Incidental Mutation 'R6374:Vars2'
| ID |
513724 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
044524-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6374 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 35970937 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 631
(V631A)
|
| 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: V631A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: V631A
| 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: ENSMUST00000164978
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000165787
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168885
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000168922
AA Change: V280A
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: V280A
| 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 |
noncoding transcript
Transcript: ENSMUST00000174129
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170701
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
| 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 |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.5%
- 20x: 92.4%
|
| Validation Efficiency |
99% (75/76) |
| 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: 77 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921509C19Rik |
A |
C |
2: 151,314,800 (GRCm39) |
S293A |
possibly damaging |
Het |
| 5430401F13Rik |
A |
T |
6: 131,529,892 (GRCm39) |
Q162L |
unknown |
Het |
| Abca8a |
A |
T |
11: 109,974,216 (GRCm39) |
Y239* |
probably null |
Het |
| Aox3 |
T |
C |
1: 58,211,320 (GRCm39) |
I959T |
probably benign |
Het |
| Atad2b |
T |
C |
12: 5,068,002 (GRCm39) |
V1000A |
probably damaging |
Het |
| Atic |
C |
T |
1: 71,604,100 (GRCm39) |
T221M |
probably damaging |
Het |
| Atp1a2 |
C |
T |
1: 172,116,942 (GRCm39) |
R225H |
probably damaging |
Het |
| BC024139 |
A |
G |
15: 76,004,657 (GRCm39) |
|
probably null |
Het |
| Bpi |
A |
T |
2: 158,113,974 (GRCm39) |
T291S |
probably damaging |
Het |
| Ccdc170 |
C |
T |
10: 4,499,746 (GRCm39) |
Q556* |
probably null |
Het |
| Cd3e |
G |
A |
9: 44,920,661 (GRCm39) |
L12F |
probably benign |
Het |
| Cdc42ep1 |
A |
T |
15: 78,731,649 (GRCm39) |
R31S |
probably damaging |
Het |
| Cyp21a1 |
G |
T |
17: 35,023,110 (GRCm39) |
|
probably null |
Het |
| Dnase1l3 |
A |
G |
14: 7,974,115 (GRCm38) |
M192T |
probably damaging |
Het |
| Dnmt1 |
A |
T |
9: 20,835,341 (GRCm39) |
H330Q |
possibly damaging |
Het |
| Enah |
T |
C |
1: 181,751,145 (GRCm39) |
E232G |
unknown |
Het |
| Etnppl |
C |
T |
3: 130,414,342 (GRCm39) |
T73I |
probably damaging |
Het |
| Fam83b |
T |
A |
9: 76,400,189 (GRCm39) |
I305F |
probably benign |
Het |
| Galnt15 |
T |
A |
14: 31,780,116 (GRCm39) |
I471N |
probably damaging |
Het |
| Gm19965 |
T |
A |
1: 116,750,021 (GRCm39) |
N567K |
probably benign |
Het |
| Golga1 |
T |
C |
2: 38,924,080 (GRCm39) |
Q435R |
probably benign |
Het |
| Gpat2 |
G |
C |
2: 127,273,838 (GRCm39) |
G294R |
possibly damaging |
Het |
| Hao1 |
T |
G |
2: 134,365,024 (GRCm39) |
D201A |
probably benign |
Het |
| Heg1 |
T |
C |
16: 33,547,499 (GRCm39) |
L786P |
possibly damaging |
Het |
| Hnrnpll |
A |
T |
17: 80,357,303 (GRCm39) |
C238S |
possibly damaging |
Het |
| Hrg |
A |
G |
16: 22,779,742 (GRCm39) |
Y340C |
probably damaging |
Het |
| Kyat3 |
A |
T |
3: 142,443,998 (GRCm39) |
I411F |
probably damaging |
Het |
| Myo1a |
T |
C |
10: 127,543,549 (GRCm39) |
Y202H |
probably damaging |
Het |
| Nags |
T |
C |
11: 102,037,337 (GRCm39) |
C143R |
possibly damaging |
Het |
| Ncoa6 |
T |
C |
2: 155,263,076 (GRCm39) |
N453D |
probably damaging |
Het |
| Nup35 |
G |
T |
2: 80,488,730 (GRCm39) |
M322I |
probably benign |
Het |
| Oprl1 |
T |
C |
2: 181,357,721 (GRCm39) |
V69A |
probably damaging |
Het |
| Or51v14 |
A |
G |
7: 103,261,128 (GRCm39) |
L144P |
probably benign |
Het |
| Pappa2 |
T |
A |
1: 158,784,215 (GRCm39) |
Y265F |
probably damaging |
Het |
| Pcsk6 |
C |
T |
7: 65,629,903 (GRCm39) |
P343L |
possibly damaging |
Het |
| Peak1 |
C |
A |
9: 56,164,950 (GRCm39) |
D993Y |
probably damaging |
Het |
| Polr2a |
T |
C |
11: 69,627,758 (GRCm39) |
Y1383C |
probably damaging |
Het |
| Ppme1 |
A |
G |
7: 99,990,272 (GRCm39) |
S226P |
probably damaging |
Het |
| Prom1 |
C |
T |
5: 44,213,325 (GRCm39) |
C127Y |
probably damaging |
Het |
| Ptpn6 |
A |
T |
6: 124,709,532 (GRCm39) |
|
probably null |
Het |
| Reln |
T |
C |
5: 22,285,712 (GRCm39) |
E419G |
probably benign |
Het |
| Rnf32 |
C |
T |
5: 29,430,266 (GRCm39) |
Q362* |
probably null |
Het |
| Sbspon |
T |
C |
1: 15,953,887 (GRCm39) |
D131G |
probably benign |
Het |
| Scyl3 |
T |
C |
1: 163,776,783 (GRCm39) |
S392P |
probably benign |
Het |
| Shtn1 |
T |
A |
19: 59,026,728 (GRCm39) |
D121V |
possibly damaging |
Het |
| Sin3a |
A |
G |
9: 57,024,765 (GRCm39) |
T1042A |
probably benign |
Het |
| Sipa1l2 |
A |
T |
8: 126,171,369 (GRCm39) |
V1371D |
probably damaging |
Het |
| Slc20a2 |
T |
C |
8: 23,055,668 (GRCm39) |
V584A |
possibly damaging |
Het |
| Smc6 |
T |
A |
12: 11,355,874 (GRCm39) |
|
probably null |
Het |
| Spata31h1 |
T |
A |
10: 82,124,731 (GRCm39) |
|
probably benign |
Het |
| Specc1 |
C |
T |
11: 62,047,418 (GRCm39) |
T849I |
possibly damaging |
Het |
| Spta1 |
T |
A |
1: 174,041,734 (GRCm39) |
L1368H |
probably damaging |
Het |
| Sqle |
A |
G |
15: 59,187,959 (GRCm39) |
E89G |
possibly damaging |
Het |
| Strbp |
A |
G |
2: 37,493,020 (GRCm39) |
V422A |
probably damaging |
Het |
| Sult6b1 |
G |
T |
17: 79,214,360 (GRCm39) |
T21K |
probably benign |
Het |
| Tex15 |
A |
G |
8: 34,065,940 (GRCm39) |
E1790G |
probably damaging |
Het |
| Tmem88b |
T |
A |
4: 155,870,221 (GRCm39) |
|
probably benign |
Het |
| Traf3ip3 |
T |
C |
1: 192,864,318 (GRCm39) |
D355G |
possibly damaging |
Het |
| Trim24 |
T |
A |
6: 37,930,484 (GRCm39) |
V576E |
probably benign |
Het |
| Trim30c |
C |
T |
7: 104,039,609 (GRCm39) |
G62D |
probably benign |
Het |
| Trim66 |
T |
G |
7: 109,085,269 (GRCm39) |
K100N |
probably benign |
Het |
| Tsnaxip1 |
A |
T |
8: 106,568,172 (GRCm39) |
T313S |
possibly damaging |
Het |
| Ugt2b37 |
A |
T |
5: 87,390,279 (GRCm39) |
I389N |
probably damaging |
Het |
| Unc13a |
C |
T |
8: 72,094,097 (GRCm39) |
V1335M |
possibly damaging |
Het |
| Urah |
A |
G |
7: 140,415,124 (GRCm39) |
T5A |
probably benign |
Het |
| Usp34 |
T |
C |
11: 23,388,914 (GRCm39) |
Y2185H |
probably damaging |
Het |
| Usp44 |
T |
C |
10: 93,692,172 (GRCm39) |
S643P |
probably benign |
Het |
| Vmn2r11 |
G |
A |
5: 109,201,679 (GRCm39) |
T275I |
possibly damaging |
Het |
| Vmn2r54 |
C |
A |
7: 12,349,420 (GRCm39) |
V721F |
probably damaging |
Het |
| Vmn2r79 |
T |
C |
7: 86,651,498 (GRCm39) |
I299T |
probably benign |
Het |
| Vps13d |
T |
C |
4: 144,849,251 (GRCm39) |
T2387A |
probably damaging |
Het |
| Washc5 |
A |
T |
15: 59,209,044 (GRCm39) |
L610Q |
probably benign |
Het |
| Zbtb21 |
T |
C |
16: 97,751,568 (GRCm39) |
E905G |
probably damaging |
Het |
| Zfhx4 |
A |
G |
3: 5,309,095 (GRCm39) |
T774A |
probably damaging |
Het |
| Zfp534 |
T |
C |
4: 147,759,299 (GRCm39) |
I457V |
probably benign |
Het |
| Zfp964 |
T |
C |
8: 70,111,994 (GRCm39) |
Y29H |
possibly damaging |
Het |
| Znrf4 |
A |
G |
17: 56,818,702 (GRCm39) |
F202L |
probably 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 |
|
|
R5217:Vars2
|
UTSW |
17 |
35,969,041 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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 |
|
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'- CCAGGGACTTGCTCATCTTC -3'
(R):5'- GACACTTGGTTCTCTTCGGC -3'
Sequencing Primer
(F):5'- GACTTGCTCATCTTCCGGCC -3'
(R):5'- TTGGCCGCGAGAGGTGAC -3'
|
| Posted On |
2018-04-27 |
Incidental Mutation