Mutagenetix > Incidental Mutation

Incidental Mutation 'R4966:Trmt2a'

384049

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

042562-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4966 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

18066711-18072636 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 18067418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 30 (C30*)

Ref Sequence

ENSEMBL: ENSMUSP00000121216 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000009321] [ENSMUST00000052325] [ENSMUST00000100099] [ENSMUST00000115640] [ENSMUST00000115645] [ENSMUST00000140206] [ENSMUST00000231509] [ENSMUST00000128045]

AlphaFold

Q8BNV1

Predicted Effect

probably benign
Transcript: ENSMUST00000009321

SMART Domains

Protein: ENSMUSP00000009321
Gene: ENSMUSG00000022718

Domain	Start	End	E-Value	Type
low complexity region	165	176	N/A	INTRINSIC
WW	302	334	7.26e-6	SMART
low complexity region	411	421	N/A	INTRINSIC
DSRM	512	577	5.68e-10	SMART
DSRM	620	685	8.26e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000052325

SMART Domains

Protein: ENSMUSP00000055288
Gene: ENSMUSG00000005732

Domain	Start	End	E-Value	Type
RanBD	1	108	4.92e-46	SMART
coiled coil region	123	153	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000059696

Predicted Effect

probably null
Transcript: ENSMUST00000100099
AA Change: C30*

SMART Domains

Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: C30*

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	380	579	1.2e-20	PFAM
Pfam:PCMT	386	482	1.1e-8	PFAM
Pfam:MTS	389	489	6.2e-9	PFAM
Pfam:Methyltransf_4	397	497	4.2e-7	PFAM
Pfam:Methyltransf_31	420	546	6.2e-15	PFAM
Pfam:Methyltransf_18	422	523	9.3e-11	PFAM
Pfam:Methyltransf_26	423	538	5.3e-12	PFAM
Pfam:Methyltransf_25	426	511	3.5e-8	PFAM
Pfam:Methyltransf_11	427	487	5.6e-6	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000115640
AA Change: C30*

SMART Domains

Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: C30*

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	380	579	2.6e-20	PFAM
Pfam:PCMT	386	482	3.4e-9	PFAM
Pfam:MTS	392	489	1e-7	PFAM
Pfam:Cons_hypoth95	405	542	2.7e-7	PFAM
Pfam:Methyltransf_31	420	547	2.1e-15	PFAM
Pfam:Methyltransf_18	422	526	2.9e-12	PFAM
Pfam:Methyltransf_4	423	499	2.6e-7	PFAM
Pfam:Methyltransf_25	426	511	1.3e-8	PFAM
Pfam:Methyltransf_11	427	489	3.6e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115645

SMART Domains

Protein: ENSMUSP00000111309
Gene: ENSMUSG00000005732

Domain	Start	End	E-Value	Type
RanBD	27	158	3.33e-75	SMART
low complexity region	183	202	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123073

Predicted Effect

probably null
Transcript: ENSMUST00000140206
AA Change: C30*

SMART Domains

Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: C30*

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	383	481	3.7e-8	PFAM
Pfam:PCMT	386	481	1.5e-6	PFAM
Pfam:MTS	389	493	2.5e-7	PFAM
Pfam:Methyltransf_31	420	491	1.5e-9	PFAM
Pfam:Methyltransf_18	422	508	4.1e-8	PFAM
Pfam:Methyltransf_26	423	523	3.1e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153292

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147273

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127239

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131211

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134035

Predicted Effect

probably benign
Transcript: ENSMUST00000231509

Predicted Effect

probably benign
Transcript: ENSMUST00000145112

SMART Domains

Protein: ENSMUSP00000117026
Gene: ENSMUSG00000022721

Domain	Start	End	E-Value	Type
Pfam:PCMT	118	220	4.2e-7	PFAM
Pfam:tRNA_U5-meth_tr	118	280	4e-16	PFAM
Pfam:MTS	129	229	5.4e-6	PFAM
Pfam:Cons_hypoth95	143	277	6.5e-5	PFAM
Pfam:PrmA	146	234	2e-4	PFAM
Pfam:Ubie_methyltran	148	223	1e-4	PFAM
Pfam:Methyltransf_31	158	271	6.1e-14	PFAM
Pfam:Methyltransf_18	160	263	8.3e-11	PFAM
Pfam:Methyltransf_4	161	237	7.1e-5	PFAM
Pfam:Methyltransf_26	161	274	2e-6	PFAM
Pfam:Methyltransf_25	164	251	5.2e-7	PFAM
Pfam:Methyltransf_11	165	227	9.4e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232015

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Predicted Effect

probably benign
Transcript: ENSMUST00000128045

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232342

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.8%
20x: 90.6%

Validation Efficiency

96% (94/98)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833420G17Rik	T	C	13: 119,610,757 (GRCm39)		probably benign	Het
9030619P08Rik	T	A	15: 75,303,267 (GRCm39)		noncoding transcript	Het
Abcb5	T	A	12: 118,850,626 (GRCm39)		probably benign	Het
Acox3	A	G	5: 35,747,080 (GRCm39)	N166D	probably damaging	Het
Actn1	T	C	12: 80,219,904 (GRCm39)	I656V	probably benign	Het
Arhgef15	A	G	11: 68,838,143 (GRCm39)	V659A	probably benign	Het
AW551984	T	C	9: 39,508,472 (GRCm39)	E348G	possibly damaging	Het
Bbs2	A	T	8: 94,807,435 (GRCm39)	V453E	probably damaging	Het
Caskin1	A	T	17: 24,726,135 (GRCm39)	D1414V	probably damaging	Het
Ccdc57	A	T	11: 120,751,978 (GRCm39)	S868T	probably benign	Het
Cdc34b	A	T	11: 94,633,087 (GRCm39)	I96F	probably damaging	Het
Ctnnd1	A	G	2: 84,452,417 (GRCm39)	F69L	possibly damaging	Het
Cyld	A	G	8: 89,468,929 (GRCm39)	I567V	possibly damaging	Het
Dact3	G	C	7: 16,620,013 (GRCm39)	V503L	unknown	Het
Dlg1	C	T	16: 31,573,626 (GRCm39)	T9I	probably benign	Het
Dnase1	T	C	16: 3,855,771 (GRCm39)		probably benign	Het
Drc7	G	A	8: 95,798,224 (GRCm39)	E490K	probably benign	Het
Drd4	T	C	7: 140,873,690 (GRCm39)	M114T	probably damaging	Het
Exoc3l4	A	G	12: 111,395,155 (GRCm39)	H591R	probably benign	Het
Fgfr1	C	A	8: 26,062,461 (GRCm39)	Y665*	probably null	Het
G2e3	A	G	12: 51,418,413 (GRCm39)	I603V	probably benign	Het
Glp2r	G	T	11: 67,648,419 (GRCm39)	Y94*	probably null	Het
Gnat1	A	T	9: 107,554,433 (GRCm39)	M115K	probably benign	Het
Gpr45	A	G	1: 43,072,280 (GRCm39)	T308A	probably benign	Het
Grm1	T	A	10: 10,595,409 (GRCm39)	K740*	probably null	Het
Gtsf2	T	C	15: 103,352,755 (GRCm39)	E88G	possibly damaging	Het
Hsh2d	C	T	8: 72,947,372 (GRCm39)	A23V	probably benign	Het
Ino80c	T	C	18: 24,239,702 (GRCm39)	D153G	probably damaging	Het
Ints11	T	C	4: 155,971,385 (GRCm39)	F278L	probably damaging	Het
Ints6	A	G	14: 62,939,911 (GRCm39)	L593P	probably damaging	Het
Map4k1	A	T	7: 28,682,427 (GRCm39)	H16L	probably benign	Het
Mipep	G	T	14: 61,022,231 (GRCm39)	R32L	probably damaging	Het
Mon1a	A	G	9: 107,779,850 (GRCm39)	E473G	probably damaging	Het
Myf5	A	T	10: 107,321,733 (GRCm39)	C20*	probably null	Het
Myh11	T	C	16: 14,023,818 (GRCm39)	E1512G	probably damaging	Het
Myo5c	T	C	9: 75,176,878 (GRCm39)	S608P	probably benign	Het
Myo9a	A	G	9: 59,779,017 (GRCm39)	D1591G	probably benign	Het
Myof	T	A	19: 37,924,300 (GRCm39)	I1306F	probably damaging	Het
Nlgn1	C	T	3: 25,974,401 (GRCm39)	G165D	possibly damaging	Het
Noc2l	C	G	4: 156,330,368 (GRCm39)	D513E	probably damaging	Het
Nup205	G	A	6: 35,220,784 (GRCm39)	R1862H	probably benign	Het
Nup210l	A	G	3: 90,014,208 (GRCm39)	H65R	probably benign	Het
Or2y16	A	G	11: 49,334,945 (GRCm39)	D89G	possibly damaging	Het
Or9k7	A	T	10: 130,046,306 (GRCm39)	M231K	probably benign	Het
Pcmtd1	C	A	1: 7,231,233 (GRCm39)	Y176*	probably null	Het
Pde6h	C	T	6: 136,938,201 (GRCm39)	T58I	possibly damaging	Het
Pkd1	T	C	17: 24,805,042 (GRCm39)		probably null	Het
Polr1e	G	A	4: 45,029,429 (GRCm39)	A297T	probably damaging	Het
Rbm34	T	C	8: 127,678,087 (GRCm39)	D269G	possibly damaging	Het
Rdx	T	C	9: 51,986,309 (GRCm39)	V372A	probably benign	Het
Reep6	T	A	10: 80,169,633 (GRCm39)	F107Y	probably benign	Het
Rere	G	T	4: 150,698,273 (GRCm39)		probably benign	Het
Rmdn2	G	T	17: 79,974,304 (GRCm39)	A266S	probably damaging	Het
Rnf32	G	A	5: 29,403,576 (GRCm39)	R7H	probably benign	Het
Rnpepl1	A	T	1: 92,844,483 (GRCm39)	N325I	probably damaging	Het
Rps6ka5	T	A	12: 100,519,325 (GRCm39)	M763L	probably benign	Het
Ryr2	T	C	13: 11,729,497 (GRCm39)	E2375G	possibly damaging	Het
Ryr2	T	C	13: 11,848,878 (GRCm39)	T361A	probably benign	Het
Serpina3j	T	A	12: 104,286,043 (GRCm39)	C399*	probably null	Het
Serpinb9	T	A	13: 33,192,847 (GRCm39)	W135R	probably damaging	Het
Sim2	T	C	16: 93,924,280 (GRCm39)	V475A	probably benign	Het
Slc24a5	G	A	2: 124,910,188 (GRCm39)	V30I	probably benign	Het
Snrnp25	A	G	11: 32,157,595 (GRCm39)	K58E	probably damaging	Het
Stx1b	T	C	7: 127,407,093 (GRCm39)	I55V	probably damaging	Het
Tacc2	T	C	7: 130,330,507 (GRCm39)	S264P	probably damaging	Het
Tbc1d4	A	T	14: 101,695,610 (GRCm39)	Y943N	probably damaging	Het
Tlr5	T	C	1: 182,801,038 (GRCm39)	I114T	probably benign	Het
Tm2d3	A	G	7: 65,347,469 (GRCm39)	N101S	possibly damaging	Het
Tmem201	G	T	4: 149,803,144 (GRCm39)	Q575K	probably benign	Het
Tmem241	A	G	18: 12,237,176 (GRCm39)	S87P	probably damaging	Het
Trak2	G	A	1: 58,958,480 (GRCm39)	T267I	probably damaging	Het
Ttbk2	A	T	2: 120,603,758 (GRCm39)	F258L	possibly damaging	Het
Ttk	T	A	9: 83,747,201 (GRCm39)	I680N	probably benign	Het
Ttn	T	C	2: 76,785,380 (GRCm39)	D665G	probably damaging	Het
Tulp4	G	A	17: 6,249,088 (GRCm39)	E36K	probably damaging	Het
Unc93b1	T	C	19: 3,992,023 (GRCm39)		probably null	Het
Uroc1	T	C	6: 90,322,376 (GRCm39)	L300P	probably damaging	Het
Vmn2r67	A	T	7: 84,785,593 (GRCm39)	V804E	probably damaging	Het
Wdr81	T	A	11: 75,336,775 (GRCm39)	Q1538L	probably benign	Het
Zfp457	T	A	13: 67,441,342 (GRCm39)	H315L	probably damaging	Het
Zfp518a	T	A	19: 40,904,295 (GRCm39)	V1408D	possibly damaging	Het
Zfp52	T	G	17: 21,780,665 (GRCm39)	L171R	probably benign	Het
Zfp712	C	T	13: 67,188,676 (GRCm39)	C617Y	probably damaging	Het
Zfp770	T	C	2: 114,027,868 (GRCm39)	N67S	probably benign	Het
Zmat4	T	C	8: 24,392,085 (GRCm39)	S83P	probably damaging	Het

Other mutations in Trmt2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Trmt2a	APN	16	18,067,351 (GRCm39)	missense	probably benign
R0050:Trmt2a	UTSW	16	18,068,707 (GRCm39)	missense	probably damaging	1.00
R0050:Trmt2a	UTSW	16	18,068,707 (GRCm39)	missense	probably damaging	1.00
R0377:Trmt2a	UTSW	16	18,067,567 (GRCm39)	missense	possibly damaging	0.68
R0699:Trmt2a	UTSW	16	18,067,393 (GRCm39)	missense	probably benign	0.01
R1034:Trmt2a	UTSW	16	18,067,573 (GRCm39)	missense	probably damaging	1.00
R1114:Trmt2a	UTSW	16	18,068,304 (GRCm39)	unclassified	probably benign
R1882:Trmt2a	UTSW	16	18,067,758 (GRCm39)	missense	possibly damaging	0.88
R1911:Trmt2a	UTSW	16	18,069,070 (GRCm39)	missense	probably benign	0.01
R2184:Trmt2a	UTSW	16	18,070,859 (GRCm39)	missense	probably benign	0.06
R3853:Trmt2a	UTSW	16	18,069,055 (GRCm39)	missense	possibly damaging	0.94
R4427:Trmt2a	UTSW	16	18,067,093 (GRCm39)	unclassified	probably benign
R4737:Trmt2a	UTSW	16	18,069,150 (GRCm39)	unclassified	probably benign
R4896:Trmt2a	UTSW	16	18,070,793 (GRCm39)	missense	probably damaging	0.99
R4903:Trmt2a	UTSW	16	18,067,418 (GRCm39)	nonsense	probably null
R4964:Trmt2a	UTSW	16	18,067,418 (GRCm39)	nonsense	probably null
R5216:Trmt2a	UTSW	16	18,070,048 (GRCm39)	missense	probably benign	0.22
R5452:Trmt2a	UTSW	16	18,068,814 (GRCm39)	missense	probably damaging	1.00
R5837:Trmt2a	UTSW	16	18,067,326 (GRCm39)	unclassified	probably benign
R6555:Trmt2a	UTSW	16	18,071,067 (GRCm39)	missense	probably benign	0.03
R6670:Trmt2a	UTSW	16	18,068,341 (GRCm39)	missense	possibly damaging	0.57
R7064:Trmt2a	UTSW	16	18,070,868 (GRCm39)	missense	probably damaging	0.99
R7718:Trmt2a	UTSW	16	18,068,487 (GRCm39)	missense	probably benign	0.16
R8302:Trmt2a	UTSW	16	18,067,813 (GRCm39)	missense	probably damaging	1.00
R8463:Trmt2a	UTSW	16	18,069,039 (GRCm39)	missense	probably damaging	1.00
R9120:Trmt2a	UTSW	16	18,067,722 (GRCm39)	missense	probably damaging	1.00
R9186:Trmt2a	UTSW	16	18,069,033 (GRCm39)	missense	probably benign	0.00
R9487:Trmt2a	UTSW	16	18,068,814 (GRCm39)	missense	probably damaging	1.00
R9710:Trmt2a	UTSW	16	18,070,041 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AAAAGAACGGGTTTCTCCAGGG -3'
(R):5'- CATGGTGGCTGTCCAAAGAG -3'

Sequencing Primer
(F):5'- TCCAGGGCTTCGTGGAG -3'
(R):5'- TTTTGTGGGACTGTAGACCAAAACG -3'

Posted On

2016-04-27