Mutagenetix > Incidental Mutation

Incidental Mutation 'R1911:Trmt2a'

210309

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

039929-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1911 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

18066711-18072636 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 18069070 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 304 (K304R)

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 benign
Transcript: ENSMUST00000100099
AA Change: K304R

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: K304R

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 benign
Transcript: ENSMUST00000115640
AA Change: K304R

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: K304R

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

probably benign
Transcript: ENSMUST00000140206
AA Change: K304R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: K304R

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: ENSMUST00000131211

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123073

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153292

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152033

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147273

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127239

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134035

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: ENSMUST00000128045

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232015

Predicted Effect

probably benign
Transcript: ENSMUST00000231509

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232342

Meta Mutation Damage Score

0.0857

Coding Region Coverage

1x: 97.3%
3x: 96.8%
10x: 95.4%
20x: 93.2%

Validation Efficiency

99% (99/100)

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	T	A	6: 91,927,050 (GRCm39)		probably benign	Het
Abca7	T	C	10: 79,842,468 (GRCm39)	V1134A	probably benign	Het
Acaa2	A	G	18: 74,925,483 (GRCm39)	E82G	probably benign	Het
Acap1	T	C	11: 69,772,548 (GRCm39)	D521G	probably damaging	Het
Adam19	T	C	11: 46,012,281 (GRCm39)	V259A	probably damaging	Het
Adss1	T	C	12: 112,599,443 (GRCm39)	V140A	probably benign	Het
Aif1	G	A	17: 35,391,127 (GRCm39)	P44L	probably benign	Het
Aldh3b1	T	G	19: 3,971,187 (GRCm39)	D159A	probably damaging	Het
Ank1	T	C	8: 23,589,666 (GRCm39)	V589A	probably damaging	Het
Ano2	G	A	6: 125,990,654 (GRCm39)	D803N	probably benign	Het
Arid1b	A	G	17: 5,393,241 (GRCm39)	E2257G	probably damaging	Het
Asb17	T	C	3: 153,550,138 (GRCm39)	Y57H	probably benign	Het
Asph	T	C	4: 9,453,335 (GRCm39)	E646G	probably damaging	Het
Aspm	T	A	1: 139,405,832 (GRCm39)	I1573K	probably benign	Het
Bcas1	C	A	2: 170,229,863 (GRCm39)	D236Y	probably damaging	Het
Bcas2	G	T	3: 103,079,113 (GRCm39)	G9*	probably null	Het
Btaf1	A	G	19: 36,964,030 (GRCm39)	Q867R	probably benign	Het
Calhm3	C	T	19: 47,143,908 (GRCm39)	V132I	possibly damaging	Het
Ccer1	A	T	10: 97,530,539 (GRCm39)	I401F	possibly damaging	Het
Cdcp3	T	C	7: 130,839,818 (GRCm39)	V580A	probably damaging	Het
Cecr2	T	A	6: 120,739,526 (GRCm39)		probably benign	Het
Cep104	G	A	4: 154,091,255 (GRCm39)	R925Q	possibly damaging	Het
Cep164	T	A	9: 45,682,104 (GRCm39)	M1900L	probably benign	Het
Crybg1	A	G	10: 43,873,673 (GRCm39)	V1145A	possibly damaging	Het
Cyp2a4	T	A	7: 26,008,399 (GRCm39)	N180K	possibly damaging	Het
Dennd4a	T	C	9: 64,796,368 (GRCm39)	L798P	probably damaging	Het
Dmxl1	T	C	18: 50,011,230 (GRCm39)	I1129T	probably benign	Het
Dnah2	T	C	11: 69,406,578 (GRCm39)	N555D	possibly damaging	Het
Dock1	T	A	7: 134,601,029 (GRCm39)	M988K	probably damaging	Het
Elp4	T	A	2: 105,533,088 (GRCm39)	H419L	probably damaging	Het
Endov	T	C	11: 119,393,177 (GRCm39)	V109A	possibly damaging	Het
Epha8	T	C	4: 136,663,625 (GRCm39)	Y477C	probably damaging	Het
Erlin1	A	G	19: 44,037,561 (GRCm39)	M188T	probably damaging	Het
Fhip1a	T	A	3: 85,568,525 (GRCm39)	D998V	probably benign	Het
Fhod3	A	T	18: 25,245,643 (GRCm39)	D1231V	possibly damaging	Het
Gimap3	T	A	6: 48,742,646 (GRCm39)	I95F	possibly damaging	Het
Gm10717	T	G	9: 3,026,317 (GRCm39)	F205C	probably damaging	Het
Grk1	C	A	8: 13,457,923 (GRCm39)	D274E	probably damaging	Het
Gsdmc2	G	A	15: 63,699,621 (GRCm39)	A269V	probably benign	Het
Krt33a	T	A	11: 99,903,175 (GRCm39)	Q289L	probably benign	Het
Krt76	T	A	15: 101,796,600 (GRCm39)	K403*	probably null	Het
Lcn4	T	C	2: 26,560,607 (GRCm39)		probably benign	Het
Mab21l1	T	C	3: 55,691,048 (GRCm39)	S212P	possibly damaging	Het
Mapk8ip3	A	C	17: 25,123,025 (GRCm39)	D610E	probably benign	Het
Mastl	G	T	2: 23,022,692 (GRCm39)	S677*	probably null	Het
Mfap3	T	C	11: 57,420,562 (GRCm39)	F181S	probably damaging	Het
Mlkl	T	C	8: 112,038,732 (GRCm39)		probably benign	Het
Mov10	G	A	3: 104,708,876 (GRCm39)		probably benign	Het
Muc5ac	T	C	7: 141,350,041 (GRCm39)	F595L	probably benign	Het
Nbas	T	A	12: 13,616,145 (GRCm39)	C2228S	probably benign	Het
Nit2	G	A	16: 56,982,046 (GRCm39)		probably benign	Het
Nod1	C	T	6: 54,921,425 (GRCm39)	V298M	probably damaging	Het
Or3a4	C	A	11: 73,945,210 (GRCm39)	R125L	probably damaging	Het
Or4c111	A	G	2: 88,843,565 (GRCm39)	L281P	probably damaging	Het
Or52b1	T	A	7: 104,978,590 (GRCm39)	I270F	probably benign	Het
Or6c210	A	T	10: 129,495,981 (GRCm39)	D102V	probably benign	Het
Or7g12	T	C	9: 18,900,196 (GRCm39)	L304P	probably damaging	Het
Osbpl5	C	A	7: 143,243,662 (GRCm39)	R864L	probably benign	Het
Pcnt	G	A	10: 76,204,650 (GRCm39)	T2585M	possibly damaging	Het
Pepd	C	T	7: 34,634,174 (GRCm39)		probably benign	Het
Pou6f2	T	C	13: 18,326,548 (GRCm39)	I341V	probably damaging	Het
Pramel32	T	C	4: 88,548,309 (GRCm39)	Q32R	possibly damaging	Het
Prune2	T	A	19: 17,091,038 (GRCm39)	F281I	probably benign	Het
Psg19	T	G	7: 18,528,193 (GRCm39)	Q183H	probably damaging	Het
Psme4	T	G	11: 30,765,658 (GRCm39)	S587A	probably benign	Het
Ptpro	T	C	6: 137,377,617 (GRCm39)		probably benign	Het
Pttg1ip2	C	A	5: 5,502,019 (GRCm39)	W144C	probably benign	Het
Rasgrp4	T	C	7: 28,838,302 (GRCm39)	V92A	probably damaging	Het
Rem1	G	A	2: 152,476,455 (GRCm39)	V238M	probably damaging	Het
Rexo5	C	T	7: 119,398,867 (GRCm39)	A68V	probably damaging	Het
Robo2	A	T	16: 73,755,213 (GRCm39)	N769K	probably damaging	Het
Sfrp5	C	T	19: 42,187,237 (GRCm39)	V278I	probably benign	Het
Sidt1	A	G	16: 44,102,234 (GRCm39)	S309P	possibly damaging	Het
Slc22a6	A	C	19: 8,599,246 (GRCm39)	Q292H	probably benign	Het
Slc4a3	G	A	1: 75,530,367 (GRCm39)	R690H	probably damaging	Het
Snx7	A	T	3: 117,623,317 (GRCm39)		probably null	Het
Spag6	T	A	2: 18,720,616 (GRCm39)	Y129*	probably null	Het
Srcap	T	C	7: 127,133,994 (GRCm39)	I905T	probably damaging	Het
St6gal1	T	G	16: 23,140,383 (GRCm39)	S185A	probably damaging	Het
Sult6b1	G	A	17: 79,196,393 (GRCm39)	H250Y	possibly damaging	Het
Tdrd6	T	G	17: 43,937,979 (GRCm39)	N1023T	probably benign	Het
Tecta	C	T	9: 42,249,232 (GRCm39)	E1877K	probably damaging	Het
Tex10	C	T	4: 48,456,800 (GRCm39)	R637Q	probably benign	Het
Tex14	T	A	11: 87,385,861 (GRCm39)	D240E	probably damaging	Het
Tex47	T	C	5: 7,355,022 (GRCm39)	Y68H	probably damaging	Het
Thbs2	A	G	17: 14,910,104 (GRCm39)	V165A	probably benign	Het
Tmem126b	T	A	7: 90,118,367 (GRCm39)	Y171F	possibly damaging	Het
Tpsg1	G	T	17: 25,592,374 (GRCm39)	M46I	probably benign	Het
Ttc28	G	T	5: 111,428,616 (GRCm39)	R1845L	possibly damaging	Het
Umodl1	A	T	17: 31,211,128 (GRCm39)	T884S	possibly damaging	Het
Vmn2r77	A	G	7: 86,461,001 (GRCm39)	K776E	probably damaging	Het
Vmn2r88	T	C	14: 51,655,671 (GRCm39)	S627P	probably damaging	Het
Vrk1	T	C	12: 106,024,236 (GRCm39)		probably null	Het
Zfp644	A	G	5: 106,783,137 (GRCm39)	M1079T	possibly damaging	Het
Znrf1	T	C	8: 112,348,233 (GRCm39)	*41Q	probably null	Het
Znrf1	T	C	8: 112,348,244 (GRCm39)	F183L	possibly 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
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
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'- GGTGAAGGCCTTCCAGGAATTC -3'
(R):5'- CTCCTCAGAGCTCAGTTTCTGTAG -3'

Sequencing Primer
(F):5'- GGAATTCATCCGGTGGGG -3'
(R):5'- CAGAGCTCAGTTTCTGTAGTAGATG -3'

Posted On

2014-06-30