Incidental Mutation 'R4861:Vars2'
| ID | 380267 |
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| Institutional Source |
Beutler Lab
|
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| Gene Symbol |
Vars2
|
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| Ensembl Gene |
ENSMUSG00000038838 |
|---|
| Gene Name | valyl-tRNA synthetase 2, mitochondrial |
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| Synonyms | Vars2l |
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| MMRRC Submission |
042472-MU
|
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| Accession Numbers | |
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| Is this an essential gene? |
Essential (E-score: 1.000)
|
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| Stock # | R4861 (G1)
|
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| Quality Score | 225 |
|---|
| Status |
Validated
|
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| Chromosome | 17 |
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| Chromosomal Location | 35655634-35667592 bp(-) (GRCm38) |
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| Type of Mutation | missense |
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| DNA Base Change (assembly) |
G to T
at 35661933 bp
|
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| Zygosity | Heterozygous |
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| Amino Acid Change |
Glutamine to Lysine
at position 13
(Q13K)
|
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| Ref Sequence |
ENSEMBL: ENSMUSP00000126794
(fasta)
|
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| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000165144]
[ENSMUST00000169093]
|
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| Predicted Effect |
probably benign
Transcript: ENSMUST00000043674
AA Change: Q456K
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
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| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: Q456K
| 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 |
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164295
|
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| Predicted Effect |
unknown
Transcript: ENSMUST00000164404
AA Change: Q75K
|
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| SMART Domains |
Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838
AA Change: Q75K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
1 |
201 |
1e-49 |
PFAM |
|
Pfam:tRNA-synt_1g
|
68 |
172 |
4e-7 |
PFAM |
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164978
|
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| Predicted Effect |
probably benign
Transcript: ENSMUST00000165144
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165787
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168885
|
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| Predicted Effect |
unknown
Transcript: ENSMUST00000168922
AA Change: Q105K
|
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| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: Q105K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
2 |
386 |
3e-105 |
PFAM |
|
Pfam:Anticodon_1
|
430 |
566 |
8.2e-29 |
PFAM |
|
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| Predicted Effect |
probably benign
Transcript: ENSMUST00000169093
AA Change: Q13K
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000126794
Gene: ENSMUSG00000038838
AA Change: Q13K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:tRNA-synt_1
|
1 |
109 |
1.7e-29 |
PFAM |
|
|---|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170701
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171536
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174129
|
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| Meta Mutation Damage Score |
0.0738
|
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| Coding Region Coverage |
- 1x: 98.8%
- 3x: 97.8%
- 10x: 94.2%
- 20x: 84.7%
|
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| Validation Efficiency |
100% (53/53) |
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| 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]
|
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| Allele List at MGI | |
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| Other mutations in this stock |
Total: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb11 |
C |
T |
2: 69,245,905 |
R1153H |
probably damaging |
Het |
| Ahcy |
T |
C |
2: 155,060,516 |
E411G |
probably benign |
Het |
| Alpi |
T |
A |
1: 87,100,469 |
I211F |
probably damaging |
Het |
| Arfgef3 |
G |
A |
10: 18,607,731 |
A1415V |
probably benign |
Het |
| Car3 |
T |
C |
3: 14,866,896 |
V109A |
probably damaging |
Het |
| Ccdc114 |
A |
G |
7: 45,942,873 |
E359G |
probably damaging |
Het |
| Cdk13 |
A |
T |
13: 17,766,586 |
V17D |
probably damaging |
Het |
| Cept1 |
A |
C |
3: 106,505,732 |
S226A |
probably damaging |
Het |
| Dbt |
A |
T |
3: 116,548,078 |
I443L |
probably benign |
Het |
| Dync1h1 |
C |
A |
12: 110,658,126 |
T3700N |
probably damaging |
Het |
| Farp2 |
T |
C |
1: 93,605,419 |
L633S |
probably damaging |
Het |
| Frmd6 |
T |
G |
12: 70,893,726 |
S382A |
probably damaging |
Het |
| Gm26727 |
T |
C |
2: 67,432,945 |
I79M |
probably damaging |
Het |
| Gm5800 |
T |
A |
14: 51,716,047 |
N37I |
probably damaging |
Het |
| Hapln1 |
G |
A |
13: 89,601,452 |
G39S |
possibly damaging |
Het |
| Ice2 |
T |
A |
9: 69,415,448 |
S408R |
probably benign |
Het |
| Lctl |
T |
C |
9: 64,119,763 |
I131T |
possibly damaging |
Het |
| Mvk |
C |
T |
5: 114,460,197 |
|
probably benign |
Het |
| Mzt1 |
T |
C |
14: 99,047,474 |
|
probably null |
Het |
| Ncoa7 |
T |
A |
10: 30,704,612 |
M117L |
probably benign |
Het |
| Npy4r |
C |
T |
14: 34,146,883 |
W149* |
probably null |
Het |
| Nr5a2 |
A |
G |
1: 136,948,720 |
|
probably null |
Het |
| Plg |
G |
A |
17: 12,395,735 |
E301K |
probably benign |
Het |
| Pnkp |
C |
T |
7: 44,862,403 |
S113L |
probably damaging |
Het |
| Rapgef2 |
T |
C |
3: 79,074,436 |
K1084R |
probably benign |
Het |
| Slc41a2 |
T |
C |
10: 83,316,458 |
Q51R |
probably damaging |
Het |
| Slc47a2 |
A |
T |
11: 61,336,233 |
C170S |
probably benign |
Het |
| Slco1b2 |
A |
T |
6: 141,671,222 |
N427I |
possibly damaging |
Het |
| Smc2 |
G |
A |
4: 52,461,090 |
R571H |
probably benign |
Het |
| Sp4 |
G |
T |
12: 118,300,811 |
|
probably null |
Het |
| Tas2r117 |
T |
C |
6: 132,803,129 |
F77L |
probably benign |
Het |
| Tbcd |
C |
T |
11: 121,601,961 |
R875C |
probably damaging |
Het |
| Thumpd2 |
A |
G |
17: 81,026,801 |
S453P |
probably benign |
Het |
|
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| Other mutations in Vars2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02106:Vars2
|
APN |
17 |
35664621 |
unclassified |
probably benign |
|
|
IGL02320:Vars2
|
APN |
17 |
35660454 |
missense |
probably benign |
0.07 |
|
IGL02580:Vars2
|
APN |
17 |
35660885 |
missense |
possibly damaging |
0.50 |
|
IGL02691:Vars2
|
APN |
17 |
35660248 |
missense |
probably damaging |
1.00 |
|
IGL03039:Vars2
|
APN |
17 |
35664121 |
missense |
probably damaging |
1.00 |
|
PIT4445001:Vars2
|
UTSW |
17 |
35666211 |
nonsense |
probably null |
|
|
R0079:Vars2
|
UTSW |
17 |
35659156 |
missense |
probably damaging |
0.99 |
|
R0152:Vars2
|
UTSW |
17 |
35660027 |
missense |
probably damaging |
1.00 |
|
R0346:Vars2
|
UTSW |
17 |
35664864 |
unclassified |
probably benign |
|
|
R0426:Vars2
|
UTSW |
17 |
35664584 |
missense |
probably damaging |
1.00 |
|
R0584:Vars2
|
UTSW |
17 |
35666686 |
missense |
possibly damaging |
0.82 |
|
R0589:Vars2
|
UTSW |
17 |
35659176 |
missense |
probably benign |
|
|
R0882:Vars2
|
UTSW |
17 |
35657299 |
missense |
probably benign |
0.41 |
|
R1234:Vars2
|
UTSW |
17 |
35667146 |
missense |
probably damaging |
1.00 |
|
R1263:Vars2
|
UTSW |
17 |
35661609 |
missense |
probably damaging |
1.00 |
|
R1559:Vars2
|
UTSW |
17 |
35666258 |
unclassified |
probably benign |
|
|
R1772:Vars2
|
UTSW |
17 |
35660084 |
missense |
probably damaging |
1.00 |
|
R1809:Vars2
|
UTSW |
17 |
35662216 |
missense |
probably damaging |
1.00 |
|
R1913:Vars2
|
UTSW |
17 |
35666922 |
missense |
probably benign |
0.02 |
|
R1986:Vars2
|
UTSW |
17 |
35660061 |
missense |
probably damaging |
1.00 |
|
R2504:Vars2
|
UTSW |
17 |
35664793 |
missense |
probably damaging |
1.00 |
|
R3426:Vars2
|
UTSW |
17 |
35661974 |
missense |
probably damaging |
1.00 |
|
R4539:Vars2
|
UTSW |
17 |
35666888 |
missense |
probably damaging |
0.99 |
|
R4751:Vars2
|
UTSW |
17 |
35659343 |
missense |
possibly damaging |
0.89 |
|
R4861:Vars2
|
UTSW |
17 |
35661933 |
missense |
probably benign |
0.00 |
|
R5028:Vars2
|
UTSW |
17 |
35659473 |
critical splice donor site |
probably null |
|
|
R5217:Vars2
|
UTSW |
17 |
35658149 |
missense |
probably damaging |
1.00 |
|
R5292:Vars2
|
UTSW |
17 |
35660786 |
missense |
probably damaging |
1.00 |
|
R6056:Vars2
|
UTSW |
17 |
35665788 |
missense |
probably benign |
0.01 |
|
R6211:Vars2
|
UTSW |
17 |
35665662 |
splice site |
probably null |
|
|
R6213:Vars2
|
UTSW |
17 |
35660440 |
missense |
probably benign |
0.27 |
|
R6374:Vars2
|
UTSW |
17 |
35660045 |
missense |
probably damaging |
1.00 |
|
R6746:Vars2
|
UTSW |
17 |
35660402 |
critical splice donor site |
probably null |
|
|
R6749:Vars2
|
UTSW |
17 |
35666713 |
missense |
probably damaging |
1.00 |
|
R6957:Vars2
|
UTSW |
17 |
35667075 |
missense |
probably benign |
0.39 |
|
R7107:Vars2
|
UTSW |
17 |
35658250 |
missense |
probably damaging |
1.00 |
|
R7428:Vars2
|
UTSW |
17 |
35666686 |
missense |
probably benign |
0.00 |
|
R7538:Vars2
|
UTSW |
17 |
35660780 |
missense |
probably damaging |
1.00 |
|
R7553:Vars2
|
UTSW |
17 |
35664788 |
missense |
possibly damaging |
0.93 |
|
R7741:Vars2
|
UTSW |
17 |
35660943 |
missense |
probably damaging |
1.00 |
|
R7784:Vars2
|
UTSW |
17 |
35658158 |
missense |
possibly damaging |
0.95 |
|
R7823:Vars2
|
UTSW |
17 |
35659136 |
missense |
probably damaging |
1.00 |
|
R7915:Vars2
|
UTSW |
17 |
35664839 |
missense |
probably damaging |
1.00 |
|
R8201:Vars2
|
UTSW |
17 |
35658310 |
missense |
probably benign |
|
|
X0021:Vars2
|
UTSW |
17 |
35659034 |
missense |
possibly damaging |
0.93 |
|
Z1176:Vars2
|
UTSW |
17 |
35664791 |
missense |
possibly damaging |
0.55 |
|
Z1177:Vars2
|
UTSW |
17 |
35663472 |
missense |
probably benign |
0.17 |
|
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| Predicted Primers |
PCR Primer
(F):5'- TGATCCCACACTTGACAGGC -3'
(R):5'- GTGTCATTGCAGAGGATGGGAC -3'
Sequencing Primer
(F):5'- ACACTTGACAGGCCAGGGTG -3'
(R):5'- ATGACATCCCTCTGTGGAGACTG -3'
|
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| Posted On | 2016-04-15 |
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