Mutagenetix > Incidental Mutation

Incidental Mutation 'R0781:Trmu'

216105

Institutional Source

Beutler Lab

Gene Symbol

Trmu

Ensembl Gene

ENSMUSG00000022386

Gene Name

tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase

Synonyms

1600025P05Rik, Mtu1, 1110005N20Rik, Trmt1

MMRRC Submission

038961-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.146) question?

Stock #

R0781 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

85763513-85781595 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to A at 85763604 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 9 (C9*)

Ref Sequence

ENSEMBL: ENSMUSP00000125704 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023019] [ENSMUST00000162491] [ENSMUST00000170629] [ENSMUST00000231074]

AlphaFold

Q9DAT5

Predicted Effect

probably null
Transcript: ENSMUST00000023019
AA Change: C9*

SMART Domains

Protein: ENSMUSP00000023019
Gene: ENSMUSG00000022386
AA Change: C9*

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: ENSMUST00000160733

SMART Domains

Protein: ENSMUSP00000125331
Gene: ENSMUSG00000022386

Domain	Start	End	E-Value	Type
Pfam:tRNA_Me_trans	4	34	8.2e-9	PFAM
Pfam:tRNA_Me_trans	41	104	5.6e-21	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000162491
AA Change: C9*

SMART Domains

Protein: ENSMUSP00000125704
Gene: ENSMUSG00000022386
AA Change: C9*

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: ENSMUST00000170629

SMART Domains

Protein: ENSMUSP00000128759
Gene: ENSMUSG00000022385

Domain	Start	End	E-Value	Type
Pfam:GTSE1_N	10	153	3e-62	PFAM
low complexity region	284	301	N/A	INTRINSIC
low complexity region	310	321	N/A	INTRINSIC
low complexity region	360	372	N/A	INTRINSIC
low complexity region	478	497	N/A	INTRINSIC
low complexity region	568	593	N/A	INTRINSIC
low complexity region	644	653	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229871

Predicted Effect

probably benign
Transcript: ENSMUST00000231074

Meta Mutation Damage Score

0.9591

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.0%
20x: 93.2%

Validation Efficiency

97% (67/69)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921513D11Rik	G	T	17: 79,935,180 (GRCm39)	A98S	probably benign	Het
Acp2	A	G	2: 91,038,767 (GRCm39)		probably null	Het
Akap13	T	G	7: 75,261,125 (GRCm39)	S447A	possibly damaging	Het
Alk	G	A	17: 72,291,740 (GRCm39)		probably benign	Het
Ankrd55	A	G	13: 112,517,767 (GRCm39)		probably benign	Het
Arhgef39	T	C	4: 43,496,834 (GRCm39)	T327A	probably benign	Het
Calhm5	T	G	10: 33,972,013 (GRCm39)	I141L	probably benign	Het
Cdan1	G	A	2: 120,551,083 (GRCm39)	A1103V	probably damaging	Het
Cdk17	T	A	10: 93,074,895 (GRCm39)	Y3*	probably null	Het
Cdon	T	C	9: 35,367,733 (GRCm39)		probably benign	Het
Cntn3	T	A	6: 102,222,119 (GRCm39)	N460I	probably benign	Het
Cntrl	T	A	2: 35,050,639 (GRCm39)	C985S	possibly damaging	Het
Col6a2	T	C	10: 76,443,574 (GRCm39)	E497G	probably benign	Het
Crybg1	A	G	10: 43,875,089 (GRCm39)	M673T	possibly damaging	Het
Csmd1	A	C	8: 15,971,174 (GRCm39)	I3047S	probably benign	Het
Cyp2u1	A	G	3: 131,087,258 (GRCm39)	I441T	possibly damaging	Het
Disp2	T	C	2: 118,620,920 (GRCm39)	S551P	probably damaging	Het
Dstyk	A	G	1: 132,381,063 (GRCm39)		probably benign	Het
Frem1	T	C	4: 82,868,557 (GRCm39)	S1457G	probably damaging	Het
Gabbr2	C	T	4: 46,718,838 (GRCm39)	C613Y	probably damaging	Het
Gdf7	C	A	12: 8,351,555 (GRCm39)		probably benign	Het
Hnrnpul2	A	G	19: 8,804,110 (GRCm39)	R570G	probably damaging	Het
Ift70a1	A	T	2: 75,810,320 (GRCm39)	C588S	probably damaging	Het
Iqcf4	T	C	9: 106,445,860 (GRCm39)	I96V	probably benign	Het
Iqck	G	A	7: 118,498,880 (GRCm39)	D173N	possibly damaging	Het
Itpr3	C	T	17: 27,329,529 (GRCm39)	H1518Y	probably benign	Het
Kdm5d	T	A	Y: 910,539 (GRCm39)	L250H	probably damaging	Het
Kntc1	C	T	5: 123,937,965 (GRCm39)		probably benign	Het
Lmtk3	T	A	7: 45,444,427 (GRCm39)		probably benign	Het
Lpin3	A	G	2: 160,735,999 (GRCm39)	D93G	probably benign	Het
Ncoa6	A	T	2: 155,253,440 (GRCm39)		probably benign	Het
Nudt7	G	A	8: 114,862,111 (GRCm39)		probably benign	Het
Nup160	A	G	2: 90,563,563 (GRCm39)		probably benign	Het
Oit3	G	A	10: 59,264,016 (GRCm39)	R373C	probably damaging	Het
Olfml2a	A	T	2: 38,849,765 (GRCm39)	I494L	probably damaging	Het
Opa3	A	G	7: 18,962,524 (GRCm39)		probably benign	Het
Or51e2	A	G	7: 102,392,214 (GRCm39)		probably benign	Het
Or5ac15	A	T	16: 58,940,187 (GRCm39)	V82D	probably damaging	Het
Or9r7	A	G	10: 129,962,522 (GRCm39)	Y135H	probably damaging	Het
Pak3	TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC	TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC	X: 142,526,889 (GRCm39)		probably benign	Het
Parp6	G	T	9: 59,556,847 (GRCm39)	C584F	probably damaging	Het
Pcgf2	A	G	11: 97,582,676 (GRCm39)		probably benign	Het
Pde3a	T	C	6: 141,405,042 (GRCm39)		probably benign	Het
Pitrm1	A	G	13: 6,608,280 (GRCm39)	D335G	probably benign	Het
Pkhd1	A	T	1: 20,187,708 (GRCm39)	N3533K	probably benign	Het
Pkp4	T	C	2: 59,169,109 (GRCm39)	L752P	probably damaging	Het
Plcb3	C	A	19: 6,939,281 (GRCm39)	E566*	probably null	Het
Ppef2	T	C	5: 92,392,689 (GRCm39)	K261R	probably benign	Het
Prdm14	A	G	1: 13,184,585 (GRCm39)	S529P	probably damaging	Het
Prune2	T	C	19: 17,102,586 (GRCm39)	S2582P	probably benign	Het
Sardh	G	A	2: 27,081,931 (GRCm39)	T865I	possibly damaging	Het
Slc26a3	A	T	12: 31,515,812 (GRCm39)	I571F	possibly damaging	Het
Slc5a5	A	T	8: 71,342,864 (GRCm39)	M232K	probably benign	Het
Slc9a1	T	A	4: 133,097,859 (GRCm39)	M2K	probably benign	Het
Spata31e3	A	T	13: 50,402,296 (GRCm39)	D83E	possibly damaging	Het
Ss18l1	G	A	2: 179,697,647 (GRCm39)	S177N	possibly damaging	Het
Svs5	A	T	2: 164,175,507 (GRCm39)	I120L	probably benign	Het
Tcl1b1	G	T	12: 105,126,074 (GRCm39)	V19F	probably damaging	Het
Tmem108	C	T	9: 103,361,889 (GRCm39)	V566M	probably damaging	Het
Vnn1	A	T	10: 23,775,499 (GRCm39)	I250F	possibly damaging	Het
Vps13c	T	A	9: 67,879,285 (GRCm39)	Y3409N	probably damaging	Het
Xrn1	T	A	9: 95,873,322 (GRCm39)	N695K	probably benign	Het
Zfp84	T	A	7: 29,470,797 (GRCm39)	M1K	probably null	Het
Zfyve26	G	A	12: 79,326,841 (GRCm39)	R761C	probably damaging	Het
Zp3r	A	G	1: 130,505,621 (GRCm39)		probably null	Het

Other mutations in Trmu

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00785:Trmu	APN	15	85,767,032 (GRCm39)	missense	probably benign	0.00
IGL02873:Trmu	APN	15	85,781,033 (GRCm39)	splice site	probably null
IGL03375:Trmu	APN	15	85,779,138 (GRCm39)	missense	possibly damaging	0.65
R0592:Trmu	UTSW	15	85,781,027 (GRCm39)	unclassified	probably benign
R1120:Trmu	UTSW	15	85,774,486 (GRCm39)	missense	possibly damaging	0.75
R1165:Trmu	UTSW	15	85,776,875 (GRCm39)	missense	probably damaging	0.99
R1443:Trmu	UTSW	15	85,781,302 (GRCm39)	splice site	probably null
R1503:Trmu	UTSW	15	85,779,220 (GRCm39)	missense	possibly damaging	0.88
R4626:Trmu	UTSW	15	85,779,186 (GRCm39)	missense	possibly damaging	0.96
R4790:Trmu	UTSW	15	85,767,006 (GRCm39)	missense	probably damaging	1.00
R5134:Trmu	UTSW	15	85,780,556 (GRCm39)	splice site	probably null
R5399:Trmu	UTSW	15	85,780,609 (GRCm39)	splice site	probably null
R5639:Trmu	UTSW	15	85,766,899 (GRCm39)	missense	probably damaging	1.00
R6831:Trmu	UTSW	15	85,779,207 (GRCm39)	missense	probably benign
R8093:Trmu	UTSW	15	85,766,921 (GRCm39)	missense	probably benign	0.08
R8276:Trmu	UTSW	15	85,766,932 (GRCm39)	missense	possibly damaging	0.88
R9163:Trmu	UTSW	15	85,781,096 (GRCm39)	missense	probably benign	0.00
RF007:Trmu	UTSW	15	85,776,770 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- ACCAACTCATCGCTGGCCTATCTG -3'
(R):5'- TGTCATCCAACGAAGGAGAACACTG -3'

Sequencing Primer
(F):5'- TATCTGGGACATGCTGCCAC -3'
(R):5'- AGGAGAACACTGGAGTGATTTTGTC -3'

Posted On

2014-07-21