Incidental Mutation 'R6213:Vars2'
| ID |
503593 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| MMRRC Submission |
044346-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6213 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35971332 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 568
(T568A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043674]
[ENSMUST00000169093]
|
| AlphaFold |
Q3U2A8 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000043674
AA Change: T568A
PolyPhen 2
Score 0.268 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: T568A
| 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 |
unknown
Transcript: ENSMUST00000164404
AA Change: T187A
|
| SMART Domains |
Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838
AA Change: T187A
| 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: T217A
|
| SMART Domains |
Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: T217A
| 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: ENSMUST00000170701
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174129
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173162
|
| Meta Mutation Damage Score |
0.1004 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.2%
- 20x: 97.3%
|
| Validation Efficiency |
|
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc5 |
A |
G |
16: 20,218,762 (GRCm39) |
Y207H |
probably damaging |
Het |
| Adcy7 |
G |
A |
8: 89,040,765 (GRCm39) |
V335M |
probably damaging |
Het |
| Apol11b |
A |
C |
15: 77,522,200 (GRCm39) |
D32E |
possibly damaging |
Het |
| Ccdc13 |
A |
G |
9: 121,627,975 (GRCm39) |
|
probably benign |
Het |
| Cdkn1b |
T |
A |
6: 134,898,206 (GRCm39) |
D108E |
probably benign |
Het |
| Cep290 |
A |
G |
10: 100,359,222 (GRCm39) |
D984G |
probably benign |
Het |
| Csde1 |
T |
C |
3: 102,947,830 (GRCm39) |
V128A |
probably damaging |
Het |
| Csmd3 |
A |
G |
15: 47,492,656 (GRCm39) |
S3162P |
probably damaging |
Het |
| D5Ertd579e |
G |
A |
5: 36,759,978 (GRCm39) |
T1394I |
probably damaging |
Het |
| Ddx6 |
T |
A |
9: 44,539,990 (GRCm39) |
L306Q |
probably damaging |
Het |
| Dmxl1 |
T |
A |
18: 49,996,082 (GRCm39) |
S403T |
possibly damaging |
Het |
| F11 |
G |
T |
8: 45,694,537 (GRCm39) |
T608K |
probably damaging |
Het |
| Flrt3 |
C |
T |
2: 140,503,085 (GRCm39) |
R181H |
probably damaging |
Het |
| Hs3st1 |
A |
T |
5: 39,771,864 (GRCm39) |
C260S |
probably damaging |
Het |
| Ighv7-1 |
A |
T |
12: 113,860,141 (GRCm39) |
S84T |
probably damaging |
Het |
| Inpp4b |
A |
G |
8: 82,724,019 (GRCm39) |
D332G |
probably damaging |
Het |
| Irf2bpl |
T |
C |
12: 86,930,367 (GRCm39) |
Q102R |
probably benign |
Het |
| Itpr3 |
T |
A |
17: 27,330,174 (GRCm39) |
D1597E |
probably benign |
Het |
| Kcnd1 |
G |
C |
X: 7,690,148 (GRCm39) |
A23P |
probably damaging |
Homo |
| Lypd8 |
A |
G |
11: 58,281,160 (GRCm39) |
T241A |
probably benign |
Het |
| Map1lc3a |
T |
C |
2: 155,118,935 (GRCm39) |
|
probably null |
Het |
| Mast1 |
G |
A |
8: 85,642,198 (GRCm39) |
T1052I |
probably damaging |
Het |
| Muc2 |
T |
C |
7: 141,305,151 (GRCm39) |
C152R |
probably damaging |
Het |
| Muc5b |
A |
T |
7: 141,415,903 (GRCm39) |
M2950L |
probably benign |
Het |
| Muc5b |
A |
G |
7: 141,421,356 (GRCm39) |
D4282G |
possibly damaging |
Het |
| Myo16 |
G |
T |
8: 10,420,963 (GRCm39) |
|
probably null |
Het |
| Myo9a |
T |
A |
9: 59,734,541 (GRCm39) |
F708I |
probably damaging |
Het |
| Nadsyn1 |
A |
T |
7: 143,353,549 (GRCm39) |
F558Y |
probably benign |
Het |
| Nat9 |
A |
T |
11: 115,075,932 (GRCm39) |
W30R |
probably damaging |
Het |
| Nipbl |
A |
G |
15: 8,364,390 (GRCm39) |
L1338S |
probably damaging |
Het |
| Nipsnap3b |
A |
G |
4: 53,017,066 (GRCm39) |
T97A |
probably benign |
Het |
| Npepps |
A |
T |
11: 97,132,823 (GRCm39) |
Y301* |
probably null |
Het |
| Nrcam |
C |
T |
12: 44,609,215 (GRCm39) |
P447S |
possibly damaging |
Het |
| Or14c41 |
A |
G |
7: 86,234,485 (GRCm39) |
M1V |
probably null |
Het |
| Or1o4 |
T |
C |
17: 37,591,264 (GRCm39) |
S16G |
probably benign |
Het |
| Or2a14 |
A |
G |
6: 43,130,821 (GRCm39) |
N194S |
possibly damaging |
Het |
| Or52b4 |
T |
C |
7: 102,184,139 (GRCm39) |
Y62H |
probably damaging |
Het |
| Pacsin3 |
G |
T |
2: 91,090,779 (GRCm39) |
V29F |
probably damaging |
Het |
| Pdzrn3 |
A |
C |
6: 101,354,805 (GRCm39) |
D15E |
probably damaging |
Het |
| Phf20l1 |
T |
C |
15: 66,504,752 (GRCm39) |
|
probably null |
Het |
| Pign |
A |
C |
1: 105,516,991 (GRCm39) |
V545G |
possibly damaging |
Het |
| Pkhd1 |
T |
C |
1: 20,593,994 (GRCm39) |
N1373S |
possibly damaging |
Het |
| Ptchd4 |
T |
A |
17: 42,688,251 (GRCm39) |
H264Q |
probably benign |
Het |
| Ptpn3 |
G |
T |
4: 57,265,012 (GRCm39) |
Q73K |
probably damaging |
Het |
| Ptrh1 |
G |
A |
2: 32,666,757 (GRCm39) |
V109I |
probably benign |
Het |
| Reg1 |
A |
T |
6: 78,404,386 (GRCm39) |
I87F |
possibly damaging |
Het |
| Rrp12 |
C |
A |
19: 41,857,217 (GRCm39) |
V1186L |
probably benign |
Het |
| Sall1 |
AGTGGTGGTGGTGGTGGTGGTGG |
AGTGGTGGTGGTGGTGGTGG |
8: 89,759,686 (GRCm39) |
|
probably benign |
Het |
| Slc23a3 |
A |
C |
1: 75,108,392 (GRCm39) |
F279V |
probably benign |
Het |
| Smtnl2 |
G |
A |
11: 72,292,225 (GRCm39) |
A274V |
probably damaging |
Het |
| Suds3 |
A |
G |
5: 117,244,727 (GRCm39) |
L115P |
probably damaging |
Het |
| Tekt2 |
G |
A |
4: 126,216,989 (GRCm39) |
A260V |
probably damaging |
Het |
| Tgfb3 |
T |
A |
12: 86,104,621 (GRCm39) |
Y391F |
probably damaging |
Het |
| Topbp1 |
T |
C |
9: 103,209,950 (GRCm39) |
S866P |
probably benign |
Het |
| Tspan14 |
A |
G |
14: 40,635,372 (GRCm39) |
Y175H |
probably benign |
Het |
| Vmn1r216 |
T |
G |
13: 23,283,339 (GRCm39) |
D7E |
probably benign |
Het |
| Vmn2r115 |
ATCTTCT |
ATCT |
17: 23,578,962 (GRCm39) |
|
probably benign |
Het |
| Zfp281 |
T |
C |
1: 136,553,250 (GRCm39) |
V76A |
probably benign |
Het |
| Zfp36l2 |
T |
C |
17: 84,493,980 (GRCm39) |
N219S |
probably damaging |
Het |
| Zfp626 |
T |
C |
7: 27,507,717 (GRCm39) |
M42T |
probably benign |
Het |
| Zscan21 |
C |
T |
5: 138,123,359 (GRCm39) |
P13S |
probably benign |
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 |
|
|
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'- AACCAAGTGTCCAGGACGTC -3'
(R):5'- TCAGATAGAGACCTGGCAGG -3'
Sequencing Primer
(F):5'- ACGTCAGGGTCTGGAGAC -3'
(R):5'- AACCTAGTGTGTGACAGTTCCCATG -3'
|
| Posted On |
2018-02-27 |
Incidental Mutation