Mutagenetix > Incidental Mutation

Incidental Mutation 'R8964:Vars2'

682650

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l, 1190004I24Rik

MMRRC Submission

068798-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8964 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35966526-35978484 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 35970699 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 678 (E678G)

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: E678G

PolyPhen 2 Score 0.456 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: E678G

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: E327G

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

0.0892

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.2%

Validation Efficiency

100% (80/80)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933402N03Rik	C	T	7: 130,740,716 (GRCm39)	V167M	probably benign	Het
Abca6	G	A	11: 110,139,363 (GRCm39)	P37L	probably benign	Het
Abca9	A	T	11: 110,038,075 (GRCm39)	Y490*	probably null	Het
Abcb11	A	G	2: 69,117,061 (GRCm39)	V529A	possibly damaging	Het
Acox2	G	T	14: 8,243,768 (GRCm38)	Y529*	probably null	Het
Acte1	A	G	7: 143,423,030 (GRCm39)	T39A	probably benign	Het
Adck2	G	T	6: 39,551,083 (GRCm39)		probably benign	Het
Agxt	T	A	1: 93,072,869 (GRCm39)	C409S	possibly damaging	Het
Ahsa1	T	A	12: 87,318,131 (GRCm39)	I164N	probably damaging	Het
Arhgef1	A	G	7: 24,622,462 (GRCm39)	E647G	probably damaging	Het
Axin1	T	G	17: 26,361,718 (GRCm39)	F21V	probably damaging	Het
B3galnt1	A	G	3: 69,482,589 (GRCm39)	I224T	probably damaging	Het
Bche	T	C	3: 73,608,406 (GRCm39)	K340R	probably benign	Het
Bpifb5	T	A	2: 154,072,198 (GRCm39)	W302R	possibly damaging	Het
Cd72	G	A	4: 43,450,218 (GRCm39)	T230I	probably damaging	Het
Cdc42ep4	T	A	11: 113,620,278 (GRCm39)	M38L	probably damaging	Het
Cdcp1	G	A	9: 123,012,561 (GRCm39)	Q329*	probably null	Het
Clps	C	A	17: 28,777,730 (GRCm39)		probably benign	Het
Cluap1	A	G	16: 3,729,334 (GRCm39)		probably benign	Het
CN725425	C	T	15: 91,119,972 (GRCm39)	S31L	possibly damaging	Het
Cnbp	T	C	6: 87,821,086 (GRCm39)	N158D	probably benign	Het
Crebbp	A	G	16: 3,909,753 (GRCm39)	F1545S	probably damaging	Het
Cyp39a1	A	T	17: 44,002,558 (GRCm39)	T258S	probably benign	Het
Dclk2	T	C	3: 86,743,698 (GRCm39)	D257G	probably damaging	Het
Dock7	A	T	4: 98,949,476 (GRCm39)	D455E		Het
Ehbp1	G	A	11: 22,101,154 (GRCm39)	Q259*	probably null	Het
Eif3a	A	T	19: 60,751,630 (GRCm39)	D1228E	unknown	Het
Has2	A	T	15: 56,531,061 (GRCm39)	D551E	probably damaging	Het
Herc1	T	A	9: 66,352,872 (GRCm39)	N2119K	probably damaging	Het
Hsdl1	C	T	8: 120,292,899 (GRCm39)	A179T	probably benign	Het
Htt	T	A	5: 35,062,720 (GRCm39)	M2818K	probably benign	Het
Il18bp	A	G	7: 101,665,591 (GRCm39)	S80P	possibly damaging	Het
Ints10	A	G	8: 69,264,631 (GRCm39)	M455V	probably benign	Het
Ipcef1	T	C	10: 6,869,789 (GRCm39)	T255A	possibly damaging	Het
Krt1	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	15: 101,758,813 (GRCm39)		probably benign	Het
Lrba	T	A	3: 86,258,552 (GRCm39)	D1346E	probably benign	Het
Mdm1	T	A	10: 118,002,585 (GRCm39)	D635E	probably damaging	Het
Met	C	T	6: 17,527,144 (GRCm39)	P532S	probably damaging	Het
Nlrc5	T	A	8: 95,232,116 (GRCm39)	M1314K	possibly damaging	Het
Notch1	A	T	2: 26,371,062 (GRCm39)	S341R	possibly damaging	Het
Nr3c2	T	G	8: 77,881,941 (GRCm39)	L670V	probably damaging	Het
Nuak1	C	T	10: 84,210,734 (GRCm39)	M451I	probably benign	Het
Nubp1	G	A	16: 10,238,894 (GRCm39)	V170I	probably benign	Het
Or5v1	G	A	17: 37,809,664 (GRCm39)	G41S	probably damaging	Het
Or9g8	T	A	2: 85,606,964 (GRCm39)	I12N	probably damaging	Het
Pamr1	T	C	2: 102,464,811 (GRCm39)	V320A	possibly damaging	Het
Pcdhb11	T	A	18: 37,556,660 (GRCm39)	N663K	probably benign	Het
Pcnx1	G	A	12: 82,039,812 (GRCm39)	G1400D		Het
Pdxk	A	T	10: 78,283,771 (GRCm39)	V141E	probably benign	Het
Pex5	A	T	6: 124,375,740 (GRCm39)	N520K	probably benign	Het
Pklr	T	C	3: 89,050,036 (GRCm39)	V337A	probably benign	Het
Polb	T	C	8: 23,143,341 (GRCm39)	D17G	probably damaging	Het
Ppp1r9b	T	C	11: 94,882,705 (GRCm39)	L111P	probably damaging	Het
Prl3d1	A	G	13: 27,283,926 (GRCm39)	E165G	possibly damaging	Het
Prpf40a	A	G	2: 53,035,906 (GRCm39)	F657S	probably damaging	Het
Ptgs2	C	T	1: 149,980,798 (GRCm39)	R455C	probably damaging	Het
Pzp	T	A	6: 128,464,462 (GRCm39)	D1355V	probably benign	Het
Rasl12	T	A	9: 65,314,913 (GRCm39)	V72D	probably damaging	Het
Rfx2	C	A	17: 57,093,696 (GRCm39)	R266L	probably damaging	Het
Rnaseh2a	T	C	8: 85,686,434 (GRCm39)	D204G	probably benign	Het
S1pr3	A	C	13: 51,573,248 (GRCm39)	K143T	probably damaging	Het
Sdr39u1	C	A	14: 56,135,170 (GRCm39)	A258S	possibly damaging	Het
Sntb2	T	A	8: 107,707,808 (GRCm39)	S191T	possibly damaging	Het
Sod3	T	A	5: 52,525,696 (GRCm39)	F132I	probably damaging	Het
Sorcs2	C	T	5: 36,386,511 (GRCm39)	V176I	possibly damaging	Het
Syne1	T	C	10: 5,060,872 (GRCm39)	I7256V		Het
Tbc1d22b	A	G	17: 29,819,202 (GRCm39)	E459G	probably damaging	Het
Tbkbp1	A	G	11: 97,037,169 (GRCm39)	S278P	probably damaging	Het
Thoc5	A	T	11: 4,860,647 (GRCm39)	E245D	possibly damaging	Het
Tmc7	G	A	7: 118,160,228 (GRCm39)	P203L	probably benign	Het
Tns2	T	C	15: 102,011,553 (GRCm39)	L11P	possibly damaging	Het
Trip11	A	G	12: 101,811,315 (GRCm39)		probably null	Het
Ttn	T	G	2: 76,551,309 (GRCm39)	Y31361S	probably damaging	Het
Vav1	C	A	17: 57,606,122 (GRCm39)	H249N	probably benign	Het
Vmn2r9	T	A	5: 108,996,031 (GRCm39)	I206L	probably benign	Het
Vps4a	T	C	8: 107,771,686 (GRCm39)	S410P	probably damaging	Het
Wdr82	T	C	9: 106,053,861 (GRCm39)	Y71H	possibly damaging	Het
Zfand1	A	G	3: 10,413,631 (GRCm39)	Y19H	probably benign	Het
Zfp365	A	T	10: 67,745,088 (GRCm39)	I230N	probably damaging	Het
Zfp763	T	C	17: 33,240,710 (GRCm39)	T40A	probably benign	Het
Zfp788	A	T	7: 41,297,003 (GRCm39)	D51V	probably 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
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
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
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'- TGGCAGTCAAGTCAAGAGGC -3'
(R):5'- AGCAAGGTAATGTACTCAGACGC -3'

Sequencing Primer
(F):5'- TCAAGTCAAGAGGCCAGGAC -3'
(R):5'- AGGTAATGTACTCAGACGCCTGTC -3'

Posted On

2021-10-11