Mutagenetix > Incidental Mutation

Incidental Mutation 'R1503:Trmu'

169491

Institutional Source

Beutler Lab

Gene Symbol

Trmu

Ensembl Gene

ENSMUSG00000022386

Gene Name

tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase

Synonyms

1600025P05Rik, Trmt1, 1110005N20Rik

MMRRC Submission

039553-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.139) question?

Stock #

R1503 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

85879312-85897394 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 85895019 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 289 (V289E)

Ref Sequence

ENSEMBL: ENSMUSP00000023019 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000016172] [ENSMUST00000023019] [ENSMUST00000162491]

AlphaFold

Q9DAT5

Predicted Effect

probably benign
Transcript: ENSMUST00000016172

SMART Domains

Protein: ENSMUSP00000016172
Gene: ENSMUSG00000016028

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
low complexity region	65	93	N/A	INTRINSIC
low complexity region	221	240	N/A	INTRINSIC
low complexity region	243	257	N/A	INTRINSIC
CA	282	366	9.51e-26	SMART
CA	390	472	1.59e-27	SMART
CA	496	578	3.8e-25	SMART
CA	602	700	2.25e-27	SMART
CA	724	802	3.14e-17	SMART
CA	826	905	2.67e-29	SMART
CA	929	1012	3.23e-28	SMART
CA	1036	1114	4.17e-22	SMART
CA	1142	1218	6.89e-1	SMART
EGF	1321	1376	3.38e-3	SMART
EGF	1381	1414	5.49e-3	SMART
EGF	1421	1456	9.7e-4	SMART
LamG	1477	1644	2.53e-33	SMART
EGF	1667	1700	6.4e-4	SMART
LamG	1726	1864	1.13e-21	SMART
EGF	1890	1923	1.84e-4	SMART
EGF	1925	1961	5.49e-3	SMART
EGF_Lam	2018	2063	7.12e-11	SMART
HormR	2066	2128	2.55e-20	SMART
Pfam:GAIN	2140	2396	1.1e-64	PFAM
GPS	2422	2475	5.03e-22	SMART
Pfam:7tm_2	2480	2712	2.6e-60	PFAM
low complexity region	2738	2753	N/A	INTRINSIC
low complexity region	2819	2852	N/A	INTRINSIC
low complexity region	2976	2988	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023019
AA Change: V289E

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000023019
Gene: ENSMUSG00000022386
AA Change: V289E

Domain	Start	End	E-Value	Type
Pfam:NAD_synthase	1	133	7.7e-7	PFAM
Pfam:ThiI	3	79	7.7e-8	PFAM
Pfam:tRNA_Me_trans	5	383	3.4e-142	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159730

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161784

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162010

Predicted Effect

probably benign
Transcript: ENSMUST00000162339

SMART Domains

Protein: ENSMUSP00000125266
Gene: ENSMUSG00000022386

Domain	Start	End	E-Value	Type
Pfam:tRNA_Me_trans	1	46	1.1e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162491

SMART Domains

Protein: ENSMUSP00000125704
Gene: ENSMUSG00000022386

Domain	Start	End	E-Value	Type
Pfam:NAD_synthase	1	88	1.1e-8	PFAM
Pfam:Asn_synthase	1	90	3e-7	PFAM
Pfam:ThiI	3	84	1.6e-10	PFAM
Pfam:tRNA_Me_trans	5	88	2.9e-34	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162601

Predicted Effect

probably benign
Transcript: ENSMUST00000226840

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.1%
20x: 92.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This nuclear gene encodes a mitochondrial tRNA-modifying enzyme. The encoded protein catalyzes the 2-thiolation of uridine on the wobble positions of tRNA(Lys), tRNA(Glu), and tRNA(Gln), resulting in the formation of 5-taurinomethyl-2-thiouridine moieties. Mutations in this gene may cause transient infantile liver failure. Polymorphisms in this gene may also influence the severity of deafness caused by mitochondrial 12S ribosomal RNA mutations. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
PHENOTYPE: Homozygous KO is embryonic lethal. Homozygous conditional KO in the liver affects mitochondrial function owing to impaired mt-tRNA modifications. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arhgef6	T	C	X: 57,338,562 (GRCm38)	M5V	probably benign	Het
Atf7ip	G	T	6: 136,606,867 (GRCm38)	V1299L	probably damaging	Het
Atp12a	A	T	14: 56,373,424 (GRCm38)	N342Y	probably damaging	Het
Atp8b5	G	A	4: 43,344,430 (GRCm38)	G439D	probably damaging	Het
Bpifb2	G	A	2: 153,889,510 (GRCm38)	D269N	possibly damaging	Het
Btd	T	G	14: 31,667,655 (GRCm38)	C444W	probably damaging	Het
Cacna1a	A	G	8: 84,601,946 (GRCm38)	D1624G	probably benign	Het
Carmil3	A	C	14: 55,498,280 (GRCm38)	N563T	probably damaging	Het
Cars	T	C	7: 143,568,989 (GRCm38)	R538G	probably benign	Het
Catsperd	A	G	17: 56,654,525 (GRCm38)	K416E	possibly damaging	Het
Cc2d2a	A	T	5: 43,695,239 (GRCm38)	Y386F	probably damaging	Het
Ccpg1	A	G	9: 72,999,478 (GRCm38)	N66S	probably benign	Het
Cd48	T	A	1: 171,695,847 (GRCm38)	L86H	probably damaging	Het
Cdan1	A	T	2: 120,729,575 (GRCm38)	H369Q	probably damaging	Het
Chil4	T	C	3: 106,206,034 (GRCm38)	D189G	probably benign	Het
Cit	T	A	5: 115,873,900 (GRCm38)	Y189N	possibly damaging	Het
Cntn3	G	A	6: 102,464,565 (GRCm38)	Q7*	probably null	Het
Csn1s2a	A	T	5: 87,775,799 (GRCm38)	I5F	possibly damaging	Het
Ctnnd1	C	T	2: 84,605,179 (GRCm38)		probably null	Het
Dmxl2	A	T	9: 54,446,988 (GRCm38)	Y391*	probably null	Het
Dnah12	T	C	14: 26,773,692 (GRCm38)	S1426P	probably damaging	Het
Dnhd1	T	G	7: 105,693,660 (GRCm38)	S1404A	possibly damaging	Het
Drosha	T	A	15: 12,848,073 (GRCm38)	C484S	probably benign	Het
Dsg4	A	T	18: 20,449,679 (GRCm38)	I125F	probably damaging	Het
Egfr	T	A	11: 16,869,301 (GRCm38)	M277K	possibly damaging	Het
Eml5	G	T	12: 98,831,174 (GRCm38)	L1059I	probably damaging	Het
Erbb4	G	T	1: 68,346,546 (GRCm38)	H295N	probably benign	Het
Etl4	T	G	2: 20,743,874 (GRCm38)	V139G	possibly damaging	Het
Fam160a1	T	A	3: 85,672,477 (GRCm38)	Y807F	possibly damaging	Het
Frem3	A	T	8: 80,687,018 (GRCm38)	E1969D	probably damaging	Het
Gdf3	T	A	6: 122,606,337 (GRCm38)	D357V	probably damaging	Het
Gimap8	T	A	6: 48,647,529 (GRCm38)		probably null	Het
Gml2	C	A	15: 74,821,352 (GRCm38)	S68*	probably null	Het
Gphn	A	G	12: 78,504,629 (GRCm38)	I248V	possibly damaging	Het
Greb1	A	T	12: 16,724,819 (GRCm38)	Y192*	probably null	Het
Hmbs	A	C	9: 44,337,432 (GRCm38)	L215W	probably benign	Het
Iglon5	T	A	7: 43,479,025 (GRCm38)	T123S	probably benign	Het
Ints2	C	T	11: 86,226,781 (GRCm38)	R705H	probably damaging	Het
Ints8	A	T	4: 11,245,842 (GRCm38)	L212Q	probably damaging	Het
Itgad	A	G	7: 128,198,121 (GRCm38)	Y846C	probably benign	Het
Kcnj1	A	G	9: 32,396,492 (GRCm38)	T51A	probably damaging	Het
Kif1bp	A	G	10: 62,559,408 (GRCm38)	V485A	probably damaging	Het
Kif9	A	T	9: 110,510,438 (GRCm38)	K449N	possibly damaging	Het
Klk11	G	A	7: 43,778,909 (GRCm38)	W241*	probably null	Het
Krt32	T	C	11: 100,084,110 (GRCm38)		probably null	Het
Loxl1	A	G	9: 58,293,640 (GRCm38)	F513S	probably damaging	Het
Mapk8ip3	A	T	17: 24,904,923 (GRCm38)	S571T	probably damaging	Het
Mcam	C	T	9: 44,141,291 (GRCm38)	R606C	probably damaging	Het
Mtss1	T	C	15: 58,951,672 (GRCm38)	N282S	probably damaging	Het
Myh13	T	A	11: 67,353,674 (GRCm38)	D1012E	probably benign	Het
Myo16	A	G	8: 10,502,817 (GRCm38)	T952A	probably benign	Het
Neb	T	C	2: 52,298,620 (GRCm38)	D874G	probably damaging	Het
Nek11	A	G	9: 105,163,204 (GRCm38)	Y553H	probably damaging	Het
Nr2c2	T	A	6: 92,105,331 (GRCm38)	V9D	probably benign	Het
Nxf1	T	A	19: 8,762,436 (GRCm38)	F51L	probably benign	Het
Olfr1260	T	C	2: 89,978,528 (GRCm38)	V250A	probably damaging	Het
Olfr1347	T	C	7: 6,488,179 (GRCm38)	I232V	probably damaging	Het
Olfr1350	A	G	7: 6,570,471 (GRCm38)	N160S	probably damaging	Het
Olfr170	A	G	16: 19,606,312 (GRCm38)	S119P	probably benign	Het
Olfr344	A	T	2: 36,568,873 (GRCm38)	I92F	probably damaging	Het
Olfr397	T	G	11: 73,964,568 (GRCm38)		probably null	Het
Olfr750	A	G	14: 51,070,734 (GRCm38)	S220P	probably damaging	Het
Pcdhb8	A	T	18: 37,356,519 (GRCm38)	N76Y	probably damaging	Het
Pdzrn4	T	A	15: 92,399,804 (GRCm38)	F217I	probably damaging	Het
Ppp1r16a	T	A	15: 76,694,399 (GRCm38)	H434Q	probably benign	Het
Prpf19	T	A	19: 10,901,022 (GRCm38)	F291I	possibly damaging	Het
R3hdm2	G	T	10: 127,471,826 (GRCm38)	E319*	probably null	Het
Sel1l3	A	G	5: 53,137,929 (GRCm38)	Y777H	probably damaging	Het
Serpinb5	G	A	1: 106,870,289 (GRCm38)	A3T	possibly damaging	Het
Skp2	C	A	15: 9,127,911 (GRCm38)	V88F	probably damaging	Het
Slc25a16	T	C	10: 62,928,376 (GRCm38)	Y71H	probably damaging	Het
Slc6a6	T	A	6: 91,740,992 (GRCm38)	I304N	probably damaging	Het
Sned1	G	A	1: 93,281,654 (GRCm38)	V830M	possibly damaging	Het
Sox17	C	A	1: 4,491,928 (GRCm38)	G222C	probably damaging	Het
Vdac2	A	G	14: 21,837,877 (GRCm38)	E96G	probably damaging	Het
Wdhd1	A	T	14: 47,247,400 (GRCm38)	D885E	probably benign	Het
Zfp646	A	G	7: 127,880,136 (GRCm38)	N495S	probably damaging	Het
Zfp663	T	C	2: 165,352,653 (GRCm38)	T549A	probably damaging	Het
Zfp935	G	A	13: 62,455,137 (GRCm38)	A83V	possibly damaging	Het

Other mutations in Trmu

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00785:Trmu	APN	15	85,882,831 (GRCm38)	missense	probably benign	0.00
IGL02873:Trmu	APN	15	85,896,832 (GRCm38)	splice site	probably null
IGL03375:Trmu	APN	15	85,894,937 (GRCm38)	missense	possibly damaging	0.65
R0592:Trmu	UTSW	15	85,896,826 (GRCm38)	unclassified	probably benign
R0781:Trmu	UTSW	15	85,879,403 (GRCm38)	nonsense	probably null
R1120:Trmu	UTSW	15	85,890,285 (GRCm38)	missense	possibly damaging	0.75
R1165:Trmu	UTSW	15	85,892,674 (GRCm38)	missense	probably damaging	0.99
R1443:Trmu	UTSW	15	85,897,101 (GRCm38)	splice site	probably null
R4626:Trmu	UTSW	15	85,894,985 (GRCm38)	missense	possibly damaging	0.96
R4790:Trmu	UTSW	15	85,882,805 (GRCm38)	missense	probably damaging	1.00
R5134:Trmu	UTSW	15	85,896,355 (GRCm38)	splice site	probably null
R5399:Trmu	UTSW	15	85,896,408 (GRCm38)	splice site	probably null
R5639:Trmu	UTSW	15	85,882,698 (GRCm38)	missense	probably damaging	1.00
R6831:Trmu	UTSW	15	85,895,006 (GRCm38)	missense	probably benign
R8093:Trmu	UTSW	15	85,882,720 (GRCm38)	missense	probably benign	0.08
R8276:Trmu	UTSW	15	85,882,731 (GRCm38)	missense	possibly damaging	0.88
R9163:Trmu	UTSW	15	85,896,895 (GRCm38)	missense	probably benign	0.00
RF007:Trmu	UTSW	15	85,892,569 (GRCm38)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- CCATAACCTCCCCATTTGTGAGAGC -3'
(R):5'- TGAGACGCCTTAGCAAGTTGCC -3'

Sequencing Primer
(F):5'- CATTTGTGAGAGCTGAGATGCAC -3'
(R):5'- TAGCAAGTTGCCCACTCTGAG -3'

Posted On

2014-04-13