Mutagenetix > Incidental Mutation

Incidental Mutation 'R7107:Vars2'

551282

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l, 1190004I24Rik

MMRRC Submission

045199-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7107 (G1)

Quality Score

168.009

Status

Validated

Chromosome

Chromosomal Location

35966526-35978484 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35969142 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 853 (L853P)

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: L853P

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

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: L853P

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

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

SMART Domains

Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838
AA Change: L502P

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

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

99% (78/79)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	A	G	11: 109,867,299 (GRCm39)	L253S	probably damaging	Het
Adgrv1	T	C	13: 81,726,261 (GRCm39)	E588G	probably benign	Het
Ahcy	G	A	2: 154,910,893 (GRCm39)	A25V	probably damaging	Het
Ank2	A	C	3: 126,797,631 (GRCm39)	L710R	probably damaging	Het
Ap1b1	A	G	11: 4,989,558 (GRCm39)	T824A	probably benign	Het
Arap2	T	A	5: 62,763,551 (GRCm39)	H1531L	probably damaging	Het
Atosb	A	T	4: 43,036,434 (GRCm39)	V99E	probably benign	Het
B3gnt7	T	C	1: 86,233,495 (GRCm39)	L247P	probably damaging	Het
Bcl6b	A	G	11: 70,117,396 (GRCm39)	C409R	probably damaging	Het
Bicdl1	T	C	5: 115,808,229 (GRCm39)	H301R	probably benign	Het
Casc3	T	A	11: 98,718,413 (GRCm39)	I491N	possibly damaging	Het
Ccdc92b	T	A	11: 74,520,887 (GRCm39)	L63Q	probably damaging	Het
Cep250	A	G	2: 155,837,314 (GRCm39)	T2319A	probably benign	Het
Chd1	T	C	17: 15,981,628 (GRCm39)	S1356P	probably damaging	Het
Chd8	A	G	14: 52,450,129 (GRCm39)	S1542P	probably benign	Het
Clec2m	A	G	6: 129,299,915 (GRCm39)	C188R	probably damaging	Het
Cntnap4	A	G	8: 113,542,120 (GRCm39)	D751G	probably damaging	Het
Cpsf4l	G	A	11: 113,593,315 (GRCm39)	R90C	possibly damaging	Het
Defa21	G	A	8: 21,515,724 (GRCm39)	A41T	probably damaging	Het
Dennd4a	G	T	9: 64,801,681 (GRCm39)	L941F	possibly damaging	Het
Dnah12	G	A	14: 26,500,869 (GRCm39)		probably null	Het
Dtx4	A	T	19: 12,450,624 (GRCm39)	C529*	probably null	Het
Entpd3	A	G	9: 120,389,665 (GRCm39)	Y317C	probably damaging	Het
Erp29	T	A	5: 121,583,381 (GRCm39)	I182F	possibly damaging	Het
Fam161a	A	G	11: 22,973,452 (GRCm39)	R445G	possibly damaging	Het
Fam76a	T	A	4: 132,631,232 (GRCm39)	M238L	possibly damaging	Het
Fn1	T	C	1: 71,666,408 (GRCm39)	Y875C	probably damaging	Het
Gnb2	A	G	5: 137,528,444 (GRCm39)		probably null	Het
Hspg2	T	C	4: 137,237,963 (GRCm39)	S229P	probably damaging	Het
Ighv6-6	A	G	12: 114,398,590 (GRCm39)	S59P	probably damaging	Het
Itpkc	C	A	7: 26,927,702 (GRCm39)	A71S	probably benign	Het
Kcnk10	G	A	12: 98,485,002 (GRCm39)	R45*	probably null	Het
Krcc1	A	G	6: 71,261,198 (GRCm39)	S77G	probably benign	Het
Lelp1	G	A	3: 92,042,821 (GRCm39)	T76I	unknown	Het
Lifr	A	T	15: 7,208,421 (GRCm39)	I600F	possibly damaging	Het
Lrrk1	T	A	7: 65,937,191 (GRCm39)	D987V	possibly damaging	Het
Muc16	C	T	9: 18,548,594 (GRCm39)	D5900N	probably benign	Het
Muc6	AGGCGCAGAAACCCTGGC	AGGC	7: 141,214,363 (GRCm39)		probably null	Het
Myo9a	A	G	9: 59,778,098 (GRCm39)	I1285V	probably benign	Het
Ndel1	T	C	11: 68,713,474 (GRCm39)	D321G	possibly damaging	Het
Nlrp4b	T	C	7: 10,449,144 (GRCm39)	V449A	probably damaging	Het
Or10q12	A	G	19: 13,746,525 (GRCm39)	E273G	probably benign	Het
Or2r11	T	C	6: 42,437,488 (GRCm39)	N155S	possibly damaging	Het
Or2y1c	T	A	11: 49,361,261 (GRCm39)	Y94*	probably null	Het
Or51k1	A	T	7: 103,661,489 (GRCm39)	L140Q	probably benign	Het
Or5k3	A	C	16: 58,969,279 (GRCm39)	D22A	probably benign	Het
Osbpl1a	G	A	18: 12,974,310 (GRCm39)	R459*	probably null	Het
Pabpc1l	A	C	2: 163,884,399 (GRCm39)	T379P	probably damaging	Het
Pde2a	A	T	7: 101,071,175 (GRCm39)	Q15L	probably benign	Het
Pdk1	A	G	2: 71,726,085 (GRCm39)	N331S	probably benign	Het
Pfdn1	A	T	18: 36,584,519 (GRCm39)		probably null	Het
Pnliprp1	T	A	19: 58,717,582 (GRCm39)	L9H	probably damaging	Het
Prl7a2	A	T	13: 27,843,076 (GRCm39)	D242E	possibly damaging	Het
Prmt9	T	A	8: 78,294,880 (GRCm39)	I408N	possibly damaging	Het
Psme4	G	A	11: 30,798,105 (GRCm39)	R1366H	probably benign	Het
Pstpip1	A	T	9: 56,035,934 (GRCm39)	D393V	probably damaging	Het
Rab5b	A	G	10: 128,519,062 (GRCm39)		probably null	Het
Rap1gap2	G	A	11: 74,283,945 (GRCm39)	R618C	probably damaging	Het
Rin1	A	G	19: 5,100,801 (GRCm39)		probably benign	Het
Sall3	G	A	18: 81,016,969 (GRCm39)	P320S	probably benign	Het
Sdk1	A	G	5: 142,067,471 (GRCm39)	T1124A	probably damaging	Het
Sirpb1c	T	A	3: 15,892,941 (GRCm39)	T88S	possibly damaging	Het
Slc35f6	T	A	5: 30,814,121 (GRCm39)	I189N	probably damaging	Het
Slc49a3	T	A	5: 108,596,581 (GRCm39)		probably null	Het
Spata31d1e	T	A	13: 59,889,997 (GRCm39)	R608*	probably null	Het
Spsb2	A	T	6: 124,787,244 (GRCm39)	Q226L	probably benign	Het
Stab2	T	C	10: 86,741,456 (GRCm39)	D1221G	possibly damaging	Het
Sugp1	G	A	8: 70,522,800 (GRCm39)	R500H	probably benign	Het
Syne1	A	G	10: 5,082,078 (GRCm39)	Y849H	probably damaging	Het
Tbck	T	A	3: 132,428,092 (GRCm39)	I249N	possibly damaging	Het
Tdrd6	A	C	17: 43,935,095 (GRCm39)	F1984L	probably benign	Het
Tnxb	T	A	17: 34,890,314 (GRCm39)	V219E	unknown	Het
Tpst1	T	A	5: 130,143,344 (GRCm39)	V294D	probably damaging	Het
Treml1	A	G	17: 48,667,247 (GRCm39)	Q44R	probably damaging	Het
Trrap	G	A	5: 144,733,945 (GRCm39)	A933T	probably benign	Het
Vmn1r10	A	T	6: 57,090,615 (GRCm39)	N69I	possibly damaging	Het
Vmn1r179	T	A	7: 23,627,819 (GRCm39)	Y3*	probably null	Het
Vmn2r38	T	A	7: 9,093,728 (GRCm39)	Y498F	probably benign	Het
Zc3h11a	T	C	1: 133,566,655 (GRCm39)	T179A	probably damaging	Het
Zmym2	A	G	14: 57,140,169 (GRCm39)	T3A	probably benign	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
R1986:Vars2	UTSW	17	35,970,953 (GRCm39)	missense	probably damaging	1.00
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
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'- GATACTCACCTGGCAAGCAG -3'
(R):5'- TAGCACGGTGTCAGTAACTTAG -3'

Sequencing Primer
(F):5'- GATCCCGTGTGAAAGCTCCAC -3'
(R):5'- GGTGTCAGTAACTTAGCATGTACCC -3'

Posted On

2019-05-15