Mutagenetix > Incidental Mutations

Incidental Mutation 'R7784:Vars2'

599472

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R7784 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35655634-35667592 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 35658158 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 884 (A884T)

Ref Sequence

ENSEMBL: ENSMUSP00000047917 (fasta)

Gene Model

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

AlphaFold

Q3U2A8

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043674
AA Change: A884T

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: A884T

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: A533T

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

Meta Mutation Damage Score

0.1010

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (66/66)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001J03Rik	A	T	5: 146,182,828		probably null	Het
3425401B19Rik	A	T	14: 32,659,840	S1389R	probably benign	Het
Abca9	A	T	11: 110,154,417	C363*	probably null	Het
Actbl2	T	A	13: 111,255,411	N93K	probably damaging	Het
Adamtsl3	T	C	7: 82,573,989	Y993H	probably damaging	Het
Adgrg1	G	A	8: 95,012,882	W653*	probably null	Het
Akap13	T	A	7: 75,610,328	V97D	probably benign	Het
C130026I21Rik	T	A	1: 85,212,474		probably null	Het
Cacna1d	T	A	14: 30,123,439	D613V	probably damaging	Het
Col10a1	C	A	10: 34,394,218	P62H	unknown	Het
Cpb2	A	T	14: 75,275,040	N298Y	probably damaging	Het
Ddc	A	G	11: 11,839,396		probably null	Het
Ddx6	T	C	9: 44,630,142		probably null	Het
Epb42	T	G	2: 121,034,435	K58N	probably benign	Het
Eps8	T	A	6: 137,499,587	I605L	probably benign	Het
Eps8l1	T	C	7: 4,472,122	L304P	probably damaging	Het
Erbb4	T	A	1: 68,075,499	I929F	probably damaging	Het
Erc2	A	T	14: 27,898,594	N393I	probably damaging	Het
Fbxw25	C	T	9: 109,650,119	D355N		Het
Ffar2	T	C	7: 30,819,258	K286E	probably benign	Het
Gabrd	A	G	4: 155,388,932		probably null	Het
Ganc	G	A	2: 120,436,668	W488*	probably null	Het
Gm5724	C	T	6: 141,713,193		probably null	Het
Ifi207	T	A	1: 173,730,132	M347L	unknown	Het
Kat6b	A	T	14: 21,660,841	I619F	probably damaging	Het
Kif26a	A	G	12: 112,178,147	R1612G	possibly damaging	Het
Kifc3	A	G	8: 95,110,692		probably null	Het
Krt39	A	T	11: 99,521,031	C76*	probably null	Het
Lcmt1	G	T	7: 123,401,495	R84L	probably benign	Het
Lrit1	A	G	14: 37,061,780	Y355C	probably benign	Het
Mad2l1	C	A	6: 66,535,413		probably null	Het
Med23	C	T	10: 24,902,448	T870M	probably damaging	Het
Mrpl2	A	G	17: 46,648,591		probably null	Het
Mtmr6	A	G	14: 60,300,445	D593G	probably benign	Het
Myo15b	G	A	11: 115,861,340	V683M		Het
Neb	T	A	2: 52,235,488	M506L		Het
Olfr103	T	C	17: 37,336,578	Y218C	probably benign	Het
Olfr103	A	G	17: 37,337,055	F59S	probably damaging	Het
Olfr1154	G	A	2: 87,903,193	T161I	probably benign	Het
Olfr434	T	A	6: 43,217,388	H158Q	possibly damaging	Het
Pdzd8	A	G	19: 59,327,863	F294L	probably damaging	Het
Rabgap1	G	A	2: 37,487,532	S347N	possibly damaging	Het
Rasgrf2	T	C	13: 91,896,082	T350A		Het
Rbp3	A	T	14: 33,954,158	H21L	probably benign	Het
Rp1	C	A	1: 4,142,658	V1069F	unknown	Het
Rtn4	T	A	11: 29,741,048	L1113*	probably null	Het
Ryr3	A	G	2: 112,775,695	F2407L	probably damaging	Het
Sept2	T	A	1: 93,497,444	D107E	probably damaging	Het
Sept4	A	G	11: 87,579,008	T7A	probably benign	Het
Slc34a3	T	A	2: 25,232,225	I123F	probably damaging	Het
Slc9a4	T	C	1: 40,600,776	Y243H	probably damaging	Het
Slco1a1	T	A	6: 141,943,388	E66V	probably damaging	Het
Spata33	A	G	8: 123,213,252	R68G	unknown	Het
Spta1	G	A	1: 174,202,451	D928N	probably damaging	Het
St8sia5	A	G	18: 77,254,550	S319G	probably benign	Het
Tmem208	A	G	8: 105,328,833	D149G	possibly damaging	Het
Trank1	A	T	9: 111,364,103	I583F	probably damaging	Het
Trio	C	T	15: 27,763,994	V2015M	probably damaging	Het
Tsc22d1	C	T	14: 76,416,701	Q207*	probably null	Het
Tshr	A	G	12: 91,505,305	D143G	probably benign	Het
Txlna	C	T	4: 129,632,157	R299H	probably damaging	Het
Ush2a	A	T	1: 188,444,592	T1318S	possibly damaging	Het
Utp14b	A	G	1: 78,664,943	K186R	probably damaging	Het
Zfp354c	TCACACTCGGCACA	TCACA	11: 50,815,240		probably benign	Het
Zfp775	A	G	6: 48,619,249	Q19R	possibly damaging	Het

Other mutations in Vars2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02106:Vars2	APN	17	35664621	unclassified	probably benign
IGL02320:Vars2	APN	17	35660454	missense	probably benign	0.07
IGL02580:Vars2	APN	17	35660885	missense	possibly damaging	0.50
IGL02691:Vars2	APN	17	35660248	missense	probably damaging	1.00
IGL03039:Vars2	APN	17	35664121	missense	probably damaging	1.00
PIT4445001:Vars2	UTSW	17	35666211	nonsense	probably null
R0079:Vars2	UTSW	17	35659156	missense	probably damaging	0.99
R0152:Vars2	UTSW	17	35660027	missense	probably damaging	1.00
R0346:Vars2	UTSW	17	35664864	unclassified	probably benign
R0426:Vars2	UTSW	17	35664584	missense	probably damaging	1.00
R0584:Vars2	UTSW	17	35666686	missense	possibly damaging	0.82
R0589:Vars2	UTSW	17	35659176	missense	probably benign
R0882:Vars2	UTSW	17	35657299	missense	probably benign	0.41
R1234:Vars2	UTSW	17	35667146	missense	probably damaging	1.00
R1263:Vars2	UTSW	17	35661609	missense	probably damaging	1.00
R1559:Vars2	UTSW	17	35666258	unclassified	probably benign
R1772:Vars2	UTSW	17	35660084	missense	probably damaging	1.00
R1809:Vars2	UTSW	17	35662216	missense	probably damaging	1.00
R1913:Vars2	UTSW	17	35666922	missense	probably benign	0.02
R1986:Vars2	UTSW	17	35660061	missense	probably damaging	1.00
R2504:Vars2	UTSW	17	35664793	missense	probably damaging	1.00
R3426:Vars2	UTSW	17	35661974	missense	probably damaging	1.00
R4539:Vars2	UTSW	17	35666888	missense	probably damaging	0.99
R4751:Vars2	UTSW	17	35659343	missense	possibly damaging	0.89
R4861:Vars2	UTSW	17	35661933	missense	probably benign	0.00
R4861:Vars2	UTSW	17	35661933	missense	probably benign	0.00
R5028:Vars2	UTSW	17	35659473	critical splice donor site	probably null
R5217:Vars2	UTSW	17	35658149	missense	probably damaging	1.00
R5292:Vars2	UTSW	17	35660786	missense	probably damaging	1.00
R6056:Vars2	UTSW	17	35665788	missense	probably benign	0.01
R6211:Vars2	UTSW	17	35665662	splice site	probably null
R6213:Vars2	UTSW	17	35660440	missense	probably benign	0.27
R6374:Vars2	UTSW	17	35660045	missense	probably damaging	1.00
R6746:Vars2	UTSW	17	35660402	critical splice donor site	probably null
R6749:Vars2	UTSW	17	35666713	missense	probably damaging	1.00
R6957:Vars2	UTSW	17	35667075	missense	probably benign	0.39
R7107:Vars2	UTSW	17	35658250	missense	probably damaging	1.00
R7428:Vars2	UTSW	17	35666686	missense	probably benign	0.00
R7538:Vars2	UTSW	17	35660780	missense	probably damaging	1.00
R7553:Vars2	UTSW	17	35664788	missense	possibly damaging	0.93
R7741:Vars2	UTSW	17	35660943	missense	probably damaging	1.00
R7823:Vars2	UTSW	17	35659136	missense	probably damaging	1.00
R7915:Vars2	UTSW	17	35664839	missense	probably damaging	1.00
R8201:Vars2	UTSW	17	35658310	missense	probably benign
R8955:Vars2	UTSW	17	35661649	missense	probably damaging	1.00
R8964:Vars2	UTSW	17	35659807	missense	possibly damaging	0.46
R9101:Vars2	UTSW	17	35659088	missense	possibly damaging	0.51
R9202:Vars2	UTSW	17	35663552	critical splice acceptor site	probably null
R9202:Vars2	UTSW	17	35666659	missense	probably damaging	1.00
X0021:Vars2	UTSW	17	35659034	missense	possibly damaging	0.93
Z1176:Vars2	UTSW	17	35664791	missense	possibly damaging	0.55
Z1177:Vars2	UTSW	17	35663472	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- GCAATTCAGTGACACAGCATC -3'
(R):5'- TGAAGCCAGTGTTGTCGAG -3'

Sequencing Primer
(F):5'- AATCCTAGCACTTACTTGGGAGGC -3'
(R):5'- CCAGTGTTGTCGAGCGTGC -3'

Posted On

2019-11-26