Mutagenetix > Incidental Mutation

Incidental Mutation 'R1986:Vars2'

220747

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l, 1190004I24Rik

MMRRC Submission

039998-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1986 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

35966526-35978484 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35970953 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 626 (W626R)

Ref Sequence

ENSEMBL: ENSMUSP00000047917 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043674] [ENSMUST00000169093]

AlphaFold

Q3U2A8

Predicted Effect

probably damaging
Transcript: ENSMUST00000043674
AA Change: W626R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: W626R

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	112	736	3.3e-179	PFAM
Pfam:tRNA-synt_1g	141	221	2e-8	PFAM
Pfam:Anticodon_1	780	932	3.6e-32	PFAM
low complexity region	1005	1015	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164295

Predicted Effect

probably benign
Transcript: ENSMUST00000164404

SMART Domains

Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	201	1e-49	PFAM
Pfam:tRNA-synt_1g	68	172	4e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164978

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165787

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168885

Predicted Effect

unknown
Transcript: ENSMUST00000168922
AA Change: W275R

SMART Domains

Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: W275R

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	2	386	3e-105	PFAM
Pfam:Anticodon_1	430	566	8.2e-29	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173162

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174129

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170701

Predicted Effect

probably benign
Transcript: ENSMUST00000169093

SMART Domains

Protein: ENSMUSP00000126794
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	109	1.7e-29	PFAM

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	G	3: 124,212,977 (GRCm39)	S105P	probably damaging	Het
9930111J21Rik2	T	A	11: 48,910,119 (GRCm39)	K771N	possibly damaging	Het
Abcc2	A	G	19: 43,818,318 (GRCm39)	E1268G	probably damaging	Het
Adamts4	T	C	1: 171,084,244 (GRCm39)	F574L	possibly damaging	Het
Adamts9	A	G	6: 92,773,375 (GRCm39)	V1165A	probably benign	Het
Agap2	A	T	10: 126,918,913 (GRCm39)	K430*	probably null	Het
Amn	G	T	12: 111,241,431 (GRCm39)	G232V	probably damaging	Het
Ank3	A	G	10: 69,703,258 (GRCm39)	E297G	probably damaging	Het
Arhgap45	T	C	10: 79,856,530 (GRCm39)	L26P	probably damaging	Het
Atp10b	C	A	11: 43,063,595 (GRCm39)	Q177K	probably benign	Het
Bbs10	A	T	10: 111,135,118 (GRCm39)	D77V	probably damaging	Het
Bltp2	A	T	11: 78,165,438 (GRCm39)	H1318L	probably damaging	Het
Bpifa1	T	A	2: 153,986,256 (GRCm39)	L127Q	probably damaging	Het
Brinp2	T	C	1: 158,074,348 (GRCm39)	N591S	probably damaging	Het
C2cd2	A	C	16: 97,671,471 (GRCm39)	V476G	probably damaging	Het
C7	T	A	15: 5,041,494 (GRCm39)	T471S	possibly damaging	Het
Cacna1b	A	T	2: 24,538,998 (GRCm39)	Y1488N	probably damaging	Het
Cadps2	A	G	6: 23,323,379 (GRCm39)	F1001L	probably damaging	Het
Ccdc188	T	C	16: 18,036,707 (GRCm39)	S216P	probably damaging	Het
Ccdc24	A	G	4: 117,729,213 (GRCm39)	L88P	probably damaging	Het
Dab1	T	C	4: 104,470,412 (GRCm39)	I65T	probably damaging	Het
Dock4	A	T	12: 40,780,062 (GRCm39)	D621V	probably damaging	Het
Drd5	A	T	5: 38,477,456 (GRCm39)	M150L	probably damaging	Het
Eef2k	T	A	7: 120,472,569 (GRCm39)	M94K	possibly damaging	Het
Epg5	A	G	18: 78,025,521 (GRCm39)		probably null	Het
Epsti1	T	C	14: 78,169,673 (GRCm39)		probably null	Het
Ern2	T	A	7: 121,770,752 (GRCm39)	D754V	probably benign	Het
Fbxo6	A	G	4: 148,230,552 (GRCm39)	Y237H	probably damaging	Het
Fbxw24	A	G	9: 109,436,124 (GRCm39)	S303P	probably damaging	Het
Fpr-rs3	A	T	17: 20,844,103 (GRCm39)		probably null	Het
Gab1	G	T	8: 81,493,010 (GRCm39)	T679K	probably damaging	Het
Gbp9	C	A	5: 105,253,590 (GRCm39)	V42F	probably damaging	Het
Gbp9	A	T	5: 105,253,652 (GRCm39)	V21E	probably damaging	Het
Gm20821	A	G	Y: 9,783,927 (GRCm39)	Q183R	probably benign	Het
Gpatch11	A	T	17: 79,151,266 (GRCm39)	I226F	probably benign	Het
Hephl1	T	G	9: 14,965,848 (GRCm39)	E1035A	probably damaging	Het
Hspa4l	T	C	3: 40,714,833 (GRCm39)	V156A	probably damaging	Het
Ifna13	A	G	4: 88,562,588 (GRCm39)	V12A	probably benign	Het
Il24	G	A	1: 130,810,268 (GRCm39)	T196I	probably benign	Het
Irgm2	A	G	11: 58,110,384 (GRCm39)	D37G	probably benign	Het
Irs1	A	G	1: 82,266,486 (GRCm39)	S577P	probably damaging	Het
Kif21b	G	A	1: 136,075,284 (GRCm39)	D166N	probably damaging	Het
Krtap4-16	T	C	11: 99,742,322 (GRCm39)	Q26R	unknown	Het
Lig1	T	A	7: 13,043,067 (GRCm39)	Y837*	probably null	Het
Lrrc69	T	C	4: 14,708,669 (GRCm39)	E225G	possibly damaging	Het
Map3k20	C	T	2: 72,271,638 (GRCm39)	Q589*	probably null	Het
Masp1	T	G	16: 23,302,211 (GRCm39)	M347L	probably benign	Het
Mgat3	A	T	15: 80,096,390 (GRCm39)	I406F	probably benign	Het
Mmp1b	T	G	9: 7,368,577 (GRCm39)	D425A	probably benign	Het
Mss51	T	C	14: 20,533,259 (GRCm39)	H404R	probably benign	Het
Myo15b	A	T	11: 115,773,701 (GRCm39)	H1911L	probably benign	Het
Nedd4l	A	G	18: 65,276,874 (GRCm39)	D102G	probably damaging	Het
Niban3	T	A	8: 72,056,404 (GRCm39)	I368N	possibly damaging	Het
Npc2	T	C	12: 84,807,523 (GRCm39)	K112E	probably benign	Het
Nuggc	T	A	14: 65,879,370 (GRCm39)	V694E	probably damaging	Het
Olfm1	T	G	2: 28,104,718 (GRCm39)	V157G	probably benign	Het
Or10h28	T	C	17: 33,488,489 (GRCm39)	S264P	probably benign	Het
Or5p55	T	C	7: 107,566,877 (GRCm39)	V91A	probably benign	Het
Otogl	T	A	10: 107,630,051 (GRCm39)		probably null	Het
Ovgp1	G	A	3: 105,882,251 (GRCm39)	C38Y	probably damaging	Het
Pisd	A	T	5: 32,894,672 (GRCm39)	S344T	probably damaging	Het
Psme4	T	C	11: 30,780,352 (GRCm39)	V840A	probably benign	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Rims2	T	A	15: 39,208,710 (GRCm39)	M171K	probably damaging	Het
Rin2	T	A	2: 145,720,860 (GRCm39)	M731K	probably damaging	Het
Scgb1b19	T	C	7: 32,987,108 (GRCm39)		probably null	Het
Serpina10	A	G	12: 103,594,514 (GRCm39)	I235T	possibly damaging	Het
Setbp1	T	A	18: 78,901,759 (GRCm39)	E636V	probably damaging	Het
Sh3d21	C	T	4: 126,056,290 (GRCm39)	E101K	probably damaging	Het
Ski	T	G	4: 155,306,148 (GRCm39)	D225A	probably damaging	Het
Slc28a2b	A	G	2: 122,357,910 (GRCm39)	T655A	probably benign	Het
Slc29a3	T	C	10: 60,559,593 (GRCm39)	Y187C	probably damaging	Het
Sort1	T	A	3: 108,253,043 (GRCm39)	D494E	possibly damaging	Het
Sphkap	A	T	1: 83,255,643 (GRCm39)	L702Q	probably damaging	Het
Srr	A	G	11: 74,799,545 (GRCm39)	I285T	probably damaging	Het
Stam2	T	C	2: 52,599,638 (GRCm39)	T257A	possibly damaging	Het
Suds3	A	T	5: 117,246,417 (GRCm39)	N112K	probably damaging	Het
Tedc2	T	A	17: 24,435,291 (GRCm39)	E366V	probably damaging	Het
Tedc2	C	A	17: 24,435,292 (GRCm39)	E366*	probably null	Het
Tesk2	T	C	4: 116,608,390 (GRCm39)	L104P	probably damaging	Het
Tie1	C	T	4: 118,336,160 (GRCm39)	R702H	probably benign	Het
Tpo	G	T	12: 30,169,465 (GRCm39)	A90E	probably damaging	Het
Trim30a	T	C	7: 104,060,672 (GRCm39)	D368G	probably damaging	Het
Ugt2a2	A	T	5: 87,608,438 (GRCm39)	M633K	possibly damaging	Het
Vmn2r10	A	T	5: 109,154,120 (GRCm39)	Y61*	probably null	Het
Vmn2r95	T	C	17: 18,671,805 (GRCm39)	V514A	probably benign	Het
Vwa5a	T	G	9: 38,649,110 (GRCm39)		probably benign	Het
Zfp365	A	T	10: 67,745,686 (GRCm39)	C31S	probably damaging	Het
Zfp397	A	T	18: 24,093,108 (GRCm39)	I198F	possibly damaging	Het
Zfp407	C	T	18: 84,577,898 (GRCm39)	A1072T	probably benign	Het
Zfp593	T	C	4: 133,972,206 (GRCm39)	E100G	possibly damaging	Het

Other mutations in Vars2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02106:Vars2	APN	17	35,975,513 (GRCm39)	unclassified	probably benign
IGL02320:Vars2	APN	17	35,971,346 (GRCm39)	missense	probably benign	0.07
IGL02580:Vars2	APN	17	35,971,777 (GRCm39)	missense	possibly damaging	0.50
IGL02691:Vars2	APN	17	35,971,140 (GRCm39)	missense	probably damaging	1.00
IGL03039:Vars2	APN	17	35,975,013 (GRCm39)	missense	probably damaging	1.00
PIT4445001:Vars2	UTSW	17	35,977,103 (GRCm39)	nonsense	probably null
R0079:Vars2	UTSW	17	35,970,048 (GRCm39)	missense	probably damaging	0.99
R0152:Vars2	UTSW	17	35,970,919 (GRCm39)	missense	probably damaging	1.00
R0346:Vars2	UTSW	17	35,975,756 (GRCm39)	unclassified	probably benign
R0426:Vars2	UTSW	17	35,975,476 (GRCm39)	missense	probably damaging	1.00
R0584:Vars2	UTSW	17	35,977,578 (GRCm39)	missense	possibly damaging	0.82
R0589:Vars2	UTSW	17	35,970,068 (GRCm39)	missense	probably benign
R0882:Vars2	UTSW	17	35,968,191 (GRCm39)	missense	probably benign	0.41
R1234:Vars2	UTSW	17	35,978,038 (GRCm39)	missense	probably damaging	1.00
R1263:Vars2	UTSW	17	35,972,501 (GRCm39)	missense	probably damaging	1.00
R1559:Vars2	UTSW	17	35,977,150 (GRCm39)	unclassified	probably benign
R1772:Vars2	UTSW	17	35,970,976 (GRCm39)	missense	probably damaging	1.00
R1809:Vars2	UTSW	17	35,973,108 (GRCm39)	missense	probably damaging	1.00
R1913:Vars2	UTSW	17	35,977,814 (GRCm39)	missense	probably benign	0.02
R2504:Vars2	UTSW	17	35,975,685 (GRCm39)	missense	probably damaging	1.00
R3426:Vars2	UTSW	17	35,972,866 (GRCm39)	missense	probably damaging	1.00
R4539:Vars2	UTSW	17	35,977,780 (GRCm39)	missense	probably damaging	0.99
R4751:Vars2	UTSW	17	35,970,235 (GRCm39)	missense	possibly damaging	0.89
R4861:Vars2	UTSW	17	35,972,825 (GRCm39)	missense	probably benign	0.00
R4861:Vars2	UTSW	17	35,972,825 (GRCm39)	missense	probably benign	0.00
R5028:Vars2	UTSW	17	35,970,365 (GRCm39)	critical splice donor site	probably null
R5217:Vars2	UTSW	17	35,969,041 (GRCm39)	missense	probably damaging	1.00
R5292:Vars2	UTSW	17	35,971,678 (GRCm39)	missense	probably damaging	1.00
R6056:Vars2	UTSW	17	35,976,680 (GRCm39)	missense	probably benign	0.01
R6211:Vars2	UTSW	17	35,976,554 (GRCm39)	splice site	probably null
R6213:Vars2	UTSW	17	35,971,332 (GRCm39)	missense	probably benign	0.27
R6374:Vars2	UTSW	17	35,970,937 (GRCm39)	missense	probably damaging	1.00
R6746:Vars2	UTSW	17	35,971,294 (GRCm39)	critical splice donor site	probably null
R6749:Vars2	UTSW	17	35,977,605 (GRCm39)	missense	probably damaging	1.00
R6957:Vars2	UTSW	17	35,977,967 (GRCm39)	missense	probably benign	0.39
R7107:Vars2	UTSW	17	35,969,142 (GRCm39)	missense	probably damaging	1.00
R7428:Vars2	UTSW	17	35,977,578 (GRCm39)	missense	probably benign	0.00
R7538:Vars2	UTSW	17	35,971,672 (GRCm39)	missense	probably damaging	1.00
R7553:Vars2	UTSW	17	35,975,680 (GRCm39)	missense	possibly damaging	0.93
R7741:Vars2	UTSW	17	35,971,835 (GRCm39)	missense	probably damaging	1.00
R7784:Vars2	UTSW	17	35,969,050 (GRCm39)	missense	possibly damaging	0.95
R7823:Vars2	UTSW	17	35,970,028 (GRCm39)	missense	probably damaging	1.00
R7915:Vars2	UTSW	17	35,975,731 (GRCm39)	missense	probably damaging	1.00
R8201:Vars2	UTSW	17	35,969,202 (GRCm39)	missense	probably benign
R8955:Vars2	UTSW	17	35,972,541 (GRCm39)	missense	probably damaging	1.00
R8964:Vars2	UTSW	17	35,970,699 (GRCm39)	missense	possibly damaging	0.46
R9101:Vars2	UTSW	17	35,969,980 (GRCm39)	missense	possibly damaging	0.51
R9202:Vars2	UTSW	17	35,977,551 (GRCm39)	missense	probably damaging	1.00
R9202:Vars2	UTSW	17	35,974,444 (GRCm39)	critical splice acceptor site	probably null
R9450:Vars2	UTSW	17	35,973,027 (GRCm39)	missense	probably damaging	0.98
X0021:Vars2	UTSW	17	35,969,926 (GRCm39)	missense	possibly damaging	0.93
Z1176:Vars2	UTSW	17	35,975,683 (GRCm39)	missense	possibly damaging	0.55
Z1177:Vars2	UTSW	17	35,974,364 (GRCm39)	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- TCCCGAACCATGGAGTGAAG -3'
(R):5'- ACGTCCTGGACACTTGGTTC -3'

Sequencing Primer
(F):5'- GAAGCACCTGCAGACACGG -3'
(R):5'- GGACACTTGGTTCTCTTCGGC -3'

Posted On

2014-08-25