Incidental Mutation 'R5217:Vars2'
| ID |
403571 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
042790-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5217 (G1)
|
| Quality Score |
199 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 35969041 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Alanine
at position 887
(P887A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000169093]
|
| AlphaFold |
Q3U2A8 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000043674
AA Change: P887A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: P887A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
112 |
736 |
3.3e-179 |
PFAM |
|
Pfam:tRNA-synt_1g
|
141 |
221 |
2e-8 |
PFAM |
|
Pfam:Anticodon_1
|
780 |
932 |
3.6e-32 |
PFAM |
|
low complexity region
|
1005 |
1015 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164295
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164404
|
| SMART Domains |
Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
1 |
201 |
1e-49 |
PFAM |
|
Pfam:tRNA-synt_1g
|
68 |
172 |
4e-7 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165787
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168885
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000168922
AA Change: P536A
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: P536A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
2 |
386 |
3e-105 |
PFAM |
|
Pfam:Anticodon_1
|
430 |
566 |
8.2e-29 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169093
|
| SMART Domains |
Protein: ENSMUSP00000126794
Gene: ENSMUSG00000038838
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
1 |
109 |
1.7e-29 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174129
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170701
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
| Meta Mutation Damage Score |
0.8528 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.7%
|
| Validation Efficiency |
100% (80/80) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 73 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933428M09Rik |
G |
T |
X: 138,080,282 (GRCm39) |
G16* |
probably null |
Het |
| Abhd11 |
T |
A |
5: 135,040,398 (GRCm39) |
W144R |
probably damaging |
Het |
| Abhd2 |
A |
G |
7: 78,973,378 (GRCm39) |
E119G |
probably benign |
Het |
| Acbd3 |
A |
G |
1: 180,553,938 (GRCm39) |
Y91C |
probably benign |
Het |
| Aox4 |
C |
A |
1: 58,285,400 (GRCm39) |
S628* |
probably null |
Het |
| Bahcc1 |
T |
A |
11: 120,165,285 (GRCm39) |
Y905* |
probably null |
Het |
| Baiap2l2 |
T |
G |
15: 79,154,687 (GRCm39) |
S211R |
probably benign |
Het |
| Cab39l |
T |
A |
14: 59,764,258 (GRCm39) |
Y206* |
probably null |
Het |
| Cacna1i |
A |
T |
15: 80,275,041 (GRCm39) |
T1830S |
possibly damaging |
Het |
| Catsperg1 |
A |
T |
7: 28,889,723 (GRCm39) |
L793* |
probably null |
Het |
| Cdh10 |
G |
T |
15: 18,966,108 (GRCm39) |
V198F |
probably damaging |
Het |
| Cenpk |
A |
T |
13: 104,385,917 (GRCm39) |
I271F |
probably damaging |
Het |
| Chchd4 |
A |
T |
6: 91,442,260 (GRCm39) |
C53S |
probably damaging |
Het |
| Cluh |
T |
G |
11: 74,550,531 (GRCm39) |
C252W |
probably damaging |
Het |
| Cmklr1 |
G |
T |
5: 113,752,710 (GRCm39) |
A97E |
probably damaging |
Het |
| Coil |
C |
A |
11: 88,871,987 (GRCm39) |
A116D |
possibly damaging |
Het |
| Eif1ad9 |
A |
G |
12: 88,296,196 (GRCm39) |
H58R |
probably benign |
Het |
| F830045P16Rik |
C |
A |
2: 129,305,493 (GRCm39) |
V294F |
probably damaging |
Het |
| Fgd6 |
T |
A |
10: 93,969,939 (GRCm39) |
M1196K |
possibly damaging |
Het |
| Gabra5 |
G |
A |
7: 57,140,604 (GRCm39) |
S31L |
probably benign |
Het |
| Gm7135 |
A |
T |
1: 97,362,790 (GRCm39) |
|
noncoding transcript |
Het |
| Gon4l |
C |
A |
3: 88,794,882 (GRCm39) |
T695K |
probably damaging |
Het |
| Hectd4 |
A |
G |
5: 121,491,614 (GRCm39) |
H3684R |
possibly damaging |
Het |
| Ica1l |
T |
A |
1: 60,054,917 (GRCm39) |
M105L |
probably benign |
Het |
| Ift70a1 |
A |
G |
2: 75,811,147 (GRCm39) |
L312P |
probably damaging |
Het |
| Igkv8-24 |
A |
T |
6: 70,194,386 (GRCm39) |
V7D |
probably damaging |
Het |
| Klf10 |
G |
A |
15: 38,296,331 (GRCm39) |
R420W |
probably damaging |
Het |
| Klrc2 |
C |
A |
6: 129,633,843 (GRCm39) |
W177C |
probably damaging |
Het |
| Krit1 |
T |
A |
5: 3,856,451 (GRCm39) |
C15* |
probably null |
Het |
| Lamc1 |
C |
A |
1: 153,103,442 (GRCm39) |
V1375L |
probably damaging |
Het |
| Lrrc37a |
C |
T |
11: 103,347,780 (GRCm39) |
V2972I |
unknown |
Het |
| Mapkapk5 |
T |
C |
5: 121,672,492 (GRCm39) |
D13G |
probably damaging |
Het |
| Mcph1 |
T |
A |
8: 18,838,489 (GRCm39) |
L804I |
probably damaging |
Het |
| Mdn1 |
C |
T |
4: 32,723,690 (GRCm39) |
P2542L |
probably damaging |
Het |
| Mrto4 |
A |
G |
4: 139,075,770 (GRCm39) |
Y119H |
probably benign |
Het |
| Nbeal2 |
G |
T |
9: 110,461,158 (GRCm39) |
A1635E |
possibly damaging |
Het |
| Ndc1 |
T |
C |
4: 107,246,773 (GRCm39) |
S399P |
probably benign |
Het |
| Ndufv2 |
A |
G |
17: 66,394,424 (GRCm39) |
I147T |
probably damaging |
Het |
| Neb |
C |
A |
2: 52,052,142 (GRCm39) |
E382* |
probably null |
Het |
| Nhsl3 |
C |
T |
4: 129,116,478 (GRCm39) |
E729K |
probably damaging |
Het |
| Nme8 |
T |
A |
13: 19,880,861 (GRCm39) |
I32F |
probably damaging |
Het |
| Obox5 |
T |
A |
7: 15,491,793 (GRCm39) |
|
probably null |
Het |
| Or8g23 |
A |
G |
9: 38,971,065 (GRCm39) |
V299A |
probably benign |
Het |
| Pcdhb19 |
A |
T |
18: 37,630,939 (GRCm39) |
M245L |
probably benign |
Het |
| Pex5l |
A |
T |
3: 33,061,477 (GRCm39) |
|
probably null |
Het |
| Phrf1 |
T |
G |
7: 140,840,616 (GRCm39) |
D1270E |
probably damaging |
Het |
| Pik3r5 |
A |
G |
11: 68,382,790 (GRCm39) |
K277E |
possibly damaging |
Het |
| Ppan |
T |
C |
9: 20,802,221 (GRCm39) |
V204A |
possibly damaging |
Het |
| Ppp1r9a |
A |
T |
6: 5,115,367 (GRCm39) |
N830I |
probably damaging |
Het |
| Pxn |
C |
G |
5: 115,682,974 (GRCm39) |
A92G |
probably benign |
Het |
| Qsox1 |
A |
G |
1: 155,666,742 (GRCm39) |
V249A |
probably benign |
Het |
| Rgl3 |
T |
A |
9: 21,898,944 (GRCm39) |
*88C |
probably null |
Het |
| Rps6kc1 |
A |
T |
1: 190,515,802 (GRCm39) |
W975R |
probably damaging |
Het |
| Sash1 |
G |
T |
10: 8,656,368 (GRCm39) |
A208D |
possibly damaging |
Het |
| Simc1 |
A |
T |
13: 54,687,709 (GRCm39) |
|
probably benign |
Het |
| Sox7 |
T |
C |
14: 64,185,449 (GRCm39) |
Y162H |
probably damaging |
Het |
| Srp72 |
T |
A |
5: 77,128,375 (GRCm39) |
L171H |
probably damaging |
Het |
| Stab1 |
T |
A |
14: 30,881,476 (GRCm39) |
Y577F |
probably benign |
Het |
| Stam2 |
G |
A |
2: 52,626,305 (GRCm39) |
|
probably benign |
Het |
| Tagln |
T |
C |
9: 45,842,177 (GRCm39) |
T139A |
probably benign |
Het |
| Thbs3 |
T |
C |
3: 89,130,471 (GRCm39) |
|
probably null |
Het |
| Tmem216 |
G |
A |
19: 10,529,155 (GRCm39) |
T131M |
possibly damaging |
Het |
| Tmprss11c |
A |
G |
5: 86,404,249 (GRCm39) |
V142A |
probably benign |
Het |
| Trarg1 |
C |
G |
11: 76,585,102 (GRCm39) |
A164G |
possibly damaging |
Het |
| Ttn |
A |
T |
2: 76,641,587 (GRCm39) |
L5176Q |
possibly damaging |
Het |
| Ubtf |
T |
C |
11: 102,199,128 (GRCm39) |
M511V |
probably null |
Het |
| Ugt2b36 |
A |
T |
5: 87,214,114 (GRCm39) |
V510E |
probably damaging |
Het |
| Vmn2r80 |
A |
G |
10: 79,004,980 (GRCm39) |
M206V |
possibly damaging |
Het |
| Zbtb5 |
A |
G |
4: 44,993,990 (GRCm39) |
F465L |
probably benign |
Het |
| Zfp119a |
G |
A |
17: 56,172,425 (GRCm39) |
Q473* |
probably null |
Het |
| Zfp607a |
T |
G |
7: 27,577,269 (GRCm39) |
I113R |
probably damaging |
Het |
| Zfp998 |
A |
T |
13: 66,581,787 (GRCm39) |
L28H |
probably damaging |
Het |
| Zmym6 |
C |
A |
4: 126,999,167 (GRCm39) |
N450K |
possibly damaging |
Het |
|
| Other mutations in Vars2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02106:Vars2
|
APN |
17 |
35,975,513 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02320:Vars2
|
APN |
17 |
35,971,346 (GRCm39) |
missense |
probably benign |
0.07 |
|
IGL02580:Vars2
|
APN |
17 |
35,971,777 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
IGL02691:Vars2
|
APN |
17 |
35,971,140 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03039:Vars2
|
APN |
17 |
35,975,013 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4445001:Vars2
|
UTSW |
17 |
35,977,103 (GRCm39) |
nonsense |
probably null |
|
|
R0079:Vars2
|
UTSW |
17 |
35,970,048 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0152:Vars2
|
UTSW |
17 |
35,970,919 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0346:Vars2
|
UTSW |
17 |
35,975,756 (GRCm39) |
unclassified |
probably benign |
|
|
R0426:Vars2
|
UTSW |
17 |
35,975,476 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0584:Vars2
|
UTSW |
17 |
35,977,578 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R0589:Vars2
|
UTSW |
17 |
35,970,068 (GRCm39) |
missense |
probably benign |
|
|
R0882:Vars2
|
UTSW |
17 |
35,968,191 (GRCm39) |
missense |
probably benign |
0.41 |
|
R1234:Vars2
|
UTSW |
17 |
35,978,038 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1263:Vars2
|
UTSW |
17 |
35,972,501 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1559:Vars2
|
UTSW |
17 |
35,977,150 (GRCm39) |
unclassified |
probably benign |
|
|
R1772:Vars2
|
UTSW |
17 |
35,970,976 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1809:Vars2
|
UTSW |
17 |
35,973,108 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1913:Vars2
|
UTSW |
17 |
35,977,814 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1986:Vars2
|
UTSW |
17 |
35,970,953 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2504:Vars2
|
UTSW |
17 |
35,975,685 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3426:Vars2
|
UTSW |
17 |
35,972,866 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4539:Vars2
|
UTSW |
17 |
35,977,780 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4751:Vars2
|
UTSW |
17 |
35,970,235 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4861:Vars2
|
UTSW |
17 |
35,972,825 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4861:Vars2
|
UTSW |
17 |
35,972,825 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5028:Vars2
|
UTSW |
17 |
35,970,365 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5292:Vars2
|
UTSW |
17 |
35,971,678 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6056:Vars2
|
UTSW |
17 |
35,976,680 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6211:Vars2
|
UTSW |
17 |
35,976,554 (GRCm39) |
splice site |
probably null |
|
|
R6213:Vars2
|
UTSW |
17 |
35,971,332 (GRCm39) |
missense |
probably benign |
0.27 |
|
R6374:Vars2
|
UTSW |
17 |
35,970,937 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6746:Vars2
|
UTSW |
17 |
35,971,294 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6749:Vars2
|
UTSW |
17 |
35,977,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6957:Vars2
|
UTSW |
17 |
35,977,967 (GRCm39) |
missense |
probably benign |
0.39 |
|
R7107:Vars2
|
UTSW |
17 |
35,969,142 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7428:Vars2
|
UTSW |
17 |
35,977,578 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7538:Vars2
|
UTSW |
17 |
35,971,672 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7553:Vars2
|
UTSW |
17 |
35,975,680 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R7741:Vars2
|
UTSW |
17 |
35,971,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7784:Vars2
|
UTSW |
17 |
35,969,050 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7823:Vars2
|
UTSW |
17 |
35,970,028 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7915:Vars2
|
UTSW |
17 |
35,975,731 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8201:Vars2
|
UTSW |
17 |
35,969,202 (GRCm39) |
missense |
probably benign |
|
|
R8955:Vars2
|
UTSW |
17 |
35,972,541 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8964:Vars2
|
UTSW |
17 |
35,970,699 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R9101:Vars2
|
UTSW |
17 |
35,969,980 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R9202:Vars2
|
UTSW |
17 |
35,977,551 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9202:Vars2
|
UTSW |
17 |
35,974,444 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R9450:Vars2
|
UTSW |
17 |
35,973,027 (GRCm39) |
missense |
probably damaging |
0.98 |
|
X0021:Vars2
|
UTSW |
17 |
35,969,926 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
Z1176:Vars2
|
UTSW |
17 |
35,975,683 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
Z1177:Vars2
|
UTSW |
17 |
35,974,364 (GRCm39) |
missense |
probably benign |
0.17 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAGCAATTCAGTGACACAGC -3'
(R):5'- TGAAGCCAGTGTTGTCGAG -3'
Sequencing Primer
(F):5'- AATCCTAGCACTTACTTGGGAGGC -3'
(R):5'- CCAGTGTTGTCGAGCGTGC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation