Mutagenetix > Incidental Mutation

Incidental Mutation 'R5170:Trmt1'

397508

Institutional Source

Beutler Lab

Gene Symbol

Trmt1

Ensembl Gene

ENSMUSG00000001909

Gene Name

tRNA methyltransferase 1

Synonyms

6720406L13Rik, D8Ertd812e

MMRRC Submission

042750-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.686) question?

Stock #

R5170 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

85412953-85426437 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 85421861 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 220 (Y220H)

Ref Sequence

ENSEMBL: ENSMUSP00000135273 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001974] [ENSMUST00000109767] [ENSMUST00000109768] [ENSMUST00000125370] [ENSMUST00000152301] [ENSMUST00000175784] [ENSMUST00000131700] [ENSMUST00000143427] [ENSMUST00000177084] [ENSMUST00000177423] [ENSMUST00000177531]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000001974
AA Change: Y217H

PolyPhen 2 Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
AA Change: Y217H

Domain	Start	End	E-Value	Type
Pfam:TRM	55	499	3.5e-151	PFAM
Pfam:Met_10	141	256	1.3e-8	PFAM
ZnF_C3H1	599	625	3.55e-6	SMART
low complexity region	648	661	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000077990

Predicted Effect

possibly damaging
Transcript: ENSMUST00000109767
AA Change: Y217H

PolyPhen 2 Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
AA Change: Y217H

Domain	Start	End	E-Value	Type
Pfam:TRM	55	499	4.9e-149	PFAM
Pfam:Met_10	142	256	3.4e-8	PFAM
ZnF_C3H1	599	625	3.55e-6	SMART
low complexity region	648	661	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000109768
AA Change: Y210H

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: Y210H

Domain	Start	End	E-Value	Type
Pfam:TRM	48	492	3.1e-149	PFAM
Pfam:Met_10	135	249	4.4e-8	PFAM
ZnF_C3H1	592	618	3.55e-6	SMART
low complexity region	641	654	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000125370
AA Change: Y217H

PolyPhen 2 Score 0.424 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
AA Change: Y217H

Domain	Start	End	E-Value	Type
Pfam:TRM	55	470	1.7e-140	PFAM
Pfam:Met_10	142	256	2.8e-8	PFAM
ZnF_C3H1	570	596	3.55e-6	SMART
low complexity region	619	632	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127915

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128022

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148118

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137953

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152301
AA Change: Y220H

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000116712
Gene: ENSMUSG00000001909
AA Change: Y220H

Domain	Start	End	E-Value	Type
Pfam:TRM	54	242	4.2e-49	PFAM
Pfam:Met_10	145	229	2.3e-7	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000175784
AA Change: Y220H

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

SMART Domains

Protein: ENSMUSP00000135273
Gene: ENSMUSG00000001909
AA Change: Y220H

Domain	Start	End	E-Value	Type
Pfam:TRM	54	221	8.6e-39	PFAM
Pfam:Met_10	144	221	5.3e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150085

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138300

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175870

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128537

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175704

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175767

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148644

Predicted Effect

probably benign
Transcript: ENSMUST00000131700

SMART Domains

Protein: ENSMUSP00000122526
Gene: ENSMUSG00000001909

Domain	Start	End	E-Value	Type
Pfam:TRM	54	108	3.9e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000143427

SMART Domains

Protein: ENSMUSP00000117140
Gene: ENSMUSG00000001909

Domain	Start	End	E-Value	Type
Pfam:TRM	47	98	3.2e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000136423

SMART Domains

Protein: ENSMUSP00000134723
Gene: ENSMUSG00000001909

Domain	Start	End	E-Value	Type
low complexity region	190	203	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000177084
AA Change: Y192H

PolyPhen 2 Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135675
Gene: ENSMUSG00000001909
AA Change: Y192H

Domain	Start	End	E-Value	Type
Pfam:TRM	29	260	4.1e-76	PFAM
Pfam:Met_10	117	231	4.1e-10	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000177423
AA Change: Y213H

PolyPhen 2 Score 0.919 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000135327
Gene: ENSMUSG00000001909
AA Change: Y213H

Domain	Start	End	E-Value	Type
Pfam:TRM	47	262	1.4e-66	PFAM
Pfam:Met_10	138	252	5.6e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177260

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175980

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176053

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177286

Predicted Effect

probably benign
Transcript: ENSMUST00000175884

Predicted Effect

probably benign
Transcript: ENSMUST00000177531

SMART Domains

Protein: ENSMUSP00000135540
Gene: ENSMUSG00000001909

Domain	Start	End	E-Value	Type
Pfam:TRM	54	174	1.8e-21	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox3	A	G	5: 35,745,969 (GRCm39)	I51V	probably benign	Het
Agbl2	A	G	2: 90,633,541 (GRCm39)	K559R	probably benign	Het
Arhgap30	A	G	1: 171,235,618 (GRCm39)	D664G	probably benign	Het
BC034090	A	G	1: 155,089,396 (GRCm39)	V798A	probably damaging	Het
Bdp1	A	T	13: 100,167,302 (GRCm39)	C2237*	probably null	Het
C3	C	T	17: 57,530,938 (GRCm39)	V388M	probably damaging	Het
Ccdc170	G	A	10: 4,464,200 (GRCm39)	E60K	probably damaging	Het
Cdh8	G	A	8: 100,006,182 (GRCm39)	T135M	probably damaging	Het
Cep131	G	T	11: 119,961,435 (GRCm39)	A572E	probably damaging	Het
Clec16a	A	G	16: 10,559,655 (GRCm39)	Y976C	probably benign	Het
Cplx3	G	A	9: 57,522,902 (GRCm39)	R153*	probably null	Het
Defa41	A	T	8: 21,691,696 (GRCm39)	D26V	probably damaging	Het
Dmpk	C	G	7: 18,821,944 (GRCm39)	L301V	probably benign	Het
Eno3	A	G	11: 70,553,040 (GRCm39)	I393V	probably benign	Het
Fbxo47	A	G	11: 97,748,520 (GRCm39)	V305A	probably benign	Het
Fry	G	A	5: 150,353,319 (GRCm39)	V1779M	probably benign	Het
Gtse1	T	C	15: 85,748,465 (GRCm39)		probably null	Het
Gucy2e	A	T	11: 69,126,396 (GRCm39)	L328Q	probably damaging	Het
Ifi207	T	C	1: 173,558,064 (GRCm39)	T225A	unknown	Het
Igkv4-80	A	C	6: 68,993,649 (GRCm39)	S81A	probably benign	Het
Lamc3	A	T	2: 31,777,356 (GRCm39)	M1L	probably benign	Het
Myo16	A	G	8: 10,619,745 (GRCm39)	D1432G	probably benign	Het
Nwd2	A	T	5: 63,963,380 (GRCm39)	N988I	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Parp14	T	C	16: 35,677,649 (GRCm39)	E773G	probably benign	Het
Psen1	T	A	12: 83,761,636 (GRCm39)	M146K	probably damaging	Het
Ptx4	G	A	17: 25,342,152 (GRCm39)	R209Q	probably benign	Het
Slc13a2	T	C	11: 78,291,634 (GRCm39)	T340A	probably damaging	Het
St8sia1	T	C	6: 142,909,434 (GRCm39)	K21E	probably damaging	Het
Stxbp1	T	C	2: 32,684,686 (GRCm39)	D581G	probably benign	Het
Sumo2	G	A	11: 115,425,486 (GRCm39)		probably benign	Het
Supt5	G	A	7: 28,015,508 (GRCm39)	P910S	probably benign	Het
Tbc1d30	T	C	10: 121,142,743 (GRCm39)	Q158R	possibly damaging	Het
Tenm2	T	A	11: 35,915,633 (GRCm39)	H1968L	probably damaging	Het
Trp73	C	T	4: 154,189,295 (GRCm39)	E60K	possibly damaging	Het
Ttn	A	G	2: 76,617,413 (GRCm39)	Y8026H	probably damaging	Het
Zar1l	A	G	5: 150,441,050 (GRCm39)		probably null	Het
Zfp740	T	C	15: 102,117,640 (GRCm39)	Y117H	probably damaging	Het
Zfp941	G	A	7: 140,392,870 (GRCm39)		probably benign	Het
Zp1	C	A	19: 10,897,918 (GRCm39)	V8F	possibly damaging	Het

Other mutations in Trmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00497:Trmt1	APN	8	85,422,138 (GRCm39)	missense	possibly damaging	0.92
IGL01959:Trmt1	APN	8	85,418,005 (GRCm39)	splice site	probably null
IGL02127:Trmt1	APN	8	85,424,100 (GRCm39)	missense	probably damaging	1.00
IGL02689:Trmt1	APN	8	85,426,385 (GRCm39)	unclassified	probably benign
IGL03087:Trmt1	APN	8	85,421,862 (GRCm39)	missense	probably damaging	1.00
IGL02835:Trmt1	UTSW	8	85,423,589 (GRCm39)	missense	probably null	1.00
PIT4418001:Trmt1	UTSW	8	85,424,299 (GRCm39)	missense	probably damaging	0.97
R0395:Trmt1	UTSW	8	85,423,741 (GRCm39)	splice site	probably null
R0964:Trmt1	UTSW	8	85,423,481 (GRCm39)	missense	probably damaging	1.00
R1881:Trmt1	UTSW	8	85,415,896 (GRCm39)	intron	probably benign
R2190:Trmt1	UTSW	8	85,416,470 (GRCm39)	nonsense	probably null
R2197:Trmt1	UTSW	8	85,417,487 (GRCm39)	missense	probably damaging	1.00
R2979:Trmt1	UTSW	8	85,423,511 (GRCm39)	missense	probably damaging	1.00
R3813:Trmt1	UTSW	8	85,421,846 (GRCm39)	unclassified	probably benign
R4407:Trmt1	UTSW	8	85,424,384 (GRCm39)	unclassified	probably benign
R4461:Trmt1	UTSW	8	85,425,778 (GRCm39)	missense	probably benign	0.01
R4588:Trmt1	UTSW	8	85,417,382 (GRCm39)	intron	probably benign
R6299:Trmt1	UTSW	8	85,423,919 (GRCm39)	nonsense	probably null
R6614:Trmt1	UTSW	8	85,415,962 (GRCm39)	missense	probably benign
R6666:Trmt1	UTSW	8	85,425,083 (GRCm39)	missense	probably damaging	1.00
R7669:Trmt1	UTSW	8	85,424,180 (GRCm39)	missense	probably benign	0.05
R7952:Trmt1	UTSW	8	85,415,969 (GRCm39)	missense	possibly damaging	0.50
R9784:Trmt1	UTSW	8	85,424,330 (GRCm39)	missense	probably damaging	0.98
Z1176:Trmt1	UTSW	8	85,425,827 (GRCm39)	missense	possibly damaging	0.95
Z1176:Trmt1	UTSW	8	85,424,869 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- CAAGAAATCAGTTAACAAGTGGCC -3'
(R):5'- ATGGACAGTGATGACCCTCC -3'

Sequencing Primer
(F):5'- GCTGGGGTTTAGCTCAGCATTAAAAC -3'
(R):5'- GTGATGACCCTCCAAACAACTCTG -3'

Posted On

2016-07-06