Mutagenetix > Incidental Mutation

Incidental Mutation 'R9487:Trmt2a'

716706

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9487 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

18066711-18072636 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 18068814 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 270 (H270R)

Ref Sequence

ENSEMBL: ENSMUSP00000111303 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000009321] [ENSMUST00000052325] [ENSMUST00000100099] [ENSMUST00000115633] [ENSMUST00000115640] [ENSMUST00000115645] [ENSMUST00000140206] [ENSMUST00000128045] [ENSMUST00000231509]

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 damaging
Transcript: ENSMUST00000100099
AA Change: H270R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: H270R

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

noncoding transcript
Transcript: ENSMUST00000115633

SMART Domains

Protein: ENSMUSP00000111296
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 damaging
Transcript: ENSMUST00000115640
AA Change: H270R

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: H270R

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

SMART Domains

Protein: ENSMUSP00000117026
Gene: ENSMUSG00000022721
AA Change: H84R

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

noncoding transcript
Transcript: ENSMUST00000127239

Predicted Effect

SMART Domains

Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: H270R

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: ENSMUST00000147273

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153292

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152033

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131211

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134035

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123073

Predicted Effect

probably benign
Transcript: ENSMUST00000128045

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232015

Predicted Effect

probably benign
Transcript: ENSMUST00000231509

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232342

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019A02Rik	C	T	1: 53,221,665 (GRCm39)	D55N	possibly damaging	Het
Abcc2	G	A	19: 43,806,471 (GRCm39)	G762S	probably damaging	Het
Acta2	C	A	19: 34,225,865 (GRCm39)	A110S	probably damaging	Het
Adam26a	T	C	8: 44,022,456 (GRCm39)	T345A	possibly damaging	Het
Anapc11	T	C	11: 120,496,250 (GRCm39)	*85R	probably null	Het
Ang2	A	C	14: 51,433,071 (GRCm39)	C104G	probably damaging	Het
Ankzf1	G	A	1: 75,174,596 (GRCm39)	V529I	probably benign	Het
Aox4	G	T	1: 58,288,097 (GRCm39)	V737F	probably benign	Het
Aqr	T	C	2: 113,934,528 (GRCm39)	N1371S	probably benign	Het
Bach1	T	A	16: 87,526,733 (GRCm39)	S732T	probably benign	Het
Bcr	T	A	10: 74,967,431 (GRCm39)	I555N	probably damaging	Het
Bicra	T	C	7: 15,705,717 (GRCm39)	T1575A	probably damaging	Het
Bop1	A	G	15: 76,338,076 (GRCm39)	L598P	probably damaging	Het
Cacna1d	A	T	14: 29,845,419 (GRCm39)	F605L	possibly damaging	Het
Capn15	C	T	17: 26,184,353 (GRCm39)	V109I	possibly damaging	Het
Cdkn1b	T	C	6: 134,897,815 (GRCm39)		probably benign	Het
Dnah2	T	C	11: 69,406,617 (GRCm39)	T542A	possibly damaging	Het
Dsc2	A	T	18: 20,180,276 (GRCm39)	I159N	probably damaging	Het
Ecel1	A	T	1: 87,075,716 (GRCm39)	V774E	probably damaging	Het
Eif5b	T	G	1: 38,084,560 (GRCm39)	C849W	probably damaging	Het
Eif5b	T	A	1: 38,058,451 (GRCm39)	L251*	probably null	Het
Ext2	T	C	2: 93,592,956 (GRCm39)	D416G	probably damaging	Het
Fancm	G	A	12: 65,153,388 (GRCm39)	W1281*	probably null	Het
Flvcr1	A	T	1: 190,743,829 (GRCm39)	I409K	possibly damaging	Het
Foxk1	T	C	5: 142,437,389 (GRCm39)		probably null	Het
Frem2	T	A	3: 53,560,905 (GRCm39)	I1201F	possibly damaging	Het
Gabra5	A	G	7: 57,157,873 (GRCm39)		probably benign	Het
Gmpr2	G	A	14: 55,915,778 (GRCm39)	V319I	probably damaging	Het
Gna12	A	T	5: 140,746,338 (GRCm39)	L369Q	probably damaging	Het
Gpr160	A	G	3: 30,950,914 (GRCm39)	R329G	probably benign	Het
H2-M10.3	T	C	17: 36,677,423 (GRCm39)	H285R	probably benign	Het
H2-M2	A	T	17: 37,793,424 (GRCm39)	V194E	probably benign	Het
Hephl1	G	A	9: 14,995,830 (GRCm39)	R431W	possibly damaging	Het
Hr	A	G	14: 70,793,877 (GRCm39)	T46A	probably benign	Het
Hr	A	G	14: 70,794,205 (GRCm39)	H126R	possibly damaging	Het
Hsf1	T	G	15: 76,382,398 (GRCm39)	D256E	probably benign	Het
Ifi208	C	T	1: 173,510,961 (GRCm39)	T372I	probably damaging	Het
Ifi47	T	G	11: 48,986,620 (GRCm39)	F129C	probably damaging	Het
Il1rl2	CTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATT	CTTTATTTTATTTTATTTTATTTTATTTTATTTTATT	1: 40,366,470 (GRCm39)		probably benign	Het
Irag2	A	G	6: 145,120,257 (GRCm39)	I491V	probably benign	Het
Itga11	A	T	9: 62,670,171 (GRCm39)	N765I	probably benign	Het
Klhl22	T	A	16: 17,589,663 (GRCm39)	I108K	probably benign	Het
Lancl1	T	G	1: 67,073,381 (GRCm39)	H34P	probably benign	Het
Lcor	C	A	19: 41,573,685 (GRCm39)	N813K	probably damaging	Het
Mbd3l1	G	A	9: 18,396,274 (GRCm39)	G133D	probably benign	Het
Med12l	T	C	3: 59,155,353 (GRCm39)	F1178L	probably benign	Het
Mrm1	A	T	11: 84,705,531 (GRCm39)	N289K	probably damaging	Het
Myf6	A	G	10: 107,330,073 (GRCm39)	Y165H	probably benign	Het
Myo1g	C	A	11: 6,456,913 (GRCm39)	C971F	probably benign	Het
Myo3a	T	C	2: 22,245,862 (GRCm39)	M3T	probably benign	Het
Nsrp1	G	A	11: 76,937,114 (GRCm39)	R361*	probably null	Het
Or10d4	A	C	9: 39,580,611 (GRCm39)	Q86P	possibly damaging	Het
Or10h1b	C	A	17: 33,395,548 (GRCm39)	H57Q	possibly damaging	Het
Or4a69	T	C	2: 89,312,756 (GRCm39)	H241R	probably damaging	Het
Or4a77	T	C	2: 89,487,731 (GRCm39)	D18G	probably damaging	Het
Or5p6	A	T	7: 107,631,163 (GRCm39)	I129N	possibly damaging	Het
Or8b41	G	A	9: 38,054,866 (GRCm39)	C140Y	probably benign	Het
Or8k53	T	A	2: 86,177,846 (GRCm39)	D88V	probably benign	Het
Oscar	T	G	7: 3,614,663 (GRCm39)	Y103S	probably damaging	Het
Pdpr	A	G	8: 111,852,925 (GRCm39)	N610S	probably benign	Het
Ppp4r3b	T	C	11: 29,124,697 (GRCm39)	I56T	probably damaging	Het
Pxdn	T	A	12: 30,044,552 (GRCm39)	V510D	possibly damaging	Het
Rab11fip5	T	C	6: 85,324,913 (GRCm39)	S465G	possibly damaging	Het
Rasgrf2	T	C	13: 92,267,759 (GRCm39)	T82A	probably benign	Het
Scmh1	G	A	4: 120,320,284 (GRCm39)	W30*	probably null	Het
Sema4g	T	C	19: 44,981,071 (GRCm39)	Y40H	probably benign	Het
Serpinf2	A	T	11: 75,323,494 (GRCm39)	M404K	probably damaging	Het
Sgk3	T	C	1: 9,950,616 (GRCm39)		probably null	Het
Slc16a5	A	T	11: 115,360,738 (GRCm39)	Y307F	possibly damaging	Het
Slc39a5	G	A	10: 128,233,628 (GRCm39)	L290F	probably damaging	Het
Snx32	A	C	19: 5,547,736 (GRCm39)	D191E	probably damaging	Het
Sp4	T	C	12: 118,262,859 (GRCm39)	I396V	probably benign	Het
Srrd	A	G	5: 112,490,765 (GRCm39)	V42A	unknown	Het
Stim1	A	G	7: 102,080,257 (GRCm39)	H547R	unknown	Het
Svep1	G	A	4: 58,070,517 (GRCm39)	A2423V	probably benign	Het
Tep1	A	G	14: 51,066,687 (GRCm39)	S2304P	possibly damaging	Het
Tkt	C	G	14: 30,281,795 (GRCm39)	S104R	probably benign	Het
Tkt	T	C	14: 30,281,796 (GRCm39)	S105P	probably damaging	Het
Tln1	A	T	4: 43,542,893 (GRCm39)	N1365K	probably damaging	Het
Topaz1	G	T	9: 122,604,707 (GRCm39)	A1104S	probably benign	Het
Ttll10	G	T	4: 156,127,616 (GRCm39)	T389K	probably benign	Het
Tubal3	A	G	13: 3,980,674 (GRCm39)	I129V	probably benign	Het
Ucp3	A	G	7: 100,131,123 (GRCm39)	E192G	probably damaging	Het
Usp47	A	G	7: 111,677,063 (GRCm39)	D448G	probably damaging	Het
Vmn2r98	T	A	17: 19,301,496 (GRCm39)	L833M	possibly damaging	Het
Vps13d	A	G	4: 144,807,869 (GRCm39)		probably null	Het
Wdr7	A	G	18: 63,910,939 (GRCm39)	D777G	possibly damaging	Het
Zcchc8	A	G	5: 123,847,300 (GRCm39)	I213T	probably damaging	Het
Zfp281	T	C	1: 136,555,143 (GRCm39)	I707T	probably damaging	Het
Zfp335	T	C	2: 164,735,395 (GRCm39)	H1158R	probably damaging	Het
Zfp692	C	T	11: 58,199,765 (GRCm39)	T118M	probably damaging	Het
Zfr2	T	A	10: 81,075,969 (GRCm39)	L192Q	probably benign	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
R4966: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
R9710:Trmt2a	UTSW	16	18,070,041 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGGGTAATCAAGGTTGAGATCTGAC -3'
(R):5'- TGCCGAGTATGGTGTGGAAC -3'

Sequencing Primer
(F):5'- GGTTGAGATCTGACTCTTTACTACAC -3'
(R):5'- CAAATATACTCAGTGTGTGCCC -3'

Posted On

2022-07-18