Incidental Mutation 'R7553:Vars2'
ID |
584582 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vars2
|
Ensembl Gene |
ENSMUSG00000038838 |
Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
Synonyms |
Vars2l, 1190004I24Rik |
MMRRC Submission |
045622-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R7553 (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 T
at 35975680 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Cysteine to Serine
at position 246
(C246S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001565]
[ENSMUST00000043674]
[ENSMUST00000160734]
[ENSMUST00000160752]
[ENSMUST00000165144]
[ENSMUST00000169093]
|
AlphaFold |
Q3U2A8 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000001565
|
SMART Domains |
Protein: ENSMUSP00000001565 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
375 |
6.4e-141 |
PFAM |
PDB:3DOM|C
|
383 |
459 |
7e-13 |
PDB |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000043674
AA Change: C246S
PolyPhen 2
Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000047917 Gene: ENSMUSG00000038838 AA Change: C246S
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 |
probably benign
Transcript: ENSMUST00000160734
|
SMART Domains |
Protein: ENSMUSP00000124335 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
375 |
1.9e-137 |
PFAM |
PDB:3DOM|C
|
383 |
459 |
7e-13 |
PDB |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160752
|
SMART Domains |
Protein: ENSMUSP00000124458 Gene: ENSMUSG00000001524
Domain | Start | End | E-Value | Type |
Pfam:Tfb2
|
22 |
160 |
6.4e-32 |
PFAM |
|
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 |
probably benign
Transcript: ENSMUST00000165144
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000168922
|
SMART Domains |
Protein: ENSMUSP00000129196 Gene: ENSMUSG00000038838
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
Validation Efficiency |
98% (62/63) |
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: 66 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcc6 |
A |
G |
7: 45,648,545 (GRCm39) |
L649P |
probably damaging |
Het |
Acad10 |
T |
C |
5: 121,777,318 (GRCm39) |
Y371C |
probably damaging |
Het |
Avp |
A |
G |
2: 130,423,098 (GRCm39) |
V71A |
probably damaging |
Het |
Bhmt |
C |
T |
13: 93,756,589 (GRCm39) |
|
probably null |
Het |
Capn15 |
T |
C |
17: 26,179,738 (GRCm39) |
E874G |
probably damaging |
Het |
Capn5 |
A |
G |
7: 97,773,231 (GRCm39) |
F591S |
probably damaging |
Het |
Ccne2 |
A |
T |
4: 11,201,348 (GRCm39) |
Q292L |
probably benign |
Het |
Cd96 |
T |
G |
16: 45,872,384 (GRCm39) |
T406P |
probably damaging |
Het |
Csnk1e |
G |
A |
15: 79,310,566 (GRCm39) |
A153V |
probably damaging |
Het |
Dlk1 |
G |
A |
12: 109,420,889 (GRCm39) |
V15I |
unknown |
Het |
Dmbt1 |
A |
G |
7: 130,706,597 (GRCm39) |
N1372S |
unknown |
Het |
Dntt |
A |
T |
19: 41,017,926 (GRCm39) |
R17W |
probably damaging |
Het |
Erich3 |
G |
T |
3: 154,439,137 (GRCm39) |
A260S |
probably benign |
Het |
Foxp2 |
C |
T |
6: 15,437,881 (GRCm39) |
S669L |
unknown |
Het |
Gm40460 |
ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
7: 141,794,450 (GRCm39) |
|
probably benign |
Het |
Grid2 |
A |
G |
6: 64,053,925 (GRCm39) |
K375E |
possibly damaging |
Het |
Grin2b |
C |
T |
6: 135,749,394 (GRCm39) |
G603S |
possibly damaging |
Het |
Hexb |
C |
T |
13: 97,334,681 (GRCm39) |
R30Q |
probably benign |
Het |
Homer3 |
A |
T |
8: 70,742,774 (GRCm39) |
T162S |
probably benign |
Het |
L3mbtl1 |
A |
G |
2: 162,790,151 (GRCm39) |
E15G |
probably benign |
Het |
Manea |
A |
T |
4: 26,327,986 (GRCm39) |
F352I |
probably damaging |
Het |
Mcf2l |
T |
A |
8: 13,047,268 (GRCm39) |
M210K |
probably benign |
Het |
Morc3 |
T |
C |
16: 93,667,824 (GRCm39) |
L734P |
probably damaging |
Het |
Mybpc2 |
A |
G |
7: 44,155,571 (GRCm39) |
V894A |
possibly damaging |
Het |
Myh4 |
T |
A |
11: 67,147,221 (GRCm39) |
M1622K |
probably damaging |
Het |
Myrf |
A |
G |
19: 10,206,240 (GRCm39) |
F59L |
probably benign |
Het |
Ndst3 |
G |
T |
3: 123,350,709 (GRCm39) |
|
probably null |
Het |
Nln |
TGGTCCAGGTAAAACTGCCCCAGCCAATCAGGTACCTTGGATAGAGGTCCAGGTAAAACTGCCCCAGCCAATCAGGTACCTTGGATAGAGGTCCAGGTAGAACTGCCCCAGC |
TGGTCCAGGTAAAACTGCCCCAGCCAATCAGGTACCTTGGATAGAGGTCCAGGTAGAACTGCCCCAGC |
13: 104,186,924 (GRCm39) |
|
probably null |
Het |
Nos3 |
A |
T |
5: 24,586,715 (GRCm39) |
D986V |
possibly damaging |
Het |
Nrp1 |
G |
A |
8: 129,158,468 (GRCm39) |
A252T |
probably damaging |
Het |
Nup205 |
G |
T |
6: 35,178,934 (GRCm39) |
R668L |
probably damaging |
Het |
Or51aa2 |
T |
C |
7: 103,188,363 (GRCm39) |
Y26C |
probably damaging |
Het |
Or5af2 |
T |
A |
11: 58,707,886 (GRCm39) |
D17E |
probably benign |
Het |
Or5p56 |
G |
A |
7: 107,589,682 (GRCm39) |
V37I |
probably benign |
Het |
Pcdhga1 |
T |
A |
18: 37,882,735 (GRCm39) |
|
probably null |
Het |
Pck1 |
A |
G |
2: 172,998,860 (GRCm39) |
I373V |
probably benign |
Het |
Pde8b |
T |
C |
13: 95,223,258 (GRCm39) |
N227S |
probably benign |
Het |
Pianp |
T |
G |
6: 124,976,214 (GRCm39) |
S8A |
unknown |
Het |
Pkd1l3 |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
8: 110,350,827 (GRCm39) |
|
probably benign |
Het |
Pla2r1 |
A |
T |
2: 60,353,243 (GRCm39) |
N239K |
possibly damaging |
Het |
Pls1 |
T |
A |
9: 95,669,140 (GRCm39) |
N27I |
probably damaging |
Het |
Prep |
T |
C |
10: 45,034,620 (GRCm39) |
*711Q |
probably null |
Het |
Prkag3 |
A |
G |
1: 74,783,894 (GRCm39) |
F330L |
probably damaging |
Het |
Prss56 |
A |
G |
1: 87,111,261 (GRCm39) |
D16G |
probably benign |
Het |
Rad17 |
A |
T |
13: 100,769,794 (GRCm39) |
F255Y |
probably damaging |
Het |
Rap1gap2 |
T |
C |
11: 74,326,548 (GRCm39) |
E173G |
probably damaging |
Het |
Retreg3 |
C |
T |
11: 100,997,216 (GRCm39) |
R88H |
possibly damaging |
Het |
Rhag |
G |
A |
17: 41,139,286 (GRCm39) |
G74R |
probably damaging |
Het |
Rybp |
A |
G |
6: 100,209,220 (GRCm39) |
S201P |
possibly damaging |
Het |
S100a10 |
G |
A |
3: 93,471,602 (GRCm39) |
C62Y |
probably benign |
Het |
Scgb2b3 |
T |
A |
7: 31,059,673 (GRCm39) |
S34C |
possibly damaging |
Het |
Serpind1 |
A |
G |
16: 17,154,539 (GRCm39) |
D122G |
probably benign |
Het |
Setdb1 |
A |
G |
3: 95,254,076 (GRCm39) |
L242P |
probably damaging |
Het |
Slc14a2 |
T |
A |
18: 78,198,803 (GRCm39) |
I776F |
probably damaging |
Het |
Slc9a1 |
A |
G |
4: 133,139,580 (GRCm39) |
E266G |
probably damaging |
Het |
Stard9 |
A |
T |
2: 120,524,289 (GRCm39) |
|
probably null |
Het |
Stpg2 |
A |
G |
3: 138,924,098 (GRCm39) |
Y167C |
probably damaging |
Het |
Tex264 |
T |
C |
9: 106,536,335 (GRCm39) |
E274G |
probably damaging |
Het |
Tigd2 |
G |
A |
6: 59,188,564 (GRCm39) |
S477N |
probably benign |
Het |
Urb1 |
A |
G |
16: 90,589,752 (GRCm39) |
L343P |
probably damaging |
Het |
Vil1 |
G |
A |
1: 74,465,891 (GRCm39) |
|
probably null |
Het |
Vmn2r61 |
C |
G |
7: 41,916,205 (GRCm39) |
L273V |
not run |
Het |
Vmn2r-ps158 |
T |
G |
7: 42,697,447 (GRCm39) |
C835G |
probably damaging |
Het |
Zfp37 |
C |
A |
4: 62,110,236 (GRCm39) |
G317V |
probably damaging |
Het |
Zfp760 |
A |
G |
17: 21,941,872 (GRCm39) |
K349R |
possibly damaging |
Het |
Zyx |
A |
T |
6: 42,327,408 (GRCm39) |
E69V |
probably null |
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 |
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 |
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'- CTGGAACGATCTGAATGTCCATAC -3'
(R):5'- TTAAAGCCATAGGACGCCCC -3'
Sequencing Primer
(F):5'- GATCTGAATGTCCATACCTGACG -3'
(R):5'- GGTTCTATCTCCATCAGCGGG -3'
|
Posted On |
2019-10-17 |