Mutagenetix > Incidental Mutation

Incidental Mutation 'R4886:Vars1'

375772

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

042492-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R4886 (G1)

Quality Score

127

Status

Not validated

Chromosome

Chromosomal Location

35219963-35235298 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 35234702 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 1177 (V1177E)

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

Domain	Start	End	E-Value	Type
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: V1177E

PolyPhen 2 Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: V1177E

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
SCOP:d1gaxa3	32	67	3e-7	SMART
PDB:1IYW\|B	36	122	4e-6	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173302

Predicted Effect

probably benign
Transcript: ENSMUST00000173584
AA Change: V1177E

PolyPhen 2 Score 0.374 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: V1177E

Domain	Start	End	E-Value	Type
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: ENSMUST00000173336

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173911

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.5%

Validation Efficiency

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9430097D07Rik	A	T	2: 32,464,630 (GRCm39)		probably benign	Het
Aagab	G	C	9: 63,543,738 (GRCm39)	A231P	possibly damaging	Het
Adgra3	C	T	5: 50,156,537 (GRCm39)	D398N	probably benign	Het
Ap3b1	A	T	13: 94,609,313 (GRCm39)	D616V	possibly damaging	Het
Apc2	T	A	10: 80,150,047 (GRCm39)	H1700Q	probably damaging	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atp2b4	T	A	1: 133,634,518 (GRCm39)	I1177L	probably benign	Het
Card6	T	C	15: 5,134,623 (GRCm39)		probably null	Het
Cdk13	A	G	13: 17,894,319 (GRCm39)	S1103P	probably benign	Het
Cdk6	G	T	5: 3,394,444 (GRCm39)	K26N	possibly damaging	Het
Cfap221	T	C	1: 119,861,934 (GRCm39)	T614A	probably damaging	Het
Cfap221	T	A	1: 119,912,488 (GRCm39)	Y133F	probably damaging	Het
Clcc1	A	G	3: 108,584,154 (GRCm39)	T513A	probably benign	Het
Clec4g	T	A	8: 3,766,419 (GRCm39)		probably benign	Het
Cntln	A	C	4: 84,889,466 (GRCm39)	E316D	probably benign	Het
Col6a4	A	G	9: 105,937,271 (GRCm39)	I1415T	probably benign	Het
Cpne2	T	A	8: 95,290,592 (GRCm39)	D392E	probably benign	Het
Cpz	T	C	5: 35,664,048 (GRCm39)	N496D	probably damaging	Het
Cyp3a59	A	G	5: 146,024,197 (GRCm39)	D61G	probably damaging	Het
Cyp4a29	T	C	4: 115,110,078 (GRCm39)	V440A	probably benign	Het
Dbn1	A	T	13: 55,625,355 (GRCm39)		probably benign	Het
Ddx46	A	G	13: 55,786,012 (GRCm39)	D64G	unknown	Het
Dhrs7c	G	A	11: 67,700,620 (GRCm39)	V56M	probably damaging	Het
Dnhd1	T	A	7: 105,364,015 (GRCm39)	H4122Q	probably benign	Het
Ecm2	A	T	13: 49,676,263 (GRCm39)	I327F	possibly damaging	Het
Elavl3	T	C	9: 21,937,614 (GRCm39)	K189E	possibly damaging	Het
Enam	A	T	5: 88,636,593 (GRCm39)	R82*	probably null	Het
Fat3	T	A	9: 15,932,626 (GRCm39)	I1436F	probably benign	Het
Glt8d2	T	C	10: 82,487,874 (GRCm39)		probably benign	Het
Grin2c	T	C	11: 115,151,616 (GRCm39)	T115A	probably damaging	Het
H6pd	C	T	4: 150,067,235 (GRCm39)	V384M	possibly damaging	Het
Hba-x	A	G	11: 32,227,008 (GRCm39)	E39G	probably benign	Het
Hcar2	G	A	5: 124,003,260 (GRCm39)	T81M	probably benign	Het
Herpud2	G	A	9: 25,036,285 (GRCm39)	P125L	probably benign	Het
Hnrnpul2	C	T	19: 8,807,191 (GRCm39)	P618S	probably benign	Het
Hpse2	T	C	19: 43,373,203 (GRCm39)	Y142C	probably damaging	Het
Iqcm	A	T	8: 76,615,228 (GRCm39)	R436S	possibly damaging	Het
Itih1	A	G	14: 30,658,658 (GRCm39)		probably null	Het
Kcnk10	T	C	12: 98,401,418 (GRCm39)	N405S	possibly damaging	Het
Klhl14	A	T	18: 21,691,029 (GRCm39)		probably null	Het
L3mbtl3	T	A	10: 26,168,668 (GRCm39)	E587V	unknown	Het
Leap2	A	T	11: 53,313,653 (GRCm39)	F40I	probably damaging	Het
Leng8	T	A	7: 4,147,930 (GRCm39)		probably null	Het
Lrrc66	A	G	5: 73,765,910 (GRCm39)	F378L	probably benign	Het
Mansc1	T	C	6: 134,587,625 (GRCm39)	H184R	probably benign	Het
Map10	T	A	8: 126,397,431 (GRCm39)	Y275N	probably damaging	Het
Med23	T	C	10: 24,750,581 (GRCm39)		probably null	Het
Mpp3	A	G	11: 101,915,962 (GRCm39)	Y55H	probably benign	Het
Mrpl17	T	C	7: 105,459,260 (GRCm39)	N112S	probably benign	Het
Nectin4	T	C	1: 171,212,383 (GRCm39)	V327A	possibly damaging	Het
Nlrp14	A	T	7: 106,781,862 (GRCm39)	H353L	probably benign	Het
Notch2	A	T	3: 98,009,735 (GRCm39)	Y554F	probably damaging	Het
Nphp3	T	C	9: 103,880,193 (GRCm39)	S72P	probably damaging	Het
Nrsn2	T	C	2: 152,211,531 (GRCm39)	K167E	probably benign	Het
Or14j8	A	T	17: 38,262,962 (GRCm39)	S318T	probably benign	Het
Or5b117	T	C	19: 13,431,885 (GRCm39)		probably null	Het
Or8g30	T	C	9: 39,230,881 (GRCm39)	T10A	probably benign	Het
Or9i2	T	A	19: 13,815,643 (GRCm39)	E298V	probably damaging	Het
Osbpl9	T	C	4: 108,925,564 (GRCm39)	N485S	probably benign	Het
Pbk	T	A	14: 66,052,650 (GRCm39)	H164Q	probably damaging	Het
Pfn2	G	T	3: 57,754,874 (GRCm39)	N10K	probably damaging	Het
Pi4ka	A	G	16: 17,176,225 (GRCm39)	S405P		Het
Pik3ca	A	G	3: 32,491,312 (GRCm39)	D133G	probably damaging	Het
Pramel27	G	T	4: 143,579,873 (GRCm39)	R486L	probably benign	Het
Prkar2a	G	A	9: 108,622,823 (GRCm39)		probably null	Het
Prl6a1	A	T	13: 27,502,983 (GRCm39)	D193V	probably damaging	Het
Psg25	A	T	7: 18,258,838 (GRCm39)	D279E	probably benign	Het
Rad21	G	T	15: 51,831,896 (GRCm39)	P395Q	probably damaging	Het
Rnf168	C	A	16: 32,118,014 (GRCm39)	T525K	probably benign	Het
Rpn2	T	C	2: 157,159,964 (GRCm39)		probably null	Het
Rreb1	G	A	13: 38,115,034 (GRCm39)	V798M	possibly damaging	Het
Scgb3a2	C	T	18: 43,899,819 (GRCm39)	P36S	probably damaging	Het
Scn3a	T	C	2: 65,291,376 (GRCm39)	D1790G	probably damaging	Het
Sec24b	A	T	3: 129,777,619 (GRCm39)	H1226Q	probably benign	Het
Sec63	T	A	10: 42,665,389 (GRCm39)	Y106*	probably null	Het
Shroom3	G	T	5: 93,090,945 (GRCm39)	V1151F	probably damaging	Het
Slc12a3	G	A	8: 95,078,438 (GRCm39)		probably null	Het
Slc6a1	T	A	6: 114,279,494 (GRCm39)	I91N	possibly damaging	Het
Slitrk6	T	C	14: 110,989,315 (GRCm39)	T131A	probably damaging	Het
Spata1	C	G	3: 146,175,529 (GRCm39)	D326H	probably damaging	Het
St8sia1	G	A	6: 142,859,860 (GRCm39)	L90F	probably damaging	Het
Thsd4	T	A	9: 59,896,313 (GRCm39)	Y657F	probably benign	Het
Thsd7a	A	T	6: 12,327,659 (GRCm39)	C1404*	probably null	Het
Tma16	A	C	8: 66,934,129 (GRCm39)	C75W	probably damaging	Het
Trgv4	T	C	13: 19,369,236 (GRCm39)	V29A	probably benign	Het
Trim3	T	A	7: 105,267,047 (GRCm39)	H444L	probably damaging	Het
Trmt10a	A	T	3: 137,854,146 (GRCm39)	K75*	probably null	Het
Ttn	T	C	2: 76,561,644 (GRCm39)	D28954G	probably damaging	Het
Uggt2	A	G	14: 119,273,376 (GRCm39)		probably null	Het
Vmn2r114	G	T	17: 23,527,008 (GRCm39)	A508E	probably benign	Het
Vmn2r19	G	T	6: 123,286,800 (GRCm39)	K144N	probably benign	Het
Wdr41	C	T	13: 95,151,682 (GRCm39)	Q281*	probably null	Het
Zfp938	T	A	10: 82,061,957 (GRCm39)	Q221L	probably benign	Het

Other mutations in Vars1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- TGCGTGCTGACTACAACCTG -3'
(R):5'- AGTACAGTGACAAAGGGCCC -3'

Sequencing Primer
(F):5'- ACCAGGCCCGACTGTAAG -3'
(R):5'- TGTGCAGGAGTCCACAGG -3'

Posted On

2016-03-17