Incidental Mutation 'R0266:Vars1'
ID 34958
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 038492-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.963) question?
Stock # R0266 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 35219963-35235298 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 35232845 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 896 (S896R)
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: S896R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: S896R

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 unknown
Transcript: ENSMUST00000173142
AA Change: S14R
SMART Domains Protein: ENSMUSP00000134669
Gene: ENSMUSG00000007029
AA Change: S14R

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: S896R

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: S896R

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: ENSMUST00000174084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173302
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173336
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173911
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 98.3%
  • 3x: 97.2%
  • 10x: 94.9%
  • 20x: 89.8%
Validation Efficiency 100% (79/79)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001K19Rik A G 12: 110,635,188 (GRCm39) S117P possibly damaging Het
Aars2 T C 17: 45,818,436 (GRCm39) probably benign Het
Acot11 T C 4: 106,607,185 (GRCm39) D466G probably damaging Het
Adgrd1 G A 5: 129,216,658 (GRCm39) A342T probably benign Het
Apbb2 A T 5: 66,459,954 (GRCm39) N714K probably benign Het
Aqp12 C A 1: 92,934,572 (GRCm39) H150N possibly damaging Het
Brinp3 T A 1: 146,558,418 (GRCm39) L114* probably null Het
Ccng2 T C 5: 93,419,148 (GRCm39) probably benign Het
Cd36 T A 5: 18,003,250 (GRCm39) R265S probably benign Het
Ces4a T C 8: 105,868,598 (GRCm39) L104S probably benign Het
Clca4b T C 3: 144,628,547 (GRCm39) I387V probably damaging Het
Cul7 T A 17: 46,965,521 (GRCm39) H566Q probably benign Het
Ddx60 A T 8: 62,486,527 (GRCm39) H1646L possibly damaging Het
Dntt T C 19: 41,047,566 (GRCm39) I503T probably damaging Het
Dynlt1a T G 17: 6,367,670 (GRCm39) E2D probably benign Het
Efemp2 G T 19: 5,528,027 (GRCm39) C78F probably damaging Het
Esco1 T C 18: 10,594,605 (GRCm39) E227G probably benign Het
Fezf2 T A 14: 12,342,607 (GRCm38) K419N probably damaging Het
Gm17541 A T 12: 4,739,487 (GRCm39) probably benign Het
Gm2381 G A 7: 42,469,372 (GRCm39) Q251* probably null Het
Gm4782 T G 6: 50,587,674 (GRCm39) S686R probably damaging Het
Grin3a G A 4: 49,665,501 (GRCm39) R1045* probably null Het
Grm8 T C 6: 27,285,895 (GRCm39) Y839C probably damaging Het
Gtf3c1 G A 7: 125,243,306 (GRCm39) P1766L possibly damaging Het
Herc2 T A 7: 55,856,326 (GRCm39) H3921Q probably damaging Het
Hes6 A T 1: 91,340,026 (GRCm39) D143E possibly damaging Het
Hmcn2 A G 2: 31,284,839 (GRCm39) E2055G probably benign Het
Hmcn2 G A 2: 31,335,365 (GRCm39) probably benign Het
Ikzf3 A G 11: 98,358,143 (GRCm39) L398P probably benign Het
Il10ra A T 9: 45,176,950 (GRCm39) I125N probably benign Het
Kcnb2 G A 1: 15,783,137 (GRCm39) probably benign Het
Krt77 T C 15: 101,777,813 (GRCm39) R81G possibly damaging Het
Lrrc40 T A 3: 157,747,298 (GRCm39) probably null Het
Man1a2 C T 3: 100,489,350 (GRCm39) R543Q probably damaging Het
Mansc1 T C 6: 134,587,670 (GRCm39) D169G probably benign Het
Mdn1 T A 4: 32,741,835 (GRCm39) S3869T probably damaging Het
Mettl14 A T 3: 123,176,475 (GRCm39) S58T probably benign Het
Mrpl4 T C 9: 20,914,610 (GRCm39) V62A probably benign Het
Myh3 A G 11: 66,984,498 (GRCm39) D1085G possibly damaging Het
Myo5c C A 9: 75,191,498 (GRCm39) probably benign Het
Naalad2 G T 9: 18,262,239 (GRCm39) probably benign Het
Nat3 A G 8: 68,000,432 (GRCm39) T104A probably benign Het
Nek4 A G 14: 30,679,253 (GRCm39) E198G probably damaging Het
Olfm1 A G 2: 28,119,619 (GRCm39) Y403C probably damaging Het
Or5w11 C A 2: 87,459,626 (GRCm39) T273K possibly damaging Het
Or7e177 A T 9: 20,212,454 (GRCm39) R320S probably benign Het
Osbpl1a T A 18: 13,004,220 (GRCm39) probably null Het
Pax7 G A 4: 139,507,047 (GRCm39) S330L possibly damaging Het
Pcdhb15 C A 18: 37,608,329 (GRCm39) D520E probably damaging Het
Pgm3 T C 9: 86,449,586 (GRCm39) T145A probably benign Het
Phox2b G A 5: 67,253,968 (GRCm39) probably null Het
Pik3r6 A T 11: 68,417,234 (GRCm39) R59* probably null Het
Pold1 A G 7: 44,190,449 (GRCm39) probably benign Het
Ppp1r21 T C 17: 88,876,500 (GRCm39) probably benign Het
Prl5a1 A G 13: 28,333,970 (GRCm39) K158E possibly damaging Het
Rag2 T G 2: 101,460,948 (GRCm39) C419W probably damaging Het
Reln A G 5: 22,193,774 (GRCm39) S1395P probably damaging Het
Retnlb T G 16: 48,639,022 (GRCm39) Y74* probably null Het
Robo3 A G 9: 37,333,936 (GRCm39) S633P probably damaging Het
Ryr1 A G 7: 28,740,104 (GRCm39) S3941P probably damaging Het
Scnn1b A G 7: 121,511,698 (GRCm39) N370S probably damaging Het
Slc6a5 C A 7: 49,588,156 (GRCm39) probably benign Het
Sort1 T A 3: 108,252,247 (GRCm39) N481K probably benign Het
Sptlc3 T A 2: 139,437,957 (GRCm39) I417K possibly damaging Het
Svil T A 18: 5,099,063 (GRCm39) probably benign Het
Taf4b T C 18: 14,946,134 (GRCm39) probably benign Het
Tchp T C 5: 114,847,394 (GRCm39) M71T possibly damaging Het
Thsd4 T A 9: 59,904,417 (GRCm39) H233L probably benign Het
Tmem217 G T 17: 29,745,573 (GRCm39) N52K possibly damaging Het
Tmem38b T C 4: 53,840,765 (GRCm39) L60S probably damaging Het
Uqcrfs1 A C 13: 30,725,146 (GRCm39) N131K probably benign Het
Vmn1r170 A T 7: 23,305,906 (GRCm39) M103L probably benign Het
Vmn2r22 T C 6: 123,614,363 (GRCm39) Y409C probably damaging Het
Vmn2r92 C T 17: 18,388,219 (GRCm39) A408V probably damaging Het
Wdr49 A T 3: 75,359,103 (GRCm39) I8N possibly damaging Het
Zfp648 T A 1: 154,080,632 (GRCm39) Y264N probably damaging Het
Zmym1 A C 4: 126,941,818 (GRCm39) F857V possibly 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
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
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'- AGCAAGTCTCTTGGCAATGTCATCG -3'
(R):5'- ACAGAGTCCAAAGCGTAGGGCATC -3'

Sequencing Primer
(F):5'- TGGCAATGTCATCGACCCC -3'
(R):5'- GGAATCCCTGCTGGAAAGTC -3'
Posted On 2013-05-09