Mutagenetix > Incidental Mutation

Incidental Mutation 'R5907:Vars'

460753

Institutional Source

Beutler Lab

Gene Symbol

Vars

Ensembl Gene

ENSMUSG00000007029

Gene Name

valyl-tRNA synthetase

Synonyms

Bat-6, Bat6, G7a, D17H6S56E, Vars2

MMRRC Submission

044104-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R5907 (G1)

Quality Score

196

Status

Validated

Chromosome

Chromosomal Location

35000987-35016322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35012376 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 655 (N655S)

Ref Sequence

ENSEMBL: ENSMUSP00000084572 (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 damaging
Transcript: ENSMUST00000087315
AA Change: N655S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: N655S

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

noncoding transcript
Transcript: ENSMUST00000173336

Predicted Effect

probably damaging
Transcript: ENSMUST00000173584
AA Change: N655S

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: N655S

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: ENSMUST00000173911

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174084

Meta Mutation Damage Score

0.7928

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.9%
20x: 93.7%

Validation Efficiency

93% (92/99)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921501E09Rik	G	T	17: 33,066,150	D559E	probably benign	Het
4931429L15Rik	A	T	9: 46,306,822	I206N	probably damaging	Het
Aadac	T	A	3: 60,039,827	D315E	probably damaging	Het
Abcc8	A	G	7: 46,123,906	F800L	probably benign	Het
Adamts16	C	A	13: 70,728,910	C1204F	probably damaging	Het
Adcy7	A	G	8: 88,312,228	T291A	possibly damaging	Het
AI182371	G	T	2: 35,086,122	Q255K	possibly damaging	Het
Aig1	A	T	10: 13,801,784		probably benign	Het
Ak5	T	C	3: 152,615,952	D266G	probably damaging	Het
Ank1	A	T	8: 23,140,204	E93D	probably damaging	Het
Bop1	T	C	15: 76,455,917	D153G	probably damaging	Het
Bub1	G	T	2: 127,819,222	N316K	probably benign	Het
Capn1	T	C	19: 5,997,797	N412S	probably benign	Het
Cdca4	A	G	12: 112,821,719	S130P	probably benign	Het
Cdh23	A	T	10: 60,428,379	D663E	probably damaging	Het
Clca3a1	T	C	3: 144,749,642		probably benign	Het
Csmd2	C	T	4: 128,197,385	P239L	probably damaging	Het
Dlg2	A	T	7: 91,997,371		probably benign	Het
Dnpep	C	T	1: 75,311,991		probably null	Het
Dopey2	A	T	16: 93,801,581	H1878L	probably damaging	Het
Dscam	C	T	16: 96,820,920	D444N	probably damaging	Het
Emc9	C	T	14: 55,582,112		probably null	Het
Ero1lb	T	A	13: 12,600,318	I346N	probably damaging	Het
Etv3	A	G	3: 87,535,543	T145A	probably benign	Het
Fam170a	T	A	18: 50,282,254		probably null	Het
Fap	A	T	2: 62,544,356	I261N	probably damaging	Het
Fbn2	T	C	18: 58,045,337	N1943S	probably damaging	Het
Glb1l3	A	T	9: 26,826,383	V466E	probably damaging	Het
Gm10521	A	T	1: 171,896,503	H127L	unknown	Het
Gm8186	G	T	17: 26,099,156	N22K	probably damaging	Het
Gpr132	A	C	12: 112,852,097	L370V	probably benign	Het
Hectd1	A	T	12: 51,798,754	H449Q	probably damaging	Het
Hook3	A	G	8: 26,044,278		probably benign	Het
Ift140	A	G	17: 25,092,371	D1180G	probably benign	Het
Isoc2b	A	T	7: 4,849,578		probably null	Het
Itga4	C	T	2: 79,322,656	H896Y	probably benign	Het
Itga7	T	C	10: 128,942,981	Y326H	probably damaging	Het
Itpr3	A	T	17: 27,117,893	E2397V	probably damaging	Het
Jtb	T	G	3: 90,235,577		probably null	Het
Klk15	A	G	7: 43,938,759	T164A	probably benign	Het
Kmt2e	C	A	5: 23,464,706	H64N	probably damaging	Het
Lamtor3	T	A	3: 137,927,293		probably benign	Het
Laptm4b	A	G	15: 34,258,684	I35V	possibly damaging	Het
Lrrc1	A	C	9: 77,434,097	L393R	probably damaging	Het
Ltn1	A	G	16: 87,381,503	S1613P	possibly damaging	Het
Mtmr4	T	A	11: 87,612,050	W920R	probably damaging	Het
Nbeal1	T	C	1: 60,228,791		probably benign	Het
Nup133	A	G	8: 123,916,299	Y761H	possibly damaging	Het
Nwd2	T	A	5: 63,805,983	V970D	probably damaging	Het
Olfr1058	A	T	2: 86,385,874	S181R	probably damaging	Het
Olfr1261	A	G	2: 89,993,957	H188R	probably benign	Het
Olfr429	T	C	1: 174,089,219	Y60H	probably benign	Het
Osbp	C	T	19: 11,973,876	L262F	probably damaging	Het
Phldb2	G	T	16: 45,825,188	D343E	probably damaging	Het
Phrf1	T	A	7: 141,260,540	M1216K	possibly damaging	Het
Phyh	A	T	2: 4,930,651		probably null	Het
Plekhf1	A	T	7: 38,222,170		probably null	Het
Rars	T	C	11: 35,828,648	N116D	probably damaging	Het
Rnf44	T	A	13: 54,682,808	Q181L	possibly damaging	Het
Rpe65	T	C	3: 159,615,682		probably null	Het
Scaf1	A	G	7: 45,013,592		probably benign	Het
Serpinb11	A	T	1: 107,372,189	R88S	probably benign	Het
Slc7a7	T	C	14: 54,379,103	N174S	probably damaging	Het
Slc9a5	T	C	8: 105,357,175		probably null	Het
Slfn1	C	A	11: 83,121,176	N39K	possibly damaging	Het
Snx20	G	A	8: 88,627,295	A269V	possibly damaging	Het
Snx6	A	G	12: 54,754,319	Y298H	probably damaging	Het
Stk32c	C	T	7: 139,120,674	R213Q	probably benign	Het
Tgfbr1	A	T	4: 47,396,555	I190F	probably damaging	Het
Ube2d2b	T	A	5: 107,830,632	F50I	probably damaging	Het
Ubl5	G	A	9: 20,646,534		probably benign	Het
Ubqln5	T	G	7: 104,128,574	T348P	possibly damaging	Het
Usp46	T	C	5: 74,037,085	D22G	probably benign	Het
Vmn2r103	A	C	17: 19,812,453	I830L	possibly damaging	Het
Vmn2r26	T	A	6: 124,039,871	N431K	probably benign	Het
Vmn2r4	G	T	3: 64,391,066	P547Q	probably damaging	Het
Yy1	T	A	12: 108,806,428		probably benign	Het
Zbtb2	A	T	10: 4,368,592	L478Q	possibly damaging	Het
Zfp12	T	C	5: 143,239,988	F17S	probably damaging	Het
Zfp219	T	A	14: 52,007,149		probably null	Het
Zfp629	G	A	7: 127,610,370	H756Y	probably damaging	Het
Zfp748	T	C	13: 67,541,173	K656R	possibly damaging	Het
Zfp958	T	A	8: 4,629,072	Y366N	probably benign	Het
Zp3	C	T	5: 135,988,523	T396I	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
R5917:Vars	UTSW	17	35012515	missense	probably damaging	0.99
R5944:Vars	UTSW	17	35013644	missense	probably damaging	1.00
R6023:Vars	UTSW	17	35001609	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'- TGACTATGAGGTTGGGCAGC -3'
(R):5'- ACAGCGCACGTACCATTGTG -3'

Sequencing Primer
(F):5'- GGCCATTAGCATCATGGACTC -3'
(R):5'- CGTACCATTGTGGCCTTAACAGAG -3'

Posted On

2017-02-28