Mutagenetix > Incidental Mutation

Incidental Mutation 'R8302:Trmt2a'

646469

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8302 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

18248679-18254772 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 18249949 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 162 (V162A)

Ref Sequence

ENSEMBL: ENSMUSP00000111303 (fasta)

Gene Model

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

probably damaging
Transcript: ENSMUST00000100099
AA Change: V162A

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

SMART Domains

Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: V162A

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 damaging
Transcript: ENSMUST00000115640
AA Change: V162A

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

SMART Domains

Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: V162A

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: ENSMUST00000128045

Predicted Effect

probably damaging
Transcript: ENSMUST00000140206
AA Change: V162A

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: V162A

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

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: ENSMUST00000231509

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	C	T	11: 109,962,580		probably null	Het
Ank3	T	C	10: 70,004,980	S1937P	possibly damaging	Het
Atg5	T	A	10: 44,286,119	D10E	probably benign	Het
Car12	A	G	9: 66,747,597	D103G	probably benign	Het
Cpa3	A	G	3: 20,222,152	Y306H	probably damaging	Het
Cyp2c40	A	G	19: 39,807,622	V104A	probably damaging	Het
Cyp2c66	A	T	19: 39,176,634	H353L	probably damaging	Het
Cyp2d22	A	G	15: 82,371,820		probably null	Het
Dcp1a	A	G	14: 30,522,926	T570A	possibly damaging	Het
Exph5	A	G	9: 53,376,476	E1619G	possibly damaging	Het
Frmd5	T	A	2: 121,547,579	T435S	unknown	Het
Gm3371	T	C	14: 44,403,724	R128G		Het
Gper1	A	G	5: 139,426,275	D125G	probably benign	Het
Il17re	C	A	6: 113,466,319	S340*	probably null	Het
Kazald1	T	A	19: 45,076,839	L53Q	probably damaging	Het
Kdm3b	A	T	18: 34,834,335	H1731L	probably damaging	Het
Kif20a	T	C	18: 34,631,977	S755P	probably damaging	Het
Lrch1	T	C	14: 74,795,332	N526S	probably benign	Het
Map3k8	T	C	18: 4,334,064	I343V	probably damaging	Het
Nabp1	A	T	1: 51,472,339	F140L	probably benign	Het
Ncor1	A	G	11: 62,333,855	S860P	probably benign	Het
Ndufaf5	T	A	2: 140,188,778	Y195N	possibly damaging	Het
Nsfl1c	T	C	2: 151,504,136	L157P	probably damaging	Het
Olfr1199	T	A	2: 88,756,643	I11F	possibly damaging	Het
Olfr170	T	A	16: 19,606,366	I100L	probably benign	Het
Olfr994	T	A	2: 85,430,086	T248S	possibly damaging	Het
Pcdh10	A	G	3: 45,381,498	Y749C	probably damaging	Het
Plcz1	T	A	6: 140,028,437	K93I	probably damaging	Het
Plpbp	T	C	8: 27,049,188	S109P		Het
Prkdc	G	A	16: 15,836,082	R3901H	probably damaging	Het
Psma6	A	T	12: 55,410,181	Y103F	probably benign	Het
Ptpn3	A	G	4: 57,218,514	F650L	probably benign	Het
Pxk	T	C	14: 8,164,094	F562S	probably damaging	Het
Rbl2	A	G	8: 91,085,445	D214G	probably damaging	Het
Rgs17	C	T	10: 5,862,525	C58Y	possibly damaging	Het
Rnf6	A	T	5: 146,211,524	V228E	probably benign	Het
Sardh	T	C	2: 27,215,110	D667G	probably benign	Het
Slc12a1	T	A	2: 125,190,289	V620D	probably damaging	Het
Slc39a7	A	G	17: 34,030,712	I153T	probably damaging	Het
Slc5a11	T	C	7: 123,247,939	V125A	probably damaging	Het
Slc9c1	T	C	16: 45,547,695	F216L	probably benign	Het
Strip1	A	T	3: 107,625,708	I208N	probably damaging	Het
Top1	T	C	2: 160,703,576	M288T	probably damaging	Het
Tpbgl	G	T	7: 99,625,567	A361E	probably damaging	Het
Wdr35	T	C	12: 9,028,110	I1167T	probably benign	Het
Wdr76	C	A	2: 121,510,563	H30N	probably benign	Het
Zan	A	G	5: 137,409,661	S3624P	unknown	Het
Zc3h7a	T	C	16: 11,137,385	K942E	probably damaging	Het
Zfp292	A	G	4: 34,810,893	V722A	possibly damaging	Het
Zfp943	A	G	17: 21,992,110	H59R	probably benign	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
R5452:Trmt2a	UTSW	16	18250950	missense	probably damaging	1.00
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
R8463:Trmt2a	UTSW	16	18251175	missense	probably damaging	1.00
R9120:Trmt2a	UTSW	16	18249858	missense	probably damaging	1.00
R9186:Trmt2a	UTSW	16	18251169	missense	probably benign	0.00
R9487:Trmt2a	UTSW	16	18250950	missense	probably damaging	1.00
R9710:Trmt2a	UTSW	16	18252177	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TCAAACTCTTTGGACAGCCAC -3'
(R):5'- CAGAACCATTGACATAAACTCTGTG -3'

Sequencing Primer
(F):5'- TTTGGACAGCCACCATGTG -3'
(R):5'- CCATTGACATAAACTCTGTGTGTATC -3'

Posted On

2020-09-02