Mutagenetix > Incidental Mutations

Incidental Mutation 'R5452:Trmt2a'

432601

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

042848-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5452 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

18248679-18254772 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 18250950 bp

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] [ENSMUST00000128045] [ENSMUST00000140206] [ENSMUST00000231509]

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

noncoding transcript
Transcript: ENSMUST00000123073

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127239

Predicted Effect

probably benign
Transcript: ENSMUST00000128045

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131211

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134035

Predicted Effect

possibly damaging
Transcript: ENSMUST00000140206
AA Change: H270R

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)

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: ENSMUST00000144536

Predicted Effect

unknown
Transcript: ENSMUST00000145112
AA Change: H84R

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: ENSMUST00000147273

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152033

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153292

Predicted Effect

probably benign
Transcript: ENSMUST00000231509

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232015

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232342

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.2%
20x: 95.1%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810474O19Rik	C	A	6: 149,329,113	S1219*	probably null	Het
Adam20	A	T	8: 40,795,764	I304F	probably damaging	Het
Adamts5	A	G	16: 85,869,912		probably null	Het
Akr1c6	A	G	13: 4,454,545	R132G	probably benign	Het
Ash1l	T	A	3: 88,984,876	M1354K	possibly damaging	Het
C6	T	C	15: 4,814,829	I911T	possibly damaging	Het
Calm2	T	C	17: 87,435,722		probably null	Het
Ccdc80	G	A	16: 45,118,165	R745Q	probably damaging	Het
Celsr3	T	C	9: 108,844,034	I2685T	possibly damaging	Het
Chkb	T	C	15: 89,429,585		probably benign	Het
Dennd5b	T	A	6: 149,041,513		probably null	Het
Dnah2	T	C	11: 69,524,383	Y175C	probably damaging	Het
Dnajc13	A	G	9: 104,192,114	S1154P	probably benign	Het
Ephb4	T	C	5: 137,361,142	S325P	probably damaging	Het
Fzd9	C	T	5: 135,250,860	R57H	probably damaging	Het
Gemin6	T	G	17: 80,227,749	V46G	probably damaging	Het
Gm9949	A	G	18: 62,180,516		probably benign	Het
Gnb4	A	T	3: 32,589,845	M188K	probably benign	Het
Hr	G	T	14: 70,556,627	G109V	probably damaging	Het
Lrp1b	A	G	2: 40,922,316	S2426P	probably damaging	Het
Map2k4	A	G	11: 65,719,587	W88R	probably damaging	Het
Map4	C	T	9: 110,037,783		probably benign	Het
Moxd2	C	T	6: 40,882,114		probably null	Het
Mrgprx1	T	C	7: 48,021,808	I64V	probably benign	Het
Olfr493	A	C	7: 108,346,105	I292S	probably damaging	Het
Padi2	T	C	4: 140,932,071	F229S	probably benign	Het
Pappa2	T	C	1: 158,838,602	N1136S	probably benign	Het
Pcdhb1	A	T	18: 37,265,758	N254I	possibly damaging	Het
Plcb2	A	G	2: 118,718,246	Y400H	probably damaging	Het
Plce1	A	C	19: 38,620,482	T412P	probably benign	Het
Prg4	T	C	1: 150,455,768		probably benign	Het
Prkdc	A	G	16: 15,768,637	N2510S	possibly damaging	Het
Psme4	T	A	11: 30,791,168	S107T	probably benign	Het
Rint1	G	T	5: 23,794,365	A51S	probably benign	Het
Rsad1	T	A	11: 94,543,689	R306S	probably damaging	Het
Sema3c	T	G	5: 17,717,070		probably null	Het
Sirt3	G	A	7: 140,865,015	T290I	probably damaging	Het
Skiv2l2	T	C	13: 112,913,181	S232G	probably null	Het
Spam1	G	A	6: 24,800,732	G490D	probably benign	Het
Speer4f2	C	T	5: 17,376,500	R147W	possibly damaging	Het
Sppl2c	A	T	11: 104,187,300	I309L	probably benign	Het
Srxn1	G	A	2: 152,105,879	V66M	probably damaging	Het
St3gal4	C	T	9: 35,053,456	R152H	probably damaging	Het
Sv2c	A	T	13: 95,978,083	F532I	probably damaging	Het
Tacc1	C	A	8: 25,164,415	K705N	probably null	Het
Tekt3	G	T	11: 63,094,793	S475I	probably damaging	Het
Tjap1	T	C	17: 46,260,175	T139A	probably damaging	Het
Tnfrsf8	T	A	4: 145,292,644	K207M	possibly damaging	Het
Tnn	T	C	1: 160,110,261	T965A	probably benign	Het
Tns2	C	T	15: 102,108,934	R281C	probably damaging	Het
Ttc21a	T	C	9: 119,950,971	L448P	probably benign	Het
Ttll4	C	A	1: 74,679,321	N110K	probably benign	Het
Ttn	T	A	2: 76,754,824	I22042F	probably damaging	Het
Ubr1	A	G	2: 120,868,302	Y1595H	possibly damaging	Het
Unc45a	G	A	7: 80,329,039	P621S	probably damaging	Het
Xrn2	A	T	2: 147,024,713		probably null	Het
Zcchc6	A	G	13: 59,800,657	Y215H	probably damaging	Het

Other mutations in Trmt2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Trmt2a	APN	16	18249487	missense	probably benign
R0050:Trmt2a	UTSW	16	18250843	missense	probably damaging	1.00
R0050:Trmt2a	UTSW	16	18250843	missense	probably damaging	1.00
R0377:Trmt2a	UTSW	16	18249703	missense	possibly damaging	0.68
R0699:Trmt2a	UTSW	16	18249529	missense	probably benign	0.01
R1034:Trmt2a	UTSW	16	18249709	missense	probably damaging	1.00
R1114:Trmt2a	UTSW	16	18250440	unclassified	probably benign
R1882:Trmt2a	UTSW	16	18249894	missense	possibly damaging	0.88
R1911:Trmt2a	UTSW	16	18251206	missense	probably benign	0.01
R2184:Trmt2a	UTSW	16	18252995	missense	probably benign	0.06
R3853:Trmt2a	UTSW	16	18251191	missense	possibly damaging	0.94
R4427:Trmt2a	UTSW	16	18249229	unclassified	probably benign
R4737:Trmt2a	UTSW	16	18251286	unclassified	probably benign
R4896:Trmt2a	UTSW	16	18252929	missense	probably damaging	0.99
R4903:Trmt2a	UTSW	16	18249554	nonsense	probably null
R4964:Trmt2a	UTSW	16	18249554	nonsense	probably null
R4966:Trmt2a	UTSW	16	18249554	nonsense	probably null
R5216:Trmt2a	UTSW	16	18252184	missense	probably benign	0.22
R5837:Trmt2a	UTSW	16	18249462	unclassified	probably benign
R6555:Trmt2a	UTSW	16	18253203	missense	probably benign	0.03
R6670:Trmt2a	UTSW	16	18250477	missense	possibly damaging	0.57
R7064:Trmt2a	UTSW	16	18253004	missense	probably damaging	0.99
R7718:Trmt2a	UTSW	16	18250623	missense	probably benign	0.16

Predicted Primers

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

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

Posted On

2016-10-06