Incidental Mutation 'PIT4445001:Vars2'
| ID |
555433 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vars2
|
| Ensembl Gene |
ENSMUSG00000038838 |
| Gene Name |
valyl-tRNA synthetase 2, mitochondrial |
| Synonyms |
Vars2l, 1190004I24Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4445001 (G1)
|
| Quality Score |
199.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
35966526-35978484 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
A to T
at 35977103 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Stop codon
at position 142
(C142*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001565]
[ENSMUST00000043674]
[ENSMUST00000160039]
[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 |
probably null
Transcript: ENSMUST00000043674
AA Change: C142*
|
| SMART Domains |
Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: C142*
| 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: ENSMUST00000160039
|
| SMART Domains |
Protein: ENSMUSP00000124683
Gene: ENSMUSG00000001524
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Tfb2
|
22 |
164 |
2.9e-44 |
PFAM |
|
| 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: 93.5%
- 3x: 90.8%
- 10x: 84.5%
- 20x: 70.9%
|
| 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: 73 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
T |
C |
11: 109,966,377 (GRCm39) |
K419E |
probably damaging |
Het |
| Adam7 |
T |
A |
14: 68,747,197 (GRCm39) |
K587N |
possibly damaging |
Het |
| Agl |
T |
C |
3: 116,565,109 (GRCm39) |
M382V |
|
Het |
| Agpat3 |
A |
T |
10: 78,109,927 (GRCm39) |
F341I |
possibly damaging |
Het |
| Ampd2 |
A |
T |
3: 107,982,328 (GRCm39) |
L767Q |
probably damaging |
Het |
| Arhgap28 |
A |
T |
17: 68,203,230 (GRCm39) |
D124E |
possibly damaging |
Het |
| Arhgap32 |
T |
C |
9: 32,172,152 (GRCm39) |
L1644P |
probably damaging |
Het |
| Asic4 |
T |
C |
1: 75,427,771 (GRCm39) |
V99A |
probably benign |
Het |
| Asns |
T |
A |
6: 7,689,277 (GRCm39) |
N75I |
probably damaging |
Het |
| Atp10a |
A |
G |
7: 58,453,215 (GRCm39) |
D798G |
probably damaging |
Het |
| Atp8a1 |
A |
G |
5: 67,780,003 (GRCm39) |
V1145A |
|
Het |
| Ccdc171 |
A |
G |
4: 83,579,984 (GRCm39) |
Q577R |
probably damaging |
Het |
| Cd247 |
T |
A |
1: 165,688,605 (GRCm39) |
D154E |
probably damaging |
Het |
| Ceacam1 |
A |
T |
7: 25,175,881 (GRCm39) |
N104K |
probably damaging |
Het |
| Chfr |
A |
G |
5: 110,299,543 (GRCm39) |
D312G |
possibly damaging |
Het |
| Ddb1 |
C |
A |
19: 10,603,334 (GRCm39) |
L881I |
probably damaging |
Het |
| Dgkh |
A |
T |
14: 78,813,382 (GRCm39) |
I1032N |
possibly damaging |
Het |
| Efcab6 |
A |
T |
15: 83,788,468 (GRCm39) |
V942D |
probably benign |
Het |
| Fmo5 |
A |
G |
3: 97,558,844 (GRCm39) |
T435A |
probably benign |
Het |
| Fpr1 |
T |
C |
17: 18,097,155 (GRCm39) |
Q278R |
probably benign |
Het |
| Fzr1 |
C |
T |
10: 81,205,228 (GRCm39) |
W256* |
probably null |
Het |
| Gabrb1 |
T |
C |
5: 72,266,125 (GRCm39) |
S261P |
probably damaging |
Het |
| Galr2 |
G |
T |
11: 116,172,474 (GRCm39) |
A55S |
probably benign |
Het |
| Gbp2 |
A |
T |
3: 142,343,227 (GRCm39) |
K581N |
probably benign |
Het |
| Gria1 |
A |
T |
11: 57,076,664 (GRCm39) |
Y89F |
probably damaging |
Het |
| Ibsp |
T |
A |
5: 104,450,170 (GRCm39) |
I26N |
possibly damaging |
Het |
| Igf1r |
T |
C |
7: 67,857,211 (GRCm39) |
F1058L |
probably damaging |
Het |
| Ighv1-16 |
A |
C |
12: 114,629,680 (GRCm39) |
C36G |
probably benign |
Het |
| Igll1 |
T |
C |
16: 16,678,783 (GRCm39) |
T176A |
probably benign |
Het |
| Ilkap |
T |
C |
1: 91,313,067 (GRCm39) |
T143A |
probably benign |
Het |
| Kdm3b |
A |
T |
18: 34,926,168 (GRCm39) |
K103* |
probably null |
Het |
| Mphosph9 |
A |
G |
5: 124,436,853 (GRCm39) |
I497T |
possibly damaging |
Het |
| Mrgpra3 |
G |
A |
7: 47,239,908 (GRCm39) |
T6I |
possibly damaging |
Het |
| Mrpl38 |
T |
C |
11: 116,023,384 (GRCm39) |
|
probably null |
Het |
| Myo3a |
A |
T |
2: 22,434,457 (GRCm39) |
E813V |
possibly damaging |
Het |
| Myo7b |
T |
C |
18: 32,095,405 (GRCm39) |
K1851R |
probably damaging |
Het |
| Myo7b |
G |
T |
18: 32,092,519 (GRCm39) |
Q2093K |
possibly damaging |
Het |
| P3h2 |
T |
A |
16: 25,803,749 (GRCm39) |
D339V |
probably benign |
Het |
| Pcdhb6 |
C |
A |
18: 37,468,300 (GRCm39) |
P407Q |
possibly damaging |
Het |
| Plch2 |
C |
A |
4: 155,093,483 (GRCm39) |
R153L |
probably damaging |
Het |
| Plppr4 |
G |
A |
3: 117,153,957 (GRCm39) |
|
probably benign |
Het |
| Ppp1r3a |
A |
G |
6: 14,717,776 (GRCm39) |
F1046S |
probably damaging |
Het |
| Pramel41 |
T |
G |
5: 94,596,366 (GRCm39) |
W468G |
probably benign |
Het |
| Prkacb |
A |
T |
3: 146,461,446 (GRCm39) |
L107M |
probably benign |
Het |
| Ranbp17 |
A |
G |
11: 33,431,020 (GRCm39) |
|
probably null |
Het |
| Rasl11b |
C |
A |
5: 74,357,994 (GRCm39) |
P88Q |
probably damaging |
Het |
| Rcc2 |
A |
G |
4: 140,448,460 (GRCm39) |
E503G |
possibly damaging |
Het |
| Rnf216 |
T |
A |
5: 143,071,758 (GRCm39) |
K407N |
probably damaging |
Het |
| Rusf1 |
A |
G |
7: 127,875,706 (GRCm39) |
V243A |
probably benign |
Het |
| Scrn3 |
G |
A |
2: 73,148,673 (GRCm39) |
M81I |
possibly damaging |
Het |
| Scube2 |
T |
C |
7: 109,408,387 (GRCm39) |
T687A |
probably benign |
Het |
| Serpinb10 |
T |
A |
1: 107,463,728 (GRCm39) |
F3L |
probably benign |
Het |
| Sgcb |
C |
T |
5: 73,797,155 (GRCm39) |
V202I |
probably damaging |
Het |
| Sgce |
A |
G |
6: 4,689,654 (GRCm39) |
V429A |
possibly damaging |
Het |
| Sh3rf2 |
T |
C |
18: 42,286,229 (GRCm39) |
V574A |
probably benign |
Het |
| Sncaip |
T |
C |
18: 53,002,016 (GRCm39) |
L179S |
probably damaging |
Het |
| Sntg2 |
A |
T |
12: 30,362,571 (GRCm39) |
D58E |
probably damaging |
Het |
| Taar3 |
T |
C |
10: 23,825,586 (GRCm39) |
I44T |
possibly damaging |
Het |
| Tmem87b |
G |
A |
2: 128,673,391 (GRCm39) |
V227I |
probably benign |
Het |
| Tnfsf9 |
T |
C |
17: 57,412,517 (GRCm39) |
L29P |
possibly damaging |
Het |
| Tnip2 |
T |
C |
5: 34,654,215 (GRCm39) |
H391R |
probably benign |
Het |
| Traf5 |
A |
G |
1: 191,729,768 (GRCm39) |
Y125H |
|
Het |
| Ttc23 |
T |
G |
7: 67,316,961 (GRCm39) |
I77M |
probably damaging |
Het |
| Ube2l3 |
T |
C |
16: 16,978,036 (GRCm39) |
N43S |
probably benign |
Het |
| Vmn2r15 |
A |
C |
5: 109,435,008 (GRCm39) |
D565E |
probably damaging |
Het |
| Vmn2r56 |
C |
T |
7: 12,449,153 (GRCm39) |
|
probably null |
Het |
| Vmn2r79 |
A |
T |
7: 86,651,408 (GRCm39) |
D269V |
possibly damaging |
Het |
| Vmn2r85 |
A |
T |
10: 130,261,572 (GRCm39) |
M255K |
probably benign |
Het |
| Wfdc6a |
T |
A |
2: 164,421,746 (GRCm39) |
*137C |
probably null |
Het |
| Wipi2 |
T |
C |
5: 142,652,639 (GRCm39) |
V417A |
probably benign |
Het |
| Xirp2 |
G |
T |
2: 67,340,116 (GRCm39) |
V786L |
possibly damaging |
Het |
| Zdhhc13 |
G |
A |
7: 48,445,697 (GRCm39) |
G26S |
probably benign |
Het |
| Zscan25 |
T |
A |
5: 145,227,422 (GRCm39) |
V362D |
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 |
|
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 |
|
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'- TGCCACAGAAACACCATGGG -3'
(R):5'- GCACAGGCTAACTTCACAGTTG -3'
Sequencing Primer
(F):5'- GGACTCTGAGCTCACTGATC -3'
(R):5'- TCCTGGAACTCTGTAGACGAG -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation