Incidental Mutation 'R6211:Vars2'
ID 503479
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) question?
Stock # R6211 (G1)
Quality Score 192.009
Status Validated
Chromosome 17
Chromosomal Location 35966526-35978484 bp(-) (GRCm39)
Type of Mutation splice site (2079 bp from exon)
DNA Base Change (assembly) A to T at 35976554 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000124335 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001565] [ENSMUST00000043674] [ENSMUST00000160734] [ENSMUST00000160752] [ENSMUST00000169093] [ENSMUST00000165144]
AlphaFold Q3U2A8
Predicted Effect probably null
Transcript: ENSMUST00000001565
SMART Domains Protein: ENSMUSP00000001565
Gene: ENSMUSG00000001524

DomainStartEndE-ValueType
Pfam:Tfb2 22 375 6.4e-141 PFAM
PDB:3DOM|C 383 459 7e-13 PDB
Predicted Effect probably null
Transcript: ENSMUST00000043674
SMART Domains Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838

DomainStartEndE-ValueType
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: ENSMUST00000160535
Predicted Effect probably null
Transcript: ENSMUST00000160734
SMART Domains Protein: ENSMUSP00000124335
Gene: ENSMUSG00000001524

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:Tfb2 22 160 6.4e-32 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162894
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162927
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164978
Predicted Effect probably benign
Transcript: ENSMUST00000164404
SMART Domains Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838

DomainStartEndE-ValueType
Pfam:tRNA-synt_1 1 201 1e-49 PFAM
Pfam:tRNA-synt_1g 68 172 4e-7 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000171536
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168885
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165787
Predicted Effect probably benign
Transcript: ENSMUST00000168922
SMART Domains Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:tRNA-synt_1 1 109 1.7e-29 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000165144
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.6%
Validation Efficiency 100% (54/54)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acin1 A T 14: 54,881,503 (GRCm39) W391R probably damaging Het
Arl6ip1 A T 7: 117,726,473 (GRCm39) S18R probably benign Het
Armc3 G A 2: 19,301,614 (GRCm39) probably null Het
Ccdc162 G T 10: 41,506,141 (GRCm39) S883* probably null Het
Cd300lg A G 11: 101,944,995 (GRCm39) M358V possibly damaging Het
Cdh23 A G 10: 60,246,600 (GRCm39) V949A possibly damaging Het
Cenpo C T 12: 4,266,733 (GRCm39) S126N probably benign Het
Chd3 A T 11: 69,243,503 (GRCm39) D1366E probably damaging Het
Chd4 A G 6: 125,078,248 (GRCm39) E169G possibly damaging Het
Clec1b A G 6: 129,378,440 (GRCm39) T24A possibly damaging Het
Clhc1 A G 11: 29,528,145 (GRCm39) I558V probably damaging Het
Col5a2 T A 1: 45,415,826 (GRCm39) R1440S probably damaging Het
Cops3 A G 11: 59,708,727 (GRCm39) probably benign Het
Cxcr4 A G 1: 128,517,187 (GRCm39) V158A probably damaging Het
Dnah7a A G 1: 53,458,795 (GRCm39) M3781T probably damaging Het
Dnai7 C T 6: 145,146,217 (GRCm39) R95Q probably damaging Het
Elovl5 C A 9: 77,888,784 (GRCm39) T217K probably damaging Het
Fbln7 G T 2: 128,737,260 (GRCm39) M358I probably damaging Het
Fbxl13 C T 5: 21,689,019 (GRCm39) R763Q possibly damaging Het
Gabrr3 C A 16: 59,268,471 (GRCm39) N361K probably benign Het
Garre1 A T 7: 33,938,429 (GRCm39) H1035Q possibly damaging Het
Gbp7 A G 3: 142,251,754 (GRCm39) M534V probably benign Het
Hcar2 G A 5: 124,003,017 (GRCm39) T162I probably benign Het
Hdc A T 2: 126,435,897 (GRCm39) L658Q probably damaging Het
Hivep3 A G 4: 119,955,602 (GRCm39) Y1306C probably damaging Het
Homer3 C T 8: 70,738,174 (GRCm39) R49C probably damaging Het
Hspa4 C T 11: 53,153,766 (GRCm39) E702K probably benign Het
Iqgap3 A G 3: 87,998,822 (GRCm39) N308D probably benign Het
Itga8 G A 2: 12,198,320 (GRCm39) T555M probably damaging Het
Lrfn5 G T 12: 61,886,256 (GRCm39) V15L probably benign Het
Lrrk1 T C 7: 65,952,458 (GRCm39) K493E possibly damaging Het
Lyzl6 A G 11: 103,525,889 (GRCm39) I77T probably damaging Het
Mavs G T 2: 131,082,311 (GRCm39) R65L probably damaging Het
Mdn1 T G 4: 32,696,269 (GRCm39) D1217E probably benign Het
Or12d13 A T 17: 37,647,599 (GRCm39) F175I possibly damaging Het
Or52h1 A T 7: 103,828,954 (GRCm39) Y220* probably null Het
Or9i1 A G 19: 13,839,938 (GRCm39) I260M probably benign Het
Otof C A 5: 30,529,244 (GRCm39) V1762L probably damaging Het
Pcdha12 T C 18: 37,153,374 (GRCm39) L31P probably damaging Het
Pxk C A 14: 8,163,952 (GRCm38) P515T probably damaging Het
Qrich2 A T 11: 116,344,368 (GRCm39) D1759E probably benign Het
Rps6ka1 A T 4: 133,596,617 (GRCm39) F33Y probably damaging Het
Rxfp2 G A 5: 149,967,591 (GRCm39) probably null Het
Slc23a4 A T 6: 34,933,896 (GRCm39) I202N probably damaging Het
Slc24a5 A T 2: 124,930,171 (GRCm39) I491F probably benign Het
Slco1a1 T A 6: 141,854,775 (GRCm39) K625N probably benign Het
Snx31 A G 15: 36,547,030 (GRCm39) V51A probably damaging Het
Sox6 G T 7: 115,400,697 (GRCm39) H48Q probably damaging Het
Tas2r109 A T 6: 132,957,587 (GRCm39) Y114* probably null Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Timm13 A C 10: 80,736,314 (GRCm39) probably null Het
Tpsb2 G A 17: 25,586,737 (GRCm39) A250T possibly damaging Het
Trpm6 T C 19: 18,760,492 (GRCm39) I131T probably damaging Het
Vmn2r35 T A 7: 7,789,527 (GRCm39) I737F probably damaging Het
Wdr46 C A 17: 34,163,459 (GRCm39) T339K probably damaging Het
Other mutations in Vars2
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- TATCGGGAGCAGCCACTTTG -3'
(R):5'- TTCAGGCCATGGTGGAGAAG -3'

Sequencing Primer
(F):5'- GCAGCCACTTTGTGAAAAATGTGTG -3'
(R):5'- CGGAGACATGAGCTGAGCC -3'
Posted On 2018-02-27