Mutagenetix > Incidental Mutation

Incidental Mutation 'R1699:Vars1'

192564

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

039732-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R1699 (G1)

Quality Score

211

Status

Not validated

Chromosome

Chromosomal Location

35219963-35235298 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35233734 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 1020 (E1020G)

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

possibly damaging
Transcript: ENSMUST00000087315
AA Change: E1020G

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: E1020G

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

possibly damaging
Transcript: ENSMUST00000173584
AA Change: E1020G

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: E1020G

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: ENSMUST00000173336

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174084

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173911

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.3%

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: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca2	A	G	2: 25,337,363 (GRCm39)	E2406G	possibly damaging	Het
Adam6b	T	A	12: 113,454,205 (GRCm39)	F341I	probably benign	Het
Adam8	A	T	7: 139,563,224 (GRCm39)	N767K	possibly damaging	Het
Aig1	T	C	10: 13,744,366 (GRCm39)	D46G	possibly damaging	Het
Alms1	A	G	6: 85,599,862 (GRCm39)	I2032V	possibly damaging	Het
Ankrd16	A	G	2: 11,789,204 (GRCm39)	I264V	probably benign	Het
Areg	T	G	5: 91,291,357 (GRCm39)	V100G	probably damaging	Het
Bcan	A	G	3: 87,896,543 (GRCm39)	Y718H	probably damaging	Het
Brsk2	T	A	7: 141,539,200 (GRCm39)	I188N	probably damaging	Het
Cdt1	T	C	8: 123,296,722 (GRCm39)	Y203H	probably damaging	Het
Cfap119	A	T	7: 127,186,028 (GRCm39)		probably null	Het
Chil3	A	C	3: 106,067,682 (GRCm39)		probably null	Het
Ciao2b	A	G	8: 105,366,718 (GRCm39)	V132A	probably damaging	Het
Cimip2c	A	G	5: 30,641,210 (GRCm39)		probably null	Het
Cth	A	G	3: 157,613,073 (GRCm39)	L253P	probably damaging	Het
Cyp11b1	A	G	15: 74,712,666 (GRCm39)	F132L	possibly damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dnah11	A	G	12: 118,154,603 (GRCm39)	S226P	probably damaging	Het
Egfr	A	T	11: 16,809,019 (GRCm39)	Q71L	probably benign	Het
Eml6	T	A	11: 29,696,282 (GRCm39)	K1940*	probably null	Het
Epn2	T	A	11: 61,414,014 (GRCm39)	K391*	probably null	Het
Erich1	A	T	8: 14,140,259 (GRCm39)	S2T	possibly damaging	Het
Evi5	A	C	5: 107,966,786 (GRCm39)	L245R	probably damaging	Het
Evpl	T	C	11: 116,118,414 (GRCm39)	Y731C	probably damaging	Het
Exoc3l	G	A	8: 106,021,645 (GRCm39)	H128Y	probably benign	Het
Extl1	G	A	4: 134,091,894 (GRCm39)	Q320*	probably null	Het
Fam91a1	T	A	15: 58,304,797 (GRCm39)	S416T	probably benign	Het
Fat3	A	T	9: 15,849,694 (GRCm39)	S3903T	probably damaging	Het
Fer1l4	A	G	2: 155,871,605 (GRCm39)	F1392L	probably benign	Het
Fstl4	T	C	11: 53,059,005 (GRCm39)	I488T	possibly damaging	Het
Gak	A	T	5: 108,752,243 (GRCm39)	Y338*	probably null	Het
Garin4	T	A	1: 190,896,018 (GRCm39)	E208D	probably benign	Het
Glp2r	T	C	11: 67,648,367 (GRCm39)	T112A	probably benign	Het
Glrb	G	A	3: 80,769,081 (GRCm39)	T180I	probably damaging	Het
Gm10118	C	T	10: 63,762,671 (GRCm39)		probably benign	Het
Gpr19	A	T	6: 134,847,192 (GRCm39)	F72I	possibly damaging	Het
Grin3b	C	A	10: 79,811,716 (GRCm39)	N740K	probably damaging	Het
Gstk1	A	T	6: 42,223,535 (GRCm39)	T42S	probably benign	Het
Hoxd1	G	A	2: 74,594,626 (GRCm39)	A294T	probably benign	Het
Hspg2	T	A	4: 137,275,323 (GRCm39)		probably null	Het
Ift74	A	T	4: 94,573,940 (GRCm39)	N472I	probably benign	Het
Il1a	C	T	2: 129,144,813 (GRCm39)	D202N	probably damaging	Het
Islr	T	C	9: 58,064,778 (GRCm39)	D243G	probably damaging	Het
Kif21a	C	T	15: 90,843,946 (GRCm39)	E1098K	probably damaging	Het
Krtap16-1	T	C	11: 99,876,852 (GRCm39)	E184G	probably damaging	Het
Lrp1b	A	G	2: 41,075,974 (GRCm39)	I1889T	possibly damaging	Het
Mcpt4	A	G	14: 56,297,416 (GRCm39)	*247Q	probably null	Het
Megf10	T	C	18: 57,410,802 (GRCm39)		probably null	Het
Mettl2	T	A	11: 105,030,544 (GRCm39)	H373Q	probably benign	Het
Mocos	A	G	18: 24,816,273 (GRCm39)	K617E	probably damaging	Het
Ms4a8a	A	G	19: 11,053,761 (GRCm39)	I115T	probably damaging	Het
Ndst1	T	C	18: 60,828,580 (GRCm39)	Y658C	probably damaging	Het
Nin	G	A	12: 70,077,712 (GRCm39)	A1031V	probably benign	Het
Nin	C	A	12: 70,092,337 (GRCm39)	K657N	possibly damaging	Het
Noc4l	G	A	5: 110,797,713 (GRCm39)	R344*	probably null	Het
Notch2	T	C	3: 98,052,443 (GRCm39)	S1980P	probably damaging	Het
Npat	C	T	9: 53,473,960 (GRCm39)	S584L	probably benign	Het
Nphp4	A	G	4: 152,581,121 (GRCm39)	T102A	probably damaging	Het
Olfml2b	A	G	1: 170,472,642 (GRCm39)	N51S	possibly damaging	Het
Or2n1e	A	G	17: 38,585,932 (GRCm39)	K90R	probably benign	Het
Or2y16	T	A	11: 49,335,116 (GRCm39)	I146N	possibly damaging	Het
Or5al1	T	C	2: 85,990,280 (GRCm39)	I145V	probably benign	Het
Or5w22	A	G	2: 87,362,427 (GRCm39)	T17A	probably benign	Het
Pced1b	T	A	15: 97,282,758 (GRCm39)	W266R	probably damaging	Het
Pdcd6ip	A	G	9: 113,507,422 (GRCm39)	V378A	probably damaging	Het
Pde8b	T	A	13: 95,169,374 (GRCm39)	K683N	probably damaging	Het
Pfas	T	G	11: 68,888,872 (GRCm39)		probably null	Het
Pirb	A	T	7: 3,720,637 (GRCm39)	L287Q	probably benign	Het
Plcd4	T	G	1: 74,587,394 (GRCm39)	S51R	probably benign	Het
Plekhh2	T	A	17: 84,884,612 (GRCm39)	Y775*	probably null	Het
Polr3a	G	A	14: 24,534,232 (GRCm39)	P91L	probably damaging	Het
Ppp4r3b	C	T	11: 29,163,765 (GRCm39)	T47I	possibly damaging	Het
Pter	A	T	2: 12,999,572 (GRCm39)	D169V	probably damaging	Het
Ptpn12	A	G	5: 21,203,168 (GRCm39)	S537P	probably benign	Het
Ptpru	T	A	4: 131,506,361 (GRCm39)	D1067V	probably damaging	Het
Rcn1	A	T	2: 105,229,350 (GRCm39)	D67E	probably damaging	Het
Rfc4	T	C	16: 22,932,983 (GRCm39)	E318G	probably benign	Het
Samd13	C	A	3: 146,368,469 (GRCm39)	R41L	probably benign	Het
Shoc1	T	C	4: 59,113,926 (GRCm39)	K13R	unknown	Het
Slc6a2	T	C	8: 93,699,440 (GRCm39)	I156T	possibly damaging	Het
Spag16	T	C	1: 70,036,015 (GRCm39)	F348L	probably benign	Het
Spag4	T	C	2: 155,907,342 (GRCm39)	Y21H	probably damaging	Het
Stam2	G	A	2: 52,593,187 (GRCm39)	A368V	possibly damaging	Het
Stc1	A	T	14: 69,275,776 (GRCm39)	M190L	probably benign	Het
Stxbp1	A	G	2: 32,690,629 (GRCm39)	L475P	probably damaging	Het
Syn3	A	T	10: 85,916,075 (GRCm39)	Y304N	probably damaging	Het
Tbc1d15	G	T	10: 115,056,219 (GRCm39)	T251K	probably benign	Het
Tbpl2	A	T	2: 23,985,057 (GRCm39)	M29K	probably benign	Het
Tead3	T	G	17: 28,553,698 (GRCm39)	Q170H	possibly damaging	Het
Tpbpb	T	C	13: 61,049,977 (GRCm39)	N51D	probably benign	Het
Tstd3	A	G	4: 21,759,400 (GRCm39)	M124T	probably benign	Het
Ttyh1	T	A	7: 4,122,695 (GRCm39)	H14Q	possibly damaging	Het
Tubgcp4	G	A	2: 121,020,374 (GRCm39)	W449*	probably null	Het
Txndc11	A	G	16: 10,905,639 (GRCm39)		probably null	Het
Usp24	T	A	4: 106,296,024 (GRCm39)	D2615E	probably damaging	Het
Vmn2r58	A	G	7: 41,509,951 (GRCm39)	I542T	probably benign	Het
Vwf	A	G	6: 125,620,032 (GRCm39)	Y1570C	probably damaging	Het
Vwf	A	T	6: 125,662,863 (GRCm39)	Y2749F	possibly damaging	Het
Zfand1	A	C	3: 10,406,115 (GRCm39)	V198G	possibly damaging	Het
Zfp536	G	A	7: 37,268,879 (GRCm39)	T179I	probably damaging	Het
Zfp599	T	C	9: 22,161,700 (GRCm39)	Y155C	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
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'- TAGTGTGATGGCCTACTGCCTGAC -3'
(R):5'- CTCCTCTGTGACAAAGGGCATGAAG -3'

Sequencing Primer
(F):5'- GCCTACTGCCTGACGTTTC -3'
(R):5'- CAGGTTTTAGACACTCCTAGAGATGG -3'

Posted On

2014-05-14