Incidental Mutation 'R0559:Vars1'
ID 45810
Institutional Source Beutler Lab
Gene Symbol Vars1
Ensembl Gene ENSMUSG00000007029
Gene Name valyl-tRNA synthetase 1
Synonyms Bat6, Vars2, G7a, Bat-6, D17H6S56E, Vars
MMRRC Submission 038751-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.963) question?
Stock # R0559 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 35219963-35235298 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 35233034 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Stop codon at position 916 (C916*)
Ref Sequence ENSEMBL: ENSMUSP00000133994 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007245] [ENSMUST00000087315] [ENSMUST00000172499] [ENSMUST00000173584]
AlphaFold Q9Z1Q9
Predicted Effect probably benign
Transcript: ENSMUST00000007245
SMART Domains Protein: ENSMUSP00000007245
Gene: ENSMUSG00000007030

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
VWA 314 499 2.59e0 SMART
low complexity region 683 701 N/A INTRINSIC
low complexity region 840 861 N/A INTRINSIC
low complexity region 864 877 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000087315
AA Change: C916*
SMART Domains Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: C916*

DomainStartEndE-ValueType
Pfam:GST_N 2 81 5.7e-16 PFAM
Pfam:GST_C 107 198 7.3e-13 PFAM
low complexity region 234 256 N/A INTRINSIC
low complexity region 261 271 N/A INTRINSIC
Pfam:tRNA-synt_1 307 938 2e-197 PFAM
Pfam:tRNA-synt_1g 336 496 6e-6 PFAM
Pfam:tRNA-synt_1_2 555 623 1.9e-11 PFAM
Pfam:Anticodon_1 983 1138 2.6e-34 PFAM
low complexity region 1153 1174 N/A INTRINSIC
low complexity region 1207 1225 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000172499
SMART Domains Protein: ENSMUSP00000133418
Gene: ENSMUSG00000007030

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
VWA 314 478 7.28e0 SMART
low complexity region 662 680 N/A INTRINSIC
low complexity region 819 840 N/A INTRINSIC
low complexity region 843 856 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172637
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172999
Predicted Effect probably null
Transcript: ENSMUST00000173142
AA Change: C34*
SMART Domains Protein: ENSMUSP00000134669
Gene: ENSMUSG00000007029
AA Change: C34*

DomainStartEndE-ValueType
SCOP:d1gaxa3 32 67 3e-7 SMART
PDB:1IYW|B 36 122 4e-6 PDB
Predicted Effect probably null
Transcript: ENSMUST00000173584
AA Change: C916*
SMART Domains Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: C916*

DomainStartEndE-ValueType
low complexity region 25 38 N/A INTRINSIC
low complexity region 44 58 N/A INTRINSIC
low complexity region 78 89 N/A INTRINSIC
Pfam:GST_C 96 198 7.8e-14 PFAM
low complexity region 234 256 N/A INTRINSIC
low complexity region 261 271 N/A INTRINSIC
Pfam:tRNA-synt_1 307 938 1.9e-200 PFAM
Pfam:tRNA-synt_1g 336 493 2.1e-7 PFAM
Pfam:tRNA-synt_1_2 555 623 1.1e-12 PFAM
Pfam:Anticodon_1 983 1138 7.2e-36 PFAM
low complexity region 1153 1174 N/A INTRINSIC
coiled coil region 1197 1225 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173911
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173336
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173302
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.5%
Validation Efficiency 97% (34/35)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this gene belongs to class-I aminoacyl-tRNA synthetase family and is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1a A T 5: 8,748,535 (GRCm39) I289F probably benign Het
Adam15 G A 3: 89,251,085 (GRCm39) A540V probably damaging Het
Adat1 T C 8: 112,709,062 (GRCm39) T254A probably damaging Het
Agtpbp1 A G 13: 59,644,814 (GRCm39) V684A probably benign Het
Ahi1 A G 10: 20,876,618 (GRCm39) probably benign Het
Arl5b T C 2: 15,077,998 (GRCm39) Y108H probably damaging Het
Cep85l A G 10: 53,224,597 (GRCm39) F331L probably benign Het
Ctnna2 T C 6: 76,892,833 (GRCm39) K785E probably damaging Het
Dgkd T A 1: 87,842,826 (GRCm39) I118N probably damaging Het
Dicer1 G A 12: 104,672,560 (GRCm39) R896W probably damaging Het
Eif1ad19 T A 12: 87,740,223 (GRCm39) H112L probably benign Het
Fbxl19 G T 7: 127,349,390 (GRCm39) W160L possibly damaging Het
H1f8 T C 6: 115,924,760 (GRCm39) Y89H probably damaging Het
Ipo5 T C 14: 121,176,053 (GRCm39) V626A probably damaging Het
Isx A G 8: 75,600,369 (GRCm39) K34R probably benign Het
Myh6 T C 14: 55,196,011 (GRCm39) E596G probably benign Het
Olfml2a T C 2: 38,849,832 (GRCm39) I516T probably damaging Het
Or14j5 C T 17: 38,161,746 (GRCm39) R88* probably null Het
Or5w12 T G 2: 87,502,244 (GRCm39) T156P possibly damaging Het
Or8b37 G T 9: 37,959,123 (GRCm39) V202L probably benign Het
Parp9 T C 16: 35,768,362 (GRCm39) F181L probably benign Het
Pkdcc G A 17: 83,523,454 (GRCm39) G187D probably benign Het
Plekhh3 C T 11: 101,055,592 (GRCm39) E483K possibly damaging Het
Ptx4 C T 17: 25,342,082 (GRCm39) Q186* probably null Het
Qsox2 T A 2: 26,104,169 (GRCm39) H287L probably benign Het
Rev3l G A 10: 39,700,483 (GRCm39) G1660D probably damaging Het
Scamp1 G T 13: 94,344,690 (GRCm39) A217E possibly damaging Het
Slc5a9 T C 4: 111,742,779 (GRCm39) I438V probably benign Het
Sort1 T C 3: 108,263,895 (GRCm39) F818S probably damaging Het
Srl G A 16: 4,314,842 (GRCm39) P267S probably benign Het
Tbc1d1 T C 5: 64,331,136 (GRCm39) I105T probably damaging Het
Tifab A G 13: 56,324,060 (GRCm39) Y128H probably benign Het
Trp53bp1 A T 2: 121,058,282 (GRCm39) S907T probably damaging Het
Ubr1 G A 2: 120,778,364 (GRCm39) R225* probably null Het
Upk3bl A G 5: 136,086,330 (GRCm39) T89A probably benign Het
Ywhaz T C 15: 36,791,208 (GRCm39) E5G possibly damaging Het
Zfp91 T C 19: 12,747,419 (GRCm39) D568G probably damaging Het
Zgpat T C 2: 181,021,985 (GRCm39) probably benign Het
Other mutations in Vars1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01520:Vars1 APN 17 35,232,849 (GRCm39) missense probably benign 0.00
IGL02160:Vars1 APN 17 35,220,478 (GRCm39) missense probably damaging 1.00
IGL02303:Vars1 APN 17 35,234,460 (GRCm39) splice site probably benign
IGL03027:Vars1 APN 17 35,232,663 (GRCm39) missense probably damaging 1.00
Maladroit UTSW 17 35,224,451 (GRCm39) missense probably benign 0.30
Whoops UTSW 17 35,232,620 (GRCm39) missense probably damaging 1.00
FR4304:Vars1 UTSW 17 35,234,965 (GRCm39) small insertion probably benign
FR4548:Vars1 UTSW 17 35,234,967 (GRCm39) small insertion probably benign
FR4548:Vars1 UTSW 17 35,234,965 (GRCm39) small insertion probably benign
FR4589:Vars1 UTSW 17 35,234,964 (GRCm39) small insertion probably benign
R0045:Vars1 UTSW 17 35,229,595 (GRCm39) missense probably damaging 1.00
R0045:Vars1 UTSW 17 35,229,595 (GRCm39) missense probably damaging 1.00
R0045:Vars1 UTSW 17 35,217,042 (GRCm39) missense probably benign 0.13
R0266:Vars1 UTSW 17 35,232,845 (GRCm39) missense probably benign 0.00
R0267:Vars1 UTSW 17 35,230,572 (GRCm39) splice site probably benign
R0391:Vars1 UTSW 17 35,230,462 (GRCm39) missense possibly damaging 0.79
R0445:Vars1 UTSW 17 35,230,785 (GRCm39) missense probably benign 0.31
R0449:Vars1 UTSW 17 35,231,703 (GRCm39) splice site probably null
R0557:Vars1 UTSW 17 35,223,960 (GRCm39) missense possibly damaging 0.90
R0730:Vars1 UTSW 17 35,233,276 (GRCm39) missense probably damaging 1.00
R0748:Vars1 UTSW 17 35,216,988 (GRCm39) missense probably damaging 1.00
R1692:Vars1 UTSW 17 35,232,701 (GRCm39) missense probably damaging 1.00
R1693:Vars1 UTSW 17 35,217,172 (GRCm39) missense probably benign 0.31
R1697:Vars1 UTSW 17 35,217,198 (GRCm39) missense probably benign 0.43
R1699:Vars1 UTSW 17 35,233,734 (GRCm39) missense possibly damaging 0.93
R1712:Vars1 UTSW 17 35,233,728 (GRCm39) missense probably damaging 1.00
R1989:Vars1 UTSW 17 35,230,814 (GRCm39) missense possibly damaging 0.94
R2349:Vars1 UTSW 17 35,234,728 (GRCm39) missense probably benign
R2365:Vars1 UTSW 17 35,234,428 (GRCm39) missense probably benign 0.01
R3790:Vars1 UTSW 17 35,218,310 (GRCm39) missense probably benign 0.34
R4615:Vars1 UTSW 17 35,232,857 (GRCm39) missense probably damaging 0.97
R4844:Vars1 UTSW 17 35,230,588 (GRCm39) missense probably damaging 1.00
R4856:Vars1 UTSW 17 35,234,702 (GRCm39) missense probably benign 0.37
R4886:Vars1 UTSW 17 35,234,702 (GRCm39) missense probably benign 0.37
R5570:Vars1 UTSW 17 35,235,214 (GRCm39) missense probably benign 0.04
R5706:Vars1 UTSW 17 35,224,457 (GRCm39) splice site probably null
R5858:Vars1 UTSW 17 35,224,451 (GRCm39) missense probably benign 0.30
R5907:Vars1 UTSW 17 35,231,352 (GRCm39) missense probably damaging 1.00
R5917:Vars1 UTSW 17 35,231,491 (GRCm39) missense probably damaging 0.99
R5944:Vars1 UTSW 17 35,232,620 (GRCm39) missense probably damaging 1.00
R6023:Vars1 UTSW 17 35,220,585 (GRCm39) missense probably damaging 1.00
R6073:Vars1 UTSW 17 35,220,505 (GRCm39) missense probably benign
R6273:Vars1 UTSW 17 35,232,719 (GRCm39) missense probably damaging 1.00
R6390:Vars1 UTSW 17 35,234,615 (GRCm39) missense probably benign 0.00
R6658:Vars1 UTSW 17 35,234,717 (GRCm39) missense probably benign 0.03
R7067:Vars1 UTSW 17 35,230,455 (GRCm39) missense probably damaging 0.98
R7387:Vars1 UTSW 17 35,223,768 (GRCm39) nonsense probably null
R7954:Vars1 UTSW 17 35,234,960 (GRCm39) missense probably benign 0.01
R8139:Vars1 UTSW 17 35,230,480 (GRCm39) missense probably benign 0.16
R8347:Vars1 UTSW 17 35,234,953 (GRCm39) missense possibly damaging 0.92
R8387:Vars1 UTSW 17 35,229,490 (GRCm39) missense probably damaging 0.99
R8855:Vars1 UTSW 17 35,234,620 (GRCm39) missense probably benign 0.00
R8866:Vars1 UTSW 17 35,234,620 (GRCm39) missense probably benign 0.00
R9131:Vars1 UTSW 17 35,223,773 (GRCm39) missense possibly damaging 0.77
R9620:Vars1 UTSW 17 35,235,001 (GRCm39) missense unknown
R9695:Vars1 UTSW 17 35,231,564 (GRCm39) missense possibly damaging 0.82
Z1177:Vars1 UTSW 17 35,230,453 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGTGGCTAGAACGATCTGACACCTC -3'
(R):5'- CGCAGGGCAAACTTGGTAGCATTC -3'

Sequencing Primer
(F):5'- TAGGGCCTCTATGACCAACTACTG -3'
(R):5'- CAAACTTGGTAGCATTCCAGAG -3'
Posted On 2013-06-11