Incidental Mutation 'R0445:Vars1'
ID 39341
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 038646-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.963) question?
Stock # R0445 (G1)
Quality Score 160
Status Validated
Chromosome 17
Chromosomal Location 35219963-35235298 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 35230785 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 557 (H557R)
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 benign
Transcript: ENSMUST00000087315
AA Change: H557R

PolyPhen 2 Score 0.110 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: H557R

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 benign
Transcript: ENSMUST00000173142
SMART Domains Protein: ENSMUSP00000134669
Gene: ENSMUSG00000007029

DomainStartEndE-ValueType
SCOP:d1gaxa3 32 67 3e-7 SMART
PDB:1IYW|B 36 122 4e-6 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000173584
AA Change: H557R

PolyPhen 2 Score 0.309 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: H557R

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: ENSMUST00000173302
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173911
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173336
Meta Mutation Damage Score 0.5321 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.3%
Validation Efficiency 100% (77/77)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700067P10Rik A C 17: 48,400,542 (GRCm39) probably null Het
A2m C T 6: 121,634,914 (GRCm39) T687I probably damaging Het
Acsbg1 A G 9: 54,523,179 (GRCm39) S483P probably damaging Het
Adam22 T A 5: 8,230,591 (GRCm39) probably benign Het
Aggf1 A G 13: 95,490,509 (GRCm39) V595A possibly damaging Het
Aplf A T 6: 87,640,734 (GRCm39) L71I probably damaging Het
Arid3c G T 4: 41,725,172 (GRCm39) P292T probably benign Het
Bltp1 T C 3: 37,054,214 (GRCm39) V3111A probably damaging Het
Brms1l T A 12: 55,908,191 (GRCm39) Y213* probably null Het
C87436 T A 6: 86,426,832 (GRCm39) S332T possibly damaging Het
Cad G A 5: 31,230,053 (GRCm39) A1454T probably benign Het
Cdkn3 T C 14: 47,004,857 (GRCm39) probably null Het
Cnot1 A G 8: 96,486,836 (GRCm39) C624R probably damaging Het
Cntnap5c A T 17: 58,411,738 (GRCm39) I541F probably benign Het
Dennd1b A G 1: 139,095,503 (GRCm39) probably benign Het
Dscam A T 16: 96,573,703 (GRCm39) I753N probably damaging Het
Eef2 C CN 10: 81,014,604 (GRCm39) probably null Het
Epg5 T A 18: 78,057,399 (GRCm39) V1826D possibly damaging Het
Epha8 T C 4: 136,659,711 (GRCm39) Y755C probably damaging Het
Esco1 A T 18: 10,574,989 (GRCm39) N694K probably damaging Het
Fermt3 T C 19: 6,980,667 (GRCm39) H300R probably benign Het
Galnt5 C A 2: 57,888,962 (GRCm39) F187L probably benign Het
Gm17067 A G 7: 42,358,046 (GRCm39) I152T probably benign Het
Gnb3 T C 6: 124,814,218 (GRCm39) D154G possibly damaging Het
Gpr155 G A 2: 73,200,488 (GRCm39) probably benign Het
Hdac3 A G 18: 38,076,777 (GRCm39) I240T probably damaging Het
Ifitm1 A T 7: 140,548,354 (GRCm39) probably null Het
Kif1b A T 4: 149,272,466 (GRCm39) L1455Q probably benign Het
Krt1 A C 15: 101,756,056 (GRCm39) L388R probably damaging Het
Lrp1 T A 10: 127,426,505 (GRCm39) K635* probably null Het
Map3k2 A G 18: 32,350,263 (GRCm39) Y371C probably damaging Het
Mcu T C 10: 59,292,467 (GRCm39) probably benign Het
Mkrn1 C T 6: 39,381,788 (GRCm39) V167I probably benign Het
Mrpl9 T A 3: 94,352,198 (GRCm39) probably benign Het
Naip2 T C 13: 100,298,395 (GRCm39) Y547C possibly damaging Het
Nup88 G A 11: 70,838,555 (GRCm39) T487I probably benign Het
Oas3 G A 5: 120,894,210 (GRCm39) R39C probably damaging Het
Obscn C T 11: 58,890,161 (GRCm39) R7457H unknown Het
Or13c25 G A 4: 52,910,849 (GRCm39) T315M probably benign Het
Or2y13 T A 11: 49,414,784 (GRCm39) V78E probably damaging Het
Paf1 T C 7: 28,095,113 (GRCm39) S118P probably damaging Het
Parp4 T A 14: 56,840,205 (GRCm39) probably null Het
Pcdh15 A T 10: 74,178,381 (GRCm39) Y157F probably damaging Het
Pex10 G A 4: 155,153,531 (GRCm39) probably null Het
Phrf1 C T 7: 140,827,244 (GRCm39) probably benign Het
Polr3a G T 14: 24,504,989 (GRCm39) D1090E probably benign Het
Ppfia4 A C 1: 134,255,027 (GRCm39) L276R probably benign Het
Rdh16f1 T C 10: 127,626,736 (GRCm39) L263S probably benign Het
Ryr3 T C 2: 112,696,399 (GRCm39) D967G probably benign Het
Shc1 G T 3: 89,333,844 (GRCm39) A226S probably damaging Het
Slc4a1 A G 11: 102,245,192 (GRCm39) V585A probably benign Het
Stk38l T A 6: 146,677,184 (GRCm39) S461T probably benign Het
Tbkbp1 A T 11: 97,040,295 (GRCm39) S40T probably damaging Het
Tet1 A G 10: 62,715,720 (GRCm39) M25T probably benign Het
Themis A G 10: 28,658,007 (GRCm39) R192G probably damaging Het
Tmem144 T C 3: 79,732,661 (GRCm39) T206A probably benign Het
Tmem74b G A 2: 151,548,879 (GRCm39) R202H probably damaging Het
Trpm1 T C 7: 63,894,590 (GRCm39) probably benign Het
Zbtb12 C A 17: 35,115,277 (GRCm39) A354E possibly damaging Het
Zfp143 A T 7: 109,660,324 (GRCm39) probably benign Het
Zftraf1 T C 15: 76,532,457 (GRCm39) H217R probably damaging 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
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
R0559:Vars1 UTSW 17 35,233,034 (GRCm39) nonsense probably null
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'- TCAGACACAGAGCCTTCTGTCACC -3'
(R):5'- GTCCGAACAGTTCTCATATCCAGCC -3'

Sequencing Primer
(F):5'- TGGCAACAACCCGGATTG -3'
(R):5'- ATATCCAGCCCCAGTCCTG -3'
Posted On 2013-05-23