Mutagenetix > Incidental Mutation

Incidental Mutation 'R6023:Vars'

479060

Institutional Source

Beutler Lab

Gene Symbol

Vars

Ensembl Gene

ENSMUSG00000007029

Gene Name

valyl-tRNA synthetase

Synonyms

Bat-6, Bat6, G7a, D17H6S56E, Vars2

MMRRC Submission

044195-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R6023 (G1)

Quality Score

145.008

Status

Validated

Chromosome

Chromosomal Location

35000987-35016322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 35001609 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 56 (R56C)

Ref Sequence

ENSEMBL: ENSMUSP00000134313 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087315] [ENSMUST00000172570] [ENSMUST00000173584] [ENSMUST00000174260]

AlphaFold

Q9Z1Q9

Predicted Effect

probably damaging
Transcript: ENSMUST00000087315
AA Change: R56C

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: R56C

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: ENSMUST00000172570

SMART Domains

Protein: ENSMUSP00000134245
Gene: ENSMUSG00000007029

Domain	Start	End	E-Value	Type
Pfam:GST_C	2	76	1.2e-13	PFAM
low complexity region	112	124	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172637

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172656

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172741

Predicted Effect

probably damaging
Transcript: ENSMUST00000173584
AA Change: R56C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: R56C

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

probably damaging
Transcript: ENSMUST00000174260
AA Change: R56C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000134313
Gene: ENSMUSG00000007029
AA Change: R56C

Domain	Start	End	E-Value	Type
Pfam:GST_N	2	81	2.2e-16	PFAM
Pfam:GST_C	96	198	2.1e-13	PFAM

Meta Mutation Damage Score

0.1482

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.3%

Validation Efficiency

100% (51/51)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc8	T	C	7: 46,108,419	N1302S	possibly damaging	Het
Aff3	A	T	1: 38,218,370	S424T	probably damaging	Het
Ap2b1	C	T	11: 83,335,398	T207M	probably damaging	Het
Appl2	T	C	10: 83,648,529	Q18R	probably null	Het
Atrn	T	C	2: 131,020,980	F1327L	probably benign	Het
Birc6	A	T	17: 74,654,377	I47F	probably benign	Het
Cdh23	A	T	10: 60,465,542	I451N	probably damaging	Het
Clec3a	A	G	8: 114,418,143	T20A	possibly damaging	Het
Cpz	T	A	5: 35,512,578	I252F	probably benign	Het
Ctc1	A	G	11: 69,022,607	D143G	probably benign	Het
Dhrs1	A	T	14: 55,743,670	Y94*	probably null	Het
Dnajc25	A	G	4: 59,013,752	K157E	possibly damaging	Het
Dpp6	T	C	5: 27,723,547	I789T	probably damaging	Het
Duox1	T	G	2: 122,337,684	F1097V	probably benign	Het
Ercc8	A	G	13: 108,178,577	T242A	probably damaging	Het
Evc2	T	A	5: 37,348,616	M93K	probably benign	Het
Glra1	A	T	11: 55,533,853	V94E	probably damaging	Het
Got1l1	A	T	8: 27,199,904	Y151*	probably null	Het
Hcrtr2	T	A	9: 76,230,604	I410F	probably benign	Het
Ighv1-72	T	A	12: 115,757,912		probably benign	Het
Kel	C	A	6: 41,697,475	E340D	probably benign	Het
Kif11	A	G	19: 37,390,710	E283G	probably damaging	Het
Klk4	T	G	7: 43,884,058	F114V	probably benign	Het
Krt7	T	C	15: 101,412,397		probably benign	Het
Lrrc74a	A	G	12: 86,758,606	I401V	probably damaging	Het
Luzp2	T	C	7: 55,058,067	S68P	possibly damaging	Het
Naip1	T	C	13: 100,426,186	T824A	probably benign	Het
Nav3	T	C	10: 109,823,515	Q747R	possibly damaging	Het
Olfr1212	A	G	2: 88,958,715	D83G	possibly damaging	Het
Olfr1342	T	A	4: 118,690,074	Y126F	probably damaging	Het
Olfr1477	A	G	19: 13,502,703	D120G	probably damaging	Het
Olfr339	A	G	2: 36,421,511	T38A	probably damaging	Het
Olfr566	T	C	7: 102,856,962	I107V	possibly damaging	Het
Olfr649	T	C	7: 104,189,673	H178R	probably damaging	Het
Olfr837	A	C	9: 19,137,725	H244P	probably damaging	Het
Pcdhb11	T	C	18: 37,422,925	I436T	possibly damaging	Het
Pfdn2	T	C	1: 171,356,751	Y65H	probably damaging	Het
Polr2h	T	C	16: 20,719,026	Y58H	probably benign	Het
Prrt4	G	A	6: 29,176,453	P291L	probably benign	Het
Psg29	G	T	7: 17,210,512	V316L	possibly damaging	Het
Rnf112	T	A	11: 61,449,729	E525V	probably damaging	Het
Sgms1	T	C	19: 32,124,373	K411R	probably benign	Het
Sh3tc1	T	A	5: 35,706,951	K631*	probably null	Het
Syne1	T	C	10: 5,443,223	M48V	probably benign	Het
Thrb	C	T	14: 18,011,209	T226I	probably damaging	Het
Trim67	A	T	8: 124,815,104	D347V	probably damaging	Het
Try4	T	C	6: 41,303,421	S60P	probably damaging	Het
Ttn	G	T	2: 76,735,400	L19876I	probably damaging	Het
Vmn1r9	A	G	6: 57,071,254	I105V	probably benign	Het
Vps8	C	A	16: 21,461,238	T313K	probably benign	Het

Other mutations in Vars

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01520:Vars	APN	17	35013873	missense	probably benign	0.00
IGL02160:Vars	APN	17	35001502	missense	probably damaging	1.00
IGL02303:Vars	APN	17	35015484	splice site	probably benign
IGL03027:Vars	APN	17	35013687	missense	probably damaging	1.00
Maladroit	UTSW	17	35005475	missense	probably benign	0.30
Whoops	UTSW	17	35013644	missense	probably damaging	1.00
FR4304:Vars	UTSW	17	35015989	small insertion	probably benign
FR4548:Vars	UTSW	17	35015989	small insertion	probably benign
FR4548:Vars	UTSW	17	35015991	small insertion	probably benign
FR4589:Vars	UTSW	17	35015988	small insertion	probably benign
R0045:Vars	UTSW	17	35010619	missense	probably damaging	1.00
R0045:Vars	UTSW	17	34998066	missense	probably benign	0.13
R0045:Vars	UTSW	17	35010619	missense	probably damaging	1.00
R0266:Vars	UTSW	17	35013869	missense	probably benign	0.00
R0267:Vars	UTSW	17	35011596	splice site	probably benign
R0391:Vars	UTSW	17	35011486	missense	possibly damaging	0.79
R0445:Vars	UTSW	17	35011809	missense	probably benign	0.31
R0449:Vars	UTSW	17	35012727	splice site	probably null
R0557:Vars	UTSW	17	35004984	missense	possibly damaging	0.90
R0559:Vars	UTSW	17	35014058	nonsense	probably null
R0730:Vars	UTSW	17	35014300	missense	probably damaging	1.00
R0748:Vars	UTSW	17	34998012	missense	probably damaging	1.00
R1692:Vars	UTSW	17	35013725	missense	probably damaging	1.00
R1693:Vars	UTSW	17	34998196	missense	probably benign	0.31
R1697:Vars	UTSW	17	34998222	missense	probably benign	0.43
R1699:Vars	UTSW	17	35014758	missense	possibly damaging	0.93
R1712:Vars	UTSW	17	35014752	missense	probably damaging	1.00
R1989:Vars	UTSW	17	35011838	missense	possibly damaging	0.94
R2349:Vars	UTSW	17	35015752	missense	probably benign
R2365:Vars	UTSW	17	35015452	missense	probably benign	0.01
R3790:Vars	UTSW	17	34999334	missense	probably benign	0.34
R4615:Vars	UTSW	17	35013881	missense	probably damaging	0.97
R4844:Vars	UTSW	17	35011612	missense	probably damaging	1.00
R4856:Vars	UTSW	17	35015726	missense	probably benign	0.37
R4886:Vars	UTSW	17	35015726	missense	probably benign	0.37
R5570:Vars	UTSW	17	35016238	missense	probably benign	0.04
R5706:Vars	UTSW	17	35005481	splice site	probably null
R5858:Vars	UTSW	17	35005475	missense	probably benign	0.30
R5907:Vars	UTSW	17	35012376	missense	probably damaging	1.00
R5917:Vars	UTSW	17	35012515	missense	probably damaging	0.99
R5944:Vars	UTSW	17	35013644	missense	probably damaging	1.00
R6073:Vars	UTSW	17	35001529	missense	probably benign
R6273:Vars	UTSW	17	35013743	missense	probably damaging	1.00
R6390:Vars	UTSW	17	35015639	missense	probably benign	0.00
R6658:Vars	UTSW	17	35015741	missense	probably benign	0.03
R7067:Vars	UTSW	17	35011479	missense	probably damaging	0.98
R7387:Vars	UTSW	17	35004792	nonsense	probably null
R7954:Vars	UTSW	17	35015984	missense	probably benign	0.01
R8139:Vars	UTSW	17	35011504	missense	probably benign	0.16
R8347:Vars	UTSW	17	35015977	missense	possibly damaging	0.92
R8387:Vars	UTSW	17	35010514	missense	probably damaging	0.99
R8855:Vars	UTSW	17	35015644	missense	probably benign	0.00
R8866:Vars	UTSW	17	35015644	missense	probably benign	0.00
R9131:Vars	UTSW	17	35004797	missense	possibly damaging	0.77
R9620:Vars	UTSW	17	35016025	missense	unknown
R9695:Vars	UTSW	17	35012588	missense	possibly damaging	0.82
Z1177:Vars	UTSW	17	35011477	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACAGCCATGTCCATCCTCTACG -3'
(R):5'- GTTTGTGTAGTCAGAATTTCTCCC -3'

Sequencing Primer
(F):5'- GTCTCTCCTCACCCCGACG -3'
(R):5'- TGACCAGGACCTCGAAGTC -3'

Posted On

2017-06-26