Incidental Mutation 'R3853:Trmt2a'
| ID |
276034 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Trmt2a
|
| Ensembl Gene |
ENSMUSG00000022721 |
| Gene Name |
TRM2 tRNA methyltransferase 2A |
| Synonyms |
Htf9c |
| MMRRC Submission |
040900-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3853 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
18066711-18072636 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 18069055 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Phenylalanine
at position 299
(Y299F)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000100099
AA Change: Y299F
PolyPhen 2
Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: Y299F
| 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 |
possibly damaging
Transcript: ENSMUST00000115640
AA Change: Y299F
PolyPhen 2
Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: Y299F
| 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: ENSMUST00000127239
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000140206
AA Change: Y299F
PolyPhen 2
Score 0.634 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: Y299F
| 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: ENSMUST00000123073
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134035
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144536
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152033
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131211
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232144
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000232342
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232293
|
| Meta Mutation Damage Score |
0.1268 |
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 98.8%
- 10x: 97.2%
- 20x: 94.4%
|
| Validation Efficiency |
96% (47/49) |
| 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2010315B03Rik |
T |
A |
9: 124,055,976 (GRCm39) |
H316L |
probably damaging |
Het |
| Cadps |
A |
G |
14: 12,509,090 (GRCm38) |
|
probably benign |
Het |
| Cluh |
A |
G |
11: 74,547,279 (GRCm39) |
D44G |
probably benign |
Het |
| Copb1 |
A |
G |
7: 113,822,551 (GRCm39) |
V726A |
probably damaging |
Het |
| Dsg4 |
T |
C |
18: 20,582,291 (GRCm39) |
V79A |
probably benign |
Het |
| Exo1 |
A |
T |
1: 175,720,554 (GRCm39) |
I291F |
probably benign |
Het |
| Eya4 |
C |
T |
10: 22,992,574 (GRCm39) |
A460T |
probably damaging |
Het |
| Gjd3 |
G |
T |
11: 102,690,952 (GRCm39) |
D350E |
probably benign |
Het |
| Hcar2 |
T |
C |
5: 124,002,475 (GRCm39) |
M343V |
probably benign |
Het |
| Ifna15 |
T |
C |
4: 88,476,046 (GRCm39) |
Y146C |
probably damaging |
Het |
| Lce3e |
C |
T |
3: 92,875,139 (GRCm39) |
Q32* |
probably null |
Het |
| Llgl1 |
T |
C |
11: 60,598,075 (GRCm39) |
L373P |
probably damaging |
Het |
| Mark2 |
A |
G |
19: 7,254,655 (GRCm39) |
C642R |
probably damaging |
Het |
| Mbd3l2 |
A |
G |
9: 18,356,092 (GRCm39) |
Q139R |
probably benign |
Het |
| Mki67 |
A |
C |
7: 135,297,859 (GRCm39) |
S2392A |
probably benign |
Het |
| Nynrin |
T |
A |
14: 56,101,562 (GRCm39) |
N410K |
probably benign |
Het |
| Or10g7 |
A |
T |
9: 39,905,450 (GRCm39) |
T115S |
probably damaging |
Het |
| Or4a71 |
A |
T |
2: 89,357,917 (GRCm39) |
M279K |
possibly damaging |
Het |
| Or5b112 |
A |
G |
19: 13,319,862 (GRCm39) |
T247A |
possibly damaging |
Het |
| Or7a38 |
T |
A |
10: 78,752,781 (GRCm39) |
Y36N |
probably damaging |
Het |
| Or8b1 |
G |
T |
9: 38,400,247 (GRCm39) |
R307S |
probably benign |
Het |
| Padi3 |
T |
C |
4: 140,518,580 (GRCm39) |
|
probably benign |
Het |
| Prkce |
A |
G |
17: 86,476,277 (GRCm39) |
D86G |
probably damaging |
Het |
| Pwwp3b |
C |
T |
X: 138,137,403 (GRCm39) |
|
probably null |
Het |
| Rad21 |
T |
G |
15: 51,835,712 (GRCm39) |
I234L |
probably benign |
Het |
| Scn4a |
A |
T |
11: 106,210,932 (GRCm39) |
M1695K |
possibly damaging |
Het |
| Sdccag8 |
T |
C |
1: 176,681,361 (GRCm39) |
S325P |
probably damaging |
Het |
| Sebox |
G |
A |
11: 78,394,975 (GRCm39) |
G106R |
probably benign |
Het |
| Serpinb9 |
A |
G |
13: 33,199,503 (GRCm39) |
E266G |
possibly damaging |
Het |
| Shoc1 |
T |
C |
4: 59,047,390 (GRCm39) |
N1410D |
possibly damaging |
Het |
| Snx14 |
T |
C |
9: 88,289,372 (GRCm39) |
|
probably benign |
Het |
| Tmc6 |
A |
T |
11: 117,663,884 (GRCm39) |
L474* |
probably null |
Het |
| Tmem132c |
T |
C |
5: 127,436,933 (GRCm39) |
Y141H |
probably benign |
Het |
| Trap1 |
G |
A |
16: 3,872,686 (GRCm39) |
R328C |
possibly damaging |
Het |
| Trim36 |
C |
A |
18: 46,305,439 (GRCm39) |
|
probably benign |
Het |
| Trrap |
A |
G |
5: 144,728,975 (GRCm39) |
K630E |
probably damaging |
Het |
| Tsnaxip1 |
A |
T |
8: 106,567,333 (GRCm39) |
|
probably benign |
Het |
| Ttc6 |
G |
T |
12: 57,775,335 (GRCm39) |
C1677F |
possibly damaging |
Het |
| Ugt2a3 |
A |
T |
5: 87,485,018 (GRCm39) |
V2D |
|
Het |
| Usp9x |
A |
G |
X: 12,964,822 (GRCm39) |
D77G |
probably benign |
Het |
| Wfs1 |
C |
A |
5: 37,125,968 (GRCm39) |
V308L |
probably benign |
Het |
| Zan |
A |
C |
5: 137,472,326 (GRCm39) |
L140R |
probably damaging |
Het |
| Zc3h3 |
A |
T |
15: 75,709,346 (GRCm39) |
S508T |
probably benign |
Het |
| Zswim3 |
A |
G |
2: 164,662,777 (GRCm39) |
Y419C |
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 |
|
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 |
|
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'- TTCCAGAGGCCACTAAGCAG -3'
(R):5'- CAGAGCTCAGTTTCTGTAGTAGATG -3'
Sequencing Primer
(F):5'- TGAAGGCCTTCCAGGAATTC -3'
(R):5'- GATATAAAACTCCCATCAGGCTATG -3'
|
| Posted On |
2015-04-06 |
Incidental Mutation