4: 88,151,021 (GRCm39) |
|
probably null |
Het |
Gabra1 |
A |
T |
11: 42,045,842 (GRCm39) |
D89E |
probably damaging |
Het |
Hip1r |
G |
T |
5: 124,127,761 (GRCm39) |
V90F |
probably damaging |
Het |
Ifi213 |
C |
A |
1: 173,396,374 (GRCm39) |
|
probably null |
Het |
Kcnj9 |
A |
G |
1: 172,153,716 (GRCm39) |
I136T |
probably benign |
Het |
Kmt2c |
A |
G |
5: 25,703,542 (GRCm39) |
S3P |
possibly damaging |
Het |
Lrrc4b |
GAGAAG |
GAG |
7: 44,111,654 (GRCm39) |
|
probably benign |
Het |
Lrrk1 |
G |
A |
7: 65,931,432 (GRCm39) |
S43L |
probably damaging |
Het |
Macf1 |
A |
G |
4: 123,391,519 (GRCm39) |
|
probably null |
Het |
Mad1l1 |
A |
G |
5: 140,289,425 (GRCm39) |
S167P |
probably benign |
Het |
Maml3 |
G |
T |
3: 51,605,179 (GRCm39) |
A64D |
probably damaging |
Het |
Mgat4c |
T |
C |
10: 102,214,020 (GRCm39) |
M1T |
probably null |
Het |
Mkrn2os |
G |
T |
6: 115,566,311 (GRCm39) |
T88K |
probably damaging |
Het |
Mob3c |
T |
C |
4: 115,688,754 (GRCm39) |
Y96H |
probably damaging |
Het |
Mpo |
T |
A |
11: 87,694,298 (GRCm39) |
I96N |
probably damaging |
Het |
Mup17 |
T |
A |
4: 61,511,860 (GRCm39) |
Y138F |
probably benign |
Het |
Myh8 |
A |
G |
11: 67,183,550 (GRCm39) |
I754V |
probably benign |
Het |
Naa30 |
T |
A |
14: 49,415,597 (GRCm39) |
L289* |
probably null |
Het |
Nap1l4 |
A |
C |
7: 143,080,921 (GRCm39) |
F292V |
probably damaging |
Het |
Nek5 |
T |
A |
8: 22,601,185 (GRCm39) |
N129Y |
probably damaging |
Het |
Nlrp9a |
A |
G |
7: 26,273,338 (GRCm39) |
E880G |
probably benign |
Het |
Nsun6 |
G |
T |
2: 15,042,995 (GRCm39) |
N155K |
probably benign |
Het |
Or2aj5 |
A |
T |
16: 19,425,407 (GRCm39) |
Y4N |
probably benign |
Het |
Or4c102 |
T |
A |
2: 88,422,943 (GRCm39) |
I265K |
probably damaging |
Het |
Or4f62 |
T |
A |
2: 111,986,722 (GRCm39) |
I142N |
probably benign |
Het |
Or52a33 |
A |
T |
7: 103,288,702 (GRCm39) |
I215K |
probably damaging |
Het |
Or52ad1 |
T |
A |
7: 102,995,316 (GRCm39) |
Y273F |
possibly damaging |
Het |
Or5p5 |
A |
T |
7: 107,413,907 (GRCm39) |
I39L |
probably benign |
Het |
Or8d23 |
T |
C |
9: 38,842,171 (GRCm39) |
S235P |
possibly damaging |
Het |
Palm3 |
G |
A |
8: 84,756,651 (GRCm39) |
S721N |
possibly damaging |
Het |
Ppp2r5d |
C |
T |
17: 46,995,025 (GRCm39) |
V559M |
probably benign |
Het |
Ptgfr |
A |
T |
3: 151,540,976 (GRCm39) |
Y177* |
probably null |
Het |
Rnase10 |
A |
T |
14: 51,247,095 (GRCm39) |
I121L |
probably benign |
Het |
Sall2 |
G |
A |
14: 52,551,896 (GRCm39) |
P431L |
probably damaging |
Het |
Sbf2 |
A |
G |
7: 109,948,130 (GRCm39) |
V1194A |
possibly damaging |
Het |
Scimp |
T |
C |
11: 70,682,402 (GRCm39) |
K105E |
possibly damaging |
Het |
Scrt2 |
A |
T |
2: 151,924,007 (GRCm39) |
D13V |
probably damaging |
Het |
Snx19 |
A |
G |
9: 30,339,404 (GRCm39) |
S181G |
possibly damaging |
Het |
Spata2 |
G |
A |
2: 167,326,234 (GRCm39) |
T195M |
possibly damaging |
Het |
Sptbn4 |
A |
G |
7: 27,067,127 (GRCm39) |
V614A |
probably damaging |
Het |
Srpk2 |
G |
A |
5: 23,723,421 (GRCm39) |
A565V |
probably damaging |
Het |
Stard9 |
A |
G |
2: 120,531,887 (GRCm39) |
I2715V |
probably benign |
Het |
Sval1 |
A |
G |
6: 41,932,425 (GRCm39) |
T92A |
possibly damaging |
Het |
Synrg |
T |
C |
11: 83,910,781 (GRCm39) |
|
probably null |
Het |
Tlr12 |
T |
C |
4: 128,510,862 (GRCm39) |
T463A |
probably benign |
Het |
Tnxb |
A |
G |
17: 34,902,351 (GRCm39) |
H945R |
probably benign |
Het |
Tnxb |
A |
T |
17: 34,912,859 (GRCm39) |
D1791V |
probably damaging |
Het |
Topaz1 |
C |
T |
9: 122,579,190 (GRCm39) |
T700I |
possibly damaging |
Het |
Trappc8 |
A |
G |
18: 20,978,708 (GRCm39) |
V796A |
probably benign |
Het |
Trpm1 |
A |
T |
7: 63,858,780 (GRCm39) |
|
probably null |
Het |
Ttll4 |
G |
T |
1: 74,724,527 (GRCm39) |
V566L |
possibly damaging |
Het |
Ttn |
T |
A |
2: 76,581,285 (GRCm39) |
N23203Y |
probably damaging |
Het |
Ttn |
A |
T |
2: 76,601,131 (GRCm39) |
Y18781N |
probably damaging |
Het |
Tuba3a |
T |
C |
6: 125,258,216 (GRCm39) |
N258S |
probably damaging |
Het |
Upk1b |
A |
T |
16: 38,604,603 (GRCm39) |
W141R |
possibly damaging |
Het |
Vcpip1 |
G |
C |
1: 9,815,788 (GRCm39) |
A865G |
probably benign |
Het |
Vmn2r22 |
A |
T |
6: 123,614,500 (GRCm39) |
F363L |
probably damaging |
Het |
Vmn2r66 |
A |
T |
7: 84,661,201 (GRCm39) |
F10I |
probably benign |
Het |
Wbp2 |
C |
T |
11: 115,971,047 (GRCm39) |
|
probably null |
Het |
Yy1 |
T |
C |
12: 108,772,534 (GRCm39) |
L270P |
probably damaging |
Het |
Zan |
A |
T |
5: 137,418,268 (GRCm39) |
C2943* |
probably null |
Het |
Zfp51 |
T |
A |
17: 21,676,582 (GRCm39) |
Y18N |
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 |
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 |
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'- TTGAGACCATGCTGGGAGAC -3'
(R):5'- CAGGGTTCTACTGCATGCTG -3'
Sequencing Primer
(F):5'- TGGCTGTAGCTGTGCACC -3'
(R):5'- CTACTGCATGCTGGGGTTCC -3'
|
Posted On |
2014-08-25 |