Mutagenetix > Incidental Mutation

Incidental Mutation 'R0391:Vars'

31732

Institutional Source

Beutler Lab

Gene Symbol

Vars

Ensembl Gene

ENSMUSG00000007029

Gene Name

valyl-tRNA synthetase

Synonyms

Bat-6, Bat6, G7a, D17H6S56E, Vars2

MMRRC Submission

038597-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.971) question?

Stock #

R0391 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35000987-35016322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 35011486 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 515 (V515A)

Ref Sequence

ENSEMBL: ENSMUSP00000133994 (fasta)

Gene Model

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

AlphaFold

Q9Z1Q9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000087315
AA Change: V515A

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000084572
Gene: ENSMUSG00000007029
AA Change: V515A

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

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

possibly damaging
Transcript: ENSMUST00000173584
AA Change: V515A

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000133994
Gene: ENSMUSG00000007029
AA Change: V515A

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

0.2975

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.9%
20x: 91.8%

Validation Efficiency

97% (97/100)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530002B09Rik	T	A	4: 122,701,177 (GRCm38)		probably benign	Het
Abcc2	G	A	19: 43,821,605 (GRCm38)		probably benign	Het
Abcc8	C	G	7: 46,122,173 (GRCm38)	G838A	probably damaging	Het
Akr1c21	G	A	13: 4,581,200 (GRCm38)	A245T	probably damaging	Het
Anapc15-ps	T	C	10: 95,673,277 (GRCm38)	E47G	probably damaging	Het
Apoa1	A	G	9: 46,229,842 (GRCm38)	T79A	probably benign	Het
Atp6v1b1	A	G	6: 83,756,921 (GRCm38)	H378R	possibly damaging	Het
C4b	A	G	17: 34,735,614 (GRCm38)		probably benign	Het
Catsperd	A	T	17: 56,662,821 (GRCm38)	E638D	probably benign	Het
Cckar	C	T	5: 53,706,253 (GRCm38)		probably null	Het
Cfap100	C	T	6: 90,405,339 (GRCm38)		probably benign	Het
Chd1	G	T	17: 15,749,894 (GRCm38)	G970C	probably damaging	Het
Col14a1	A	G	15: 55,446,259 (GRCm38)		probably benign	Het
Col17a1	C	T	19: 47,663,824 (GRCm38)	V698M	probably damaging	Het
Cpeb1	T	C	7: 81,361,725 (GRCm38)	D156G	possibly damaging	Het
Cryl1	A	G	14: 57,303,775 (GRCm38)	Y151H	possibly damaging	Het
Csmd3	C	A	15: 47,657,573 (GRCm38)	V1881L	probably damaging	Het
Ctnnal1	C	T	4: 56,847,921 (GRCm38)	A73T	probably damaging	Het
Cyp2c37	T	C	19: 39,994,506 (GRCm38)	S180P	probably damaging	Het
Cyp2c54	T	C	19: 40,072,169 (GRCm38)	T123A	possibly damaging	Het
Dennd6b	T	C	15: 89,187,214 (GRCm38)	D304G	probably damaging	Het
Dnmt3l	T	C	10: 78,051,916 (GRCm38)		probably benign	Het
Eci1	G	A	17: 24,433,260 (GRCm38)		probably null	Het
Efhc1	A	G	1: 20,960,188 (GRCm38)	Y115C	probably damaging	Het
Ern1	T	A	11: 106,407,178 (GRCm38)	K706*	probably null	Het
Fam129c	T	A	8: 71,602,499 (GRCm38)		probably benign	Het
Ghrl	T	C	6: 113,719,338 (GRCm38)	E31G	probably damaging	Het
Gpr108	A	C	17: 57,243,101 (GRCm38)	V179G	probably benign	Het
Henmt1	A	G	3: 108,958,535 (GRCm38)		probably benign	Het
Ift172	A	G	5: 31,286,667 (GRCm38)	V69A	probably damaging	Het
Il17ra	T	C	6: 120,476,979 (GRCm38)		probably benign	Het
Il17rb	G	T	14: 30,006,155 (GRCm38)		probably null	Het
Il17rb	T	C	14: 30,004,347 (GRCm38)	N95D	probably benign	Het
Iqub	G	A	6: 24,446,155 (GRCm38)	L757F	probably benign	Het
Itpr1	T	C	6: 108,378,167 (GRCm38)	V473A	probably benign	Het
Itpr2	T	G	6: 146,229,773 (GRCm38)	N1978H	probably damaging	Het
Klk1b26	T	A	7: 44,012,727 (GRCm38)	F3Y	probably damaging	Het
Lars	A	G	18: 42,251,363 (GRCm38)	V50A	probably benign	Het
Lax1	G	T	1: 133,680,066 (GRCm38)	H312Q	probably benign	Het
Lctl	T	C	9: 64,122,314 (GRCm38)		probably benign	Het
Lrp2	G	A	2: 69,460,337 (GRCm38)		probably benign	Het
Lrp2	T	A	2: 69,456,858 (GRCm38)	D3745V	probably damaging	Het
Lvrn	A	T	18: 46,850,466 (GRCm38)	H92L	probably benign	Het
March1	A	G	8: 66,418,973 (GRCm38)	T385A	probably damaging	Het
Marf1	C	T	16: 14,142,534 (GRCm38)	A549T	probably damaging	Het
Mbd5	T	C	2: 49,272,416 (GRCm38)	V970A	possibly damaging	Het
Mccc1	A	G	3: 35,963,570 (GRCm38)		probably benign	Het
Mpp4	A	T	1: 59,143,829 (GRCm38)		probably benign	Het
Mrnip	G	A	11: 50,199,920 (GRCm38)	A304T	probably damaging	Het
Muc5b	T	C	7: 141,865,082 (GRCm38)	S3922P	possibly damaging	Het
Myh3	T	A	11: 67,096,507 (GRCm38)		probably benign	Het
Nbea	A	T	3: 56,037,277 (GRCm38)	H555Q	probably damaging	Het
Nlrp9c	A	T	7: 26,371,476 (GRCm38)		probably benign	Het
Nmur1	A	T	1: 86,387,678 (GRCm38)	V178E	probably damaging	Het
Nod2	T	G	8: 88,663,778 (GRCm38)	S238A	probably benign	Het
Ogfod1	A	T	8: 94,063,023 (GRCm38)	T451S	probably damaging	Het
Olfr145	G	A	9: 37,897,842 (GRCm38)	G146D	probably benign	Het
Olfr23	T	C	11: 73,941,109 (GRCm38)	F288L	probably damaging	Het
Olfr372	C	T	8: 72,058,400 (GRCm38)	T240M	probably damaging	Het
Olfr716	T	A	7: 107,148,187 (GRCm38)	Y290*	probably null	Het
Pcdh20	T	C	14: 88,468,668 (GRCm38)	I399V	probably benign	Het
Pdlim1	G	T	19: 40,243,573 (GRCm38)	H120Q	probably damaging	Het
Plg	T	C	17: 12,419,081 (GRCm38)	V798A	probably damaging	Het
Polr2c	A	G	8: 94,857,775 (GRCm38)	I39V	possibly damaging	Het
Ppfia2	C	A	10: 106,830,714 (GRCm38)		probably benign	Het
Ppp1r3a	A	T	6: 14,719,697 (GRCm38)	I406N	probably benign	Het
Psg28	A	T	7: 18,426,173 (GRCm38)	M366K	probably benign	Het
Rad54b	T	C	4: 11,601,702 (GRCm38)	I419T	probably damaging	Het
Rnf43	A	G	11: 87,731,282 (GRCm38)	Q403R	possibly damaging	Het
Sema6a	G	A	18: 47,290,045 (GRCm38)		probably null	Het
Slc28a3	A	G	13: 58,569,415 (GRCm38)		probably benign	Het
Smad2	A	T	18: 76,289,037 (GRCm38)		probably null	Het
Smad4	G	A	18: 73,658,649 (GRCm38)	P274S	probably benign	Het
Smchd1	A	T	17: 71,403,154 (GRCm38)	V906D	probably damaging	Het
Soat2	C	A	15: 102,158,753 (GRCm38)	R320S	possibly damaging	Het
Spata33	C	T	8: 123,221,887 (GRCm38)	A57V	probably damaging	Het
Stab1	A	G	14: 31,143,418 (GRCm38)	L1814P	probably benign	Het
Stab2	T	C	10: 86,947,144 (GRCm38)	K680R	probably benign	Het
Stil	A	G	4: 115,041,172 (GRCm38)		probably null	Het
Sympk	T	A	7: 19,046,849 (GRCm38)	L759H	probably benign	Het
Tet1	A	T	10: 62,814,546 (GRCm38)		probably null	Het
Tfpi2	A	T	6: 3,965,460 (GRCm38)	N117K	probably benign	Het
Tle3	A	G	9: 61,416,661 (GRCm38)	Y766C	probably damaging	Het
Trpt1	C	A	19: 6,997,930 (GRCm38)		probably null	Het
Tshz1	A	G	18: 84,016,049 (GRCm38)	F78S	possibly damaging	Het
Ttc1	T	C	11: 43,738,808 (GRCm38)	D177G	probably damaging	Het
Ttc13	T	A	8: 124,674,401 (GRCm38)	Y741F	probably damaging	Het
Ulk3	C	T	9: 57,594,832 (GRCm38)	S462L	probably benign	Het
Utrn	C	T	10: 12,525,333 (GRCm38)		probably benign	Het
V1rd19	A	C	7: 24,003,585 (GRCm38)	T159P	probably damaging	Het
Vmn1r85	A	G	7: 13,084,588 (GRCm38)	Y210H	probably benign	Het
Vmn2r89	A	G	14: 51,455,978 (GRCm38)	T262A	probably damaging	Het
Vps53	G	A	11: 76,121,579 (GRCm38)	T209I	probably benign	Het
Wdfy2	T	C	14: 62,925,133 (GRCm38)	F95L	possibly damaging	Het
Wwp1	G	T	4: 19,627,911 (GRCm38)	S694Y	probably damaging	Het
Zbtb8b	T	A	4: 129,432,670 (GRCm38)	D201V	probably damaging	Het
Zmym5	A	C	14: 56,804,451 (GRCm38)	N123K	possibly damaging	Het

Other mutations in Vars

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01520:Vars	APN	17	35,013,873 (GRCm38)	missense	probably benign	0.00
IGL02160:Vars	APN	17	35,001,502 (GRCm38)	missense	probably damaging	1.00
IGL02303:Vars	APN	17	35,015,484 (GRCm38)	splice site	probably benign
IGL03027:Vars	APN	17	35,013,687 (GRCm38)	missense	probably damaging	1.00
Maladroit	UTSW	17	35,005,475 (GRCm38)	missense	probably benign	0.30
Whoops	UTSW	17	35,013,644 (GRCm38)	missense	probably damaging	1.00
FR4304:Vars	UTSW	17	35,015,989 (GRCm38)	small insertion	probably benign
FR4548:Vars	UTSW	17	35,015,991 (GRCm38)	small insertion	probably benign
FR4548:Vars	UTSW	17	35,015,989 (GRCm38)	small insertion	probably benign
FR4589:Vars	UTSW	17	35,015,988 (GRCm38)	small insertion	probably benign
R0045:Vars	UTSW	17	35,010,619 (GRCm38)	missense	probably damaging	1.00
R0045:Vars	UTSW	17	35,010,619 (GRCm38)	missense	probably damaging	1.00
R0045:Vars	UTSW	17	34,998,066 (GRCm38)	missense	probably benign	0.13
R0266:Vars	UTSW	17	35,013,869 (GRCm38)	missense	probably benign	0.00
R0267:Vars	UTSW	17	35,011,596 (GRCm38)	splice site	probably benign
R0445:Vars	UTSW	17	35,011,809 (GRCm38)	missense	probably benign	0.31
R0449:Vars	UTSW	17	35,012,727 (GRCm38)	splice site	probably null
R0557:Vars	UTSW	17	35,004,984 (GRCm38)	missense	possibly damaging	0.90
R0559:Vars	UTSW	17	35,014,058 (GRCm38)	nonsense	probably null
R0730:Vars	UTSW	17	35,014,300 (GRCm38)	missense	probably damaging	1.00
R0748:Vars	UTSW	17	34,998,012 (GRCm38)	missense	probably damaging	1.00
R1692:Vars	UTSW	17	35,013,725 (GRCm38)	missense	probably damaging	1.00
R1693:Vars	UTSW	17	34,998,196 (GRCm38)	missense	probably benign	0.31
R1697:Vars	UTSW	17	34,998,222 (GRCm38)	missense	probably benign	0.43
R1699:Vars	UTSW	17	35,014,758 (GRCm38)	missense	possibly damaging	0.93
R1712:Vars	UTSW	17	35,014,752 (GRCm38)	missense	probably damaging	1.00
R1989:Vars	UTSW	17	35,011,838 (GRCm38)	missense	possibly damaging	0.94
R2349:Vars	UTSW	17	35,015,752 (GRCm38)	missense	probably benign
R2365:Vars	UTSW	17	35,015,452 (GRCm38)	missense	probably benign	0.01
R3790:Vars	UTSW	17	34,999,334 (GRCm38)	missense	probably benign	0.34
R4615:Vars	UTSW	17	35,013,881 (GRCm38)	missense	probably damaging	0.97
R4844:Vars	UTSW	17	35,011,612 (GRCm38)	missense	probably damaging	1.00
R4856:Vars	UTSW	17	35,015,726 (GRCm38)	missense	probably benign	0.37
R4886:Vars	UTSW	17	35,015,726 (GRCm38)	missense	probably benign	0.37
R5570:Vars	UTSW	17	35,016,238 (GRCm38)	missense	probably benign	0.04
R5706:Vars	UTSW	17	35,005,481 (GRCm38)	splice site	probably null
R5858:Vars	UTSW	17	35,005,475 (GRCm38)	missense	probably benign	0.30
R5907:Vars	UTSW	17	35,012,376 (GRCm38)	missense	probably damaging	1.00
R5917:Vars	UTSW	17	35,012,515 (GRCm38)	missense	probably damaging	0.99
R5944:Vars	UTSW	17	35,013,644 (GRCm38)	missense	probably damaging	1.00
R6023:Vars	UTSW	17	35,001,609 (GRCm38)	missense	probably damaging	1.00
R6073:Vars	UTSW	17	35,001,529 (GRCm38)	missense	probably benign
R6273:Vars	UTSW	17	35,013,743 (GRCm38)	missense	probably damaging	1.00
R6390:Vars	UTSW	17	35,015,639 (GRCm38)	missense	probably benign	0.00
R6658:Vars	UTSW	17	35,015,741 (GRCm38)	missense	probably benign	0.03
R7067:Vars	UTSW	17	35,011,479 (GRCm38)	missense	probably damaging	0.98
R7387:Vars	UTSW	17	35,004,792 (GRCm38)	nonsense	probably null
R7954:Vars	UTSW	17	35,015,984 (GRCm38)	missense	probably benign	0.01
R8139:Vars	UTSW	17	35,011,504 (GRCm38)	missense	probably benign	0.16
R8347:Vars	UTSW	17	35,015,977 (GRCm38)	missense	possibly damaging	0.92
R8387:Vars	UTSW	17	35,010,514 (GRCm38)	missense	probably damaging	0.99
R8855:Vars	UTSW	17	35,015,644 (GRCm38)	missense	probably benign	0.00
R8866:Vars	UTSW	17	35,015,644 (GRCm38)	missense	probably benign	0.00
R9131:Vars	UTSW	17	35,004,797 (GRCm38)	missense	possibly damaging	0.77
R9620:Vars	UTSW	17	35,016,025 (GRCm38)	missense	unknown
R9695:Vars	UTSW	17	35,012,588 (GRCm38)	missense	possibly damaging	0.82
Z1177:Vars	UTSW	17	35,011,477 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCCTTTGTTAGGCTCCACGAAGAAG -3'
(R):5'- ACGTCTCCCAGCATGGTCTCAATC -3'

Sequencing Primer
(F):5'- CAGCCATTTCTGACATTGAGG -3'
(R):5'- TCCGGGTTGTTGCCACC -3'

Posted On

2013-04-24