Mutagenetix > Incidental Mutation

Incidental Mutation 'R2979:Trmt1'

257041

Institutional Source

Beutler Lab

Gene Symbol

Trmt1

Ensembl Gene

ENSMUSG00000001909

Gene Name

tRNA methyltransferase 1

Synonyms

6720406L13Rik, D8Ertd812e

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.686) question?

Stock #

R2979 (G1)

Quality Score

218

Status

Not validated

Chromosome

Chromosomal Location

85412953-85426437 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 85423511 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 301 (Y301C)

Ref Sequence

ENSEMBL: ENSMUSP00000105390 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001974] [ENSMUST00000037165] [ENSMUST00000109767] [ENSMUST00000109768] [ENSMUST00000125370] [ENSMUST00000175784] [ENSMUST00000131700] [ENSMUST00000143427] [ENSMUST00000152301] [ENSMUST00000177084] [ENSMUST00000177423]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000001974
AA Change: Y308C

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

SMART Domains

Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
AA Change: Y308C

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

probably benign
Transcript: ENSMUST00000037165

SMART Domains

Protein: ENSMUSP00000046010
Gene: ENSMUSG00000034041

Domain	Start	End	E-Value	Type
low complexity region	23	39	N/A	INTRINSIC
HLH	155	207	3.97e-18	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000077990

Predicted Effect

probably damaging
Transcript: ENSMUST00000109767
AA Change: Y308C

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

SMART Domains

Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
AA Change: Y308C

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

probably damaging
Transcript: ENSMUST00000109768
AA Change: Y301C

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

SMART Domains

Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: Y301C

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 damaging
Transcript: ENSMUST00000125370
AA Change: Y308C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
AA Change: Y308C

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: ENSMUST00000128022

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138300

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137953

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177260

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148118

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148644

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175767

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175704

Predicted Effect

probably benign
Transcript: ENSMUST00000175784

SMART Domains

Protein: ENSMUSP00000135273
Gene: ENSMUSG00000001909

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

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: ENSMUST00000152301

SMART Domains

Protein: ENSMUSP00000116712
Gene: ENSMUSG00000001909

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 benign
Transcript: ENSMUST00000177084

SMART Domains

Protein: ENSMUSP00000135675
Gene: ENSMUSG00000001909

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

probably benign
Transcript: ENSMUST00000175884

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

noncoding transcript
Transcript: ENSMUST00000177286

Predicted Effect

probably benign
Transcript: ENSMUST00000177423

SMART Domains

Protein: ENSMUSP00000135327
Gene: ENSMUSG00000001909

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

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 19 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Afm	A	G	5: 90,670,022 (GRCm39)	I48V	probably benign	Het
Arhgef1	A	G	7: 24,607,176 (GRCm39)	E16G	unknown	Het
Cps1	T	C	1: 67,243,863 (GRCm39)		probably null	Het
Dnah9	T	C	11: 66,008,414 (GRCm39)	K804E	possibly damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Gm18025	G	T	12: 34,340,970 (GRCm39)	P41Q	probably damaging	Het
Kdm4c	A	T	4: 74,291,965 (GRCm39)	R861*	probably null	Het
Klhl2	C	T	8: 65,275,730 (GRCm39)	V58I	probably damaging	Het
Msl1	G	A	11: 98,691,050 (GRCm39)	G178E	possibly damaging	Het
Nacad	T	A	11: 6,551,424 (GRCm39)	Q589L	probably benign	Het
Pros1	A	G	16: 62,734,229 (GRCm39)	D345G	probably damaging	Het
Sh3tc2	A	G	18: 62,122,556 (GRCm39)	Y439C	probably damaging	Het
Smarcad1	T	A	6: 65,051,995 (GRCm39)	M376K	probably benign	Het
Srd5a1	T	C	13: 69,748,418 (GRCm39)	Q127R	probably damaging	Het
Synm	T	G	7: 67,386,008 (GRCm39)	R551S	probably damaging	Het
Ttc23l	G	A	15: 10,537,652 (GRCm39)	S206L	probably benign	Het
Txnl1	T	C	18: 63,804,691 (GRCm39)	T268A	probably benign	Het
Zbbx	C	A	3: 74,985,793 (GRCm39)	E420*	probably null	Het
Zc3h7a	A	T	16: 10,976,837 (GRCm39)	V153E	probably 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
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
R5170:Trmt1	UTSW	8	85,421,861 (GRCm39)	missense	probably damaging	1.00
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'- AACTGACATGGCTCTGTAGATGG -3'
(R):5'- AGGAGAGATCATGAGTCCCTG -3'

Sequencing Primer
(F):5'- CATGGCTCTGTAGATGGAGAAACTG -3'
(R):5'- GATCATGAGTCCCTGATATGGTCAC -3'

Posted On

2015-01-11