Incidental Mutation 'R2504:Vars2'
ID 252276
Institutional Source Beutler Lab
Gene Symbol Vars2
Ensembl Gene ENSMUSG00000038838
Gene Name valyl-tRNA synthetase 2, mitochondrial
Synonyms Vars2l, 1190004I24Rik
MMRRC Submission 040412-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2504 (G1)
Quality Score 127
Status Not validated
Chromosome 17
Chromosomal Location 35966526-35978484 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 35975685 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 244 (R244Q)
Ref Sequence ENSEMBL: ENSMUSP00000047917 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001565] [ENSMUST00000043674] [ENSMUST00000160734] [ENSMUST00000160752] [ENSMUST00000169093] [ENSMUST00000165144]
AlphaFold Q3U2A8
Predicted Effect probably benign
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 damaging
Transcript: ENSMUST00000043674
AA Change: R244Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: R244Q

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 benign
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: ENSMUST00000162927
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165787
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164978
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174129
Predicted Effect noncoding transcript
Transcript: ENSMUST00000171536
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173162
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168885
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: 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 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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.4%
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: 113 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatk T C 11: 119,909,681 (GRCm39) D28G probably benign Het
Abcg1 T A 17: 31,311,369 (GRCm39) S125T probably damaging Het
Actbl2 T C 13: 111,392,717 (GRCm39) S351P possibly damaging Het
Ankrd34b A G 13: 92,575,569 (GRCm39) probably null Het
BC051665 C T 13: 60,930,468 (GRCm39) V295I probably benign Het
C1qtnf2 A G 11: 43,381,983 (GRCm39) N265S probably damaging Het
Ccdc14 C T 16: 34,542,220 (GRCm39) R573* probably null Het
Cd55b A T 1: 130,337,612 (GRCm39) Y247N probably damaging Het
Celsr2 A T 3: 108,320,907 (GRCm39) V635E probably benign Het
Clec16a T C 16: 10,377,551 (GRCm39) probably benign Het
Clec4b1 A G 6: 123,042,904 (GRCm39) Y41C probably damaging Het
Cntn5 A T 9: 10,172,126 (GRCm39) D19E probably benign Het
Cop1 A G 1: 159,060,375 (GRCm39) N53S probably damaging Het
Cplane1 G A 15: 8,248,700 (GRCm39) E1750K probably damaging Het
Csad A T 15: 102,097,102 (GRCm39) M1K probably null Het
Cyb5rl A G 4: 106,938,142 (GRCm39) I200V probably benign Het
Cyp26a1 A G 19: 37,686,790 (GRCm39) T81A probably damaging Het
Cyp2d12 A T 15: 82,443,237 (GRCm39) H433L probably benign Het
D7Ertd443e T A 7: 133,951,208 (GRCm39) probably null Het
Dennd1b A G 1: 139,097,908 (GRCm39) probably benign Het
Dmap1 G T 4: 117,532,495 (GRCm39) T357K probably damaging Het
Dzip1 G T 14: 119,118,456 (GRCm39) T759K probably benign Het
Elmo2 A G 2: 165,140,607 (GRCm39) V300A probably damaging Het
Eml5 T C 12: 98,810,364 (GRCm39) D864G possibly damaging Het
Ep400 A G 5: 110,816,511 (GRCm39) V2670A probably damaging Het
Epha3 T A 16: 63,423,988 (GRCm39) I534F probably damaging Het
Epha4 A C 1: 77,359,628 (GRCm39) Y742D probably damaging Het
Ergic2 A G 6: 148,106,272 (GRCm39) probably null Het
Ero1a A T 14: 45,536,545 (GRCm39) probably null Het
Fam229a A G 4: 129,385,279 (GRCm39) D70G probably damaging Het
Fbn2 C T 18: 58,226,431 (GRCm39) R781Q probably damaging Het
Fbxo16 A T 14: 65,508,163 (GRCm39) probably benign Het
Fbxo39 T A 11: 72,208,111 (GRCm39) S154R probably benign Het
Fer T A 17: 64,298,575 (GRCm39) probably null Het
Filip1l A T 16: 57,391,410 (GRCm39) D428V probably damaging Het
Filip1l A G 16: 57,391,025 (GRCm39) I538V possibly damaging Het
Fsip2 T C 2: 82,809,954 (GRCm39) I2091T possibly damaging Het
Glyat A C 19: 12,628,762 (GRCm39) T186P possibly damaging Het
Gm10604 A G 4: 11,980,083 (GRCm39) S74P unknown Het
Gm4787 T G 12: 81,425,911 (GRCm39) K82N possibly damaging Het
Hectd4 T C 5: 121,358,683 (GRCm39) I50T unknown Het
Hectd4 T C 5: 121,402,030 (GRCm39) S373P possibly damaging Het
Hmcn1 A T 1: 150,562,618 (GRCm39) C2313* probably null Het
Hrob T C 11: 102,146,122 (GRCm39) Y133H possibly damaging Het
Igfn1 A T 1: 135,897,054 (GRCm39) S1171T probably benign Het
Ints8 T C 4: 11,241,642 (GRCm39) D267G probably benign Het
Itln1 A G 1: 171,356,727 (GRCm39) C251R probably damaging Het
Jcad C T 18: 4,674,026 (GRCm39) T596M probably damaging Het
Kcnj16 C T 11: 110,916,409 (GRCm39) T357M probably benign Het
Kif13a G A 13: 46,967,676 (GRCm39) T346M probably damaging Het
Klhl24 G A 16: 19,938,917 (GRCm39) A491T probably benign Het
Kntc1 C T 5: 123,916,410 (GRCm39) Q748* probably null Het
Krt25 T A 11: 99,208,122 (GRCm39) K369* probably null Het
Krt75 C T 15: 101,476,466 (GRCm39) R433Q probably benign Het
Krt76 A G 15: 101,793,293 (GRCm39) F582L unknown Het
Lysmd1 G A 3: 95,045,708 (GRCm39) V182I probably benign Het
Mab21l2 T A 3: 86,454,862 (GRCm39) E46V probably damaging Het
Magi2 A T 5: 20,563,934 (GRCm39) K355N probably damaging Het
Marchf10 T C 11: 105,276,398 (GRCm39) D630G probably damaging Het
Mast4 A T 13: 102,875,147 (GRCm39) I1215N probably damaging Het
Nckap1 G A 2: 80,360,562 (GRCm39) T523I probably benign Het
Nexmif T A X: 103,127,999 (GRCm39) D1306V probably damaging Het
Nfkb1 A C 3: 135,295,090 (GRCm39) I918R possibly damaging Het
Nt5el A G 13: 105,246,250 (GRCm39) I270M probably benign Het
Nup50 A T 15: 84,817,859 (GRCm39) T93S probably benign Het
Nwd2 T C 5: 63,961,717 (GRCm39) Y434H probably benign Het
Or13a28 T C 7: 140,218,397 (GRCm39) V261A probably benign Het
Osbpl1a C A 18: 13,038,088 (GRCm39) V288L probably benign Het
Pan3 A G 5: 147,463,846 (GRCm39) E562G possibly damaging Het
Pappa T A 4: 65,099,126 (GRCm39) Y548* probably null Het
Phf3 A T 1: 30,849,870 (GRCm39) L1181Q probably damaging Het
Phip T C 9: 82,797,392 (GRCm39) H537R possibly damaging Het
Pkhd1l1 T C 15: 44,348,824 (GRCm39) I240T probably damaging Het
Pole G A 5: 110,438,368 (GRCm39) probably null Het
Polq T A 16: 36,832,304 (GRCm39) S15T unknown Het
Prrt2 T C 7: 126,619,396 (GRCm39) E23G possibly damaging Het
Prss37 A T 6: 40,494,760 (GRCm39) probably null Het
Prune2 T C 19: 16,977,400 (GRCm39) L45P probably damaging Het
Psd A T 19: 46,313,352 (GRCm39) M6K possibly damaging Het
Psmd1 A G 1: 86,017,719 (GRCm39) E510G possibly damaging Het
Ptch1 T G 13: 63,672,773 (GRCm39) E944A probably benign Het
Pxdn T A 12: 30,053,405 (GRCm39) I1194N probably damaging Het
Rbp3 C T 14: 33,677,975 (GRCm39) T641M probably damaging Het
Rgmb C A 17: 16,027,909 (GRCm39) R270L probably benign Het
Rpgrip1l A G 8: 92,007,344 (GRCm39) probably null Het
Rps2 G A 17: 24,939,353 (GRCm39) probably benign Het
Rsbn1l G T 5: 21,107,364 (GRCm39) A550E probably damaging Het
S1pr4 C T 10: 81,335,138 (GRCm39) R112H probably benign Het
Scfd2 T C 5: 74,691,838 (GRCm39) N148S probably damaging Het
Scin C T 12: 40,131,705 (GRCm39) M276I probably benign Het
Sec24d T C 3: 123,147,255 (GRCm39) I708T possibly damaging Het
Skint11 T A 4: 114,086,009 (GRCm39) F41I possibly damaging Het
Slc15a4 A T 5: 127,694,303 (GRCm39) F44Y possibly damaging Het
Slc6a18 A G 13: 73,823,925 (GRCm39) Y72H probably benign Het
Slc7a11 A T 3: 50,332,195 (GRCm39) probably null Het
Slc7a14 G T 3: 31,291,650 (GRCm39) N209K possibly damaging Het
Sstr2 T C 11: 113,515,257 (GRCm39) C59R probably damaging Het
Stab1 A G 14: 30,884,997 (GRCm39) probably null Het
Stag1 G T 9: 100,748,263 (GRCm39) S475I probably damaging Het
Stxbp5l A G 16: 36,936,029 (GRCm39) Y1183H probably damaging Het
Svep1 A T 4: 58,135,628 (GRCm39) probably null Het
Tm9sf2 A G 14: 122,396,096 (GRCm39) T653A probably benign Het
Tmeff1 T C 4: 48,662,059 (GRCm39) S366P possibly damaging Het
Tnnt2 G T 1: 135,779,803 (GRCm39) W300L probably damaging Het
Traj32 A G 14: 54,423,560 (GRCm39) probably benign Het
Trp53bp2 A T 1: 182,269,204 (GRCm39) M223L probably benign Het
Tsga10 G A 1: 37,854,758 (GRCm39) T246M probably damaging Het
Txn2 A T 15: 77,810,870 (GRCm39) probably benign Het
Ubr3 T A 2: 69,768,542 (GRCm39) F450I probably damaging Het
Usp47 T C 7: 111,703,677 (GRCm39) probably null Het
Xrra1 T A 7: 99,546,803 (GRCm39) F251L probably damaging Het
Zfp804a G A 2: 82,087,863 (GRCm39) R564Q probably benign Het
Zfp983 T C 17: 21,877,883 (GRCm39) C29R 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
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'- GGAACGATCTGAATGTCCATACC -3'
(R):5'- TTTAAAGCCATAGGACGCCC -3'

Sequencing Primer
(F):5'- GATCTGAATGTCCATACCTGACG -3'
(R):5'- GGTTCTATCTCCATCAGCGGG -3'
Posted On 2014-12-04