Incidental Mutation 'R6666:Trmt1'
| ID |
526979 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Trmt1
|
| Ensembl Gene |
ENSMUSG00000001909 |
| Gene Name |
tRNA methyltransferase 1 |
| Synonyms |
6720406L13Rik, D8Ertd812e |
| MMRRC Submission |
044786-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.737)
|
| Stock # |
R6666 (G1)
|
| Quality Score |
133.008 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
85412953-85426437 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 85425083 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 493
(L493P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135510
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001974]
[ENSMUST00000037165]
[ENSMUST00000109767]
[ENSMUST00000109768]
[ENSMUST00000125370]
[ENSMUST00000131700]
[ENSMUST00000143427]
[ENSMUST00000175784]
[ENSMUST00000177084]
[ENSMUST00000152301]
[ENSMUST00000177423]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000001974
AA Change: L522P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
AA Change: L522P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
55 |
499 |
3.5e-151 |
PFAM |
|
Pfam:Met_10
|
141 |
256 |
1.3e-8 |
PFAM |
|
ZnF_C3H1
|
599 |
625 |
3.55e-6 |
SMART |
|
low complexity region
|
648 |
661 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037165
|
| SMART Domains |
Protein: ENSMUSP00000046010
Gene: ENSMUSG00000034041
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
23 |
39 |
N/A |
INTRINSIC |
|
HLH
|
155 |
207 |
3.97e-18 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000109767
AA Change: L522P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
AA Change: L522P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
55 |
499 |
4.9e-149 |
PFAM |
|
Pfam:Met_10
|
142 |
256 |
3.4e-8 |
PFAM |
|
ZnF_C3H1
|
599 |
625 |
3.55e-6 |
SMART |
|
low complexity region
|
648 |
661 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000109768
AA Change: L515P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: L515P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
48 |
492 |
3.1e-149 |
PFAM |
|
Pfam:Met_10
|
135 |
249 |
4.4e-8 |
PFAM |
|
ZnF_C3H1
|
592 |
618 |
3.55e-6 |
SMART |
|
low complexity region
|
641 |
654 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000125370
AA Change: L493P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
AA Change: L493P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
55 |
470 |
1.7e-140 |
PFAM |
|
Pfam:Met_10
|
142 |
256 |
2.8e-8 |
PFAM |
|
ZnF_C3H1
|
570 |
596 |
3.55e-6 |
SMART |
|
low complexity region
|
619 |
632 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128022
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131700
|
| SMART Domains |
Protein: ENSMUSP00000122526
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
54 |
108 |
3.9e-12 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000136423
AA Change: L19P
|
| SMART Domains |
Protein: ENSMUSP00000134723
Gene: ENSMUSG00000001909
AA Change: L19P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
190 |
203 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143427
|
| SMART Domains |
Protein: ENSMUSP00000117140
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
47 |
98 |
3.2e-12 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000175784
|
| SMART Domains |
Protein: ENSMUSP00000135273
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
54 |
221 |
8.6e-39 |
PFAM |
|
Pfam:Met_10
|
144 |
221 |
5.3e-7 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148644
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138300
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177260
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177286
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177084
|
| SMART Domains |
Protein: ENSMUSP00000135675
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
29 |
260 |
4.1e-76 |
PFAM |
|
Pfam:Met_10
|
117 |
231 |
4.1e-10 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148118
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152301
|
| SMART Domains |
Protein: ENSMUSP00000116712
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
54 |
242 |
4.2e-49 |
PFAM |
|
Pfam:Met_10
|
145 |
229 |
2.3e-7 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000175884
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175767
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175704
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137953
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177423
|
| SMART Domains |
Protein: ENSMUSP00000135327
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
47 |
262 |
1.4e-66 |
PFAM |
|
Pfam:Met_10
|
138 |
252 |
5.6e-9 |
PFAM |
|
| Meta Mutation Damage Score |
0.9454 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.2%
|
| Validation Efficiency |
100% (46/46) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700020N01Rik |
C |
A |
10: 21,469,228 (GRCm39) |
|
probably null |
Het |
| Arhgap24 |
A |
G |
5: 102,700,163 (GRCm39) |
|
probably null |
Het |
| Atp12a |
G |
T |
14: 56,610,821 (GRCm39) |
V322L |
probably benign |
Het |
| Capza1 |
A |
C |
3: 104,735,922 (GRCm39) |
|
probably null |
Het |
| Cela3a |
A |
T |
4: 137,131,175 (GRCm39) |
S188T |
probably benign |
Het |
| Cplx1 |
G |
T |
5: 108,668,031 (GRCm39) |
Y123* |
probably null |
Het |
| Ddias |
A |
T |
7: 92,507,289 (GRCm39) |
D875E |
probably benign |
Het |
| Dnah3 |
T |
C |
7: 119,670,172 (GRCm39) |
E715G |
probably benign |
Het |
| Fam83e |
A |
G |
7: 45,376,426 (GRCm39) |
T380A |
probably benign |
Het |
| Fancd2 |
T |
C |
6: 113,562,470 (GRCm39) |
V1270A |
probably damaging |
Het |
| Foxh1 |
A |
G |
15: 76,552,613 (GRCm39) |
F367S |
probably damaging |
Het |
| Gpat2 |
G |
C |
2: 127,273,838 (GRCm39) |
G294R |
possibly damaging |
Het |
| Gprc5a |
A |
G |
6: 135,056,473 (GRCm39) |
I307V |
probably benign |
Het |
| Gtpbp3 |
A |
G |
8: 71,943,582 (GRCm39) |
D212G |
possibly damaging |
Het |
| Helb |
A |
G |
10: 119,920,856 (GRCm39) |
V1029A |
probably damaging |
Het |
| Il22ra1 |
A |
T |
4: 135,477,772 (GRCm39) |
H281L |
probably damaging |
Het |
| Il2rb |
TAGTCA |
TAGTCAGTCA |
15: 78,366,034 (GRCm39) |
|
probably null |
Het |
| Itga3 |
T |
C |
11: 94,956,652 (GRCm39) |
T170A |
probably benign |
Het |
| Kdm3a |
T |
C |
6: 71,588,974 (GRCm39) |
E345G |
probably benign |
Het |
| Kif11 |
T |
C |
19: 37,398,214 (GRCm39) |
I680T |
probably benign |
Het |
| Klhl28 |
C |
T |
12: 64,990,301 (GRCm39) |
D547N |
probably benign |
Het |
| Limk2 |
T |
A |
11: 3,310,493 (GRCm39) |
E49D |
probably damaging |
Het |
| Lmbrd2 |
T |
A |
15: 9,151,656 (GRCm39) |
F120I |
probably benign |
Het |
| Mefv |
T |
A |
16: 3,525,862 (GRCm39) |
N802Y |
possibly damaging |
Het |
| Ms4a2 |
C |
T |
19: 11,595,787 (GRCm39) |
S168N |
probably benign |
Het |
| Myct1 |
T |
C |
10: 5,554,333 (GRCm39) |
S67P |
probably damaging |
Het |
| Myh4 |
A |
G |
11: 67,142,638 (GRCm39) |
E933G |
probably damaging |
Het |
| Naif1 |
C |
A |
2: 32,344,863 (GRCm39) |
T189K |
probably damaging |
Het |
| Nppb |
A |
G |
4: 148,070,463 (GRCm39) |
I11V |
probably benign |
Het |
| Nr3c1 |
T |
C |
18: 39,620,200 (GRCm39) |
D29G |
probably damaging |
Het |
| Nrcam |
A |
G |
12: 44,618,338 (GRCm39) |
Y782C |
probably damaging |
Het |
| Or1af1 |
A |
T |
2: 37,110,331 (GRCm39) |
I277F |
probably damaging |
Het |
| Or51e1 |
T |
C |
7: 102,359,135 (GRCm39) |
|
probably null |
Het |
| Or9m1 |
T |
A |
2: 87,733,852 (GRCm39) |
H56L |
probably damaging |
Het |
| Parp1 |
A |
G |
1: 180,413,516 (GRCm39) |
T375A |
probably benign |
Het |
| Pcdhgb1 |
G |
T |
18: 37,814,546 (GRCm39) |
E346* |
probably null |
Het |
| Pds5b |
G |
T |
5: 150,701,631 (GRCm39) |
S754I |
probably damaging |
Het |
| Scnn1g |
G |
A |
7: 121,366,611 (GRCm39) |
D603N |
probably benign |
Het |
| Slitrk5 |
A |
G |
14: 111,917,534 (GRCm39) |
D386G |
probably damaging |
Het |
| Vrk1 |
A |
G |
12: 106,024,910 (GRCm39) |
E262G |
probably damaging |
Het |
| Wfs1 |
T |
C |
5: 37,124,963 (GRCm39) |
T567A |
possibly damaging |
Het |
| Zbtb11 |
A |
T |
16: 55,826,615 (GRCm39) |
K846I |
probably damaging |
Het |
| Zfp318 |
A |
G |
17: 46,720,140 (GRCm39) |
T1113A |
probably benign |
Het |
| Zfp654 |
A |
T |
16: 64,606,596 (GRCm39) |
S535R |
probably benign |
Het |
|
| Other mutations in Trmt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00497:Trmt1
|
APN |
8 |
85,422,138 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
IGL01959:Trmt1
|
APN |
8 |
85,418,005 (GRCm39) |
splice site |
probably null |
|
|
IGL02127:Trmt1
|
APN |
8 |
85,424,100 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02689:Trmt1
|
APN |
8 |
85,426,385 (GRCm39) |
unclassified |
probably benign |
|
|
IGL03087:Trmt1
|
APN |
8 |
85,421,862 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02835:Trmt1
|
UTSW |
8 |
85,423,589 (GRCm39) |
missense |
probably null |
1.00 |
|
PIT4418001:Trmt1
|
UTSW |
8 |
85,424,299 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0395:Trmt1
|
UTSW |
8 |
85,423,741 (GRCm39) |
splice site |
probably null |
|
|
R0964:Trmt1
|
UTSW |
8 |
85,423,481 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1881:Trmt1
|
UTSW |
8 |
85,415,896 (GRCm39) |
intron |
probably benign |
|
|
R2190:Trmt1
|
UTSW |
8 |
85,416,470 (GRCm39) |
nonsense |
probably null |
|
|
R2197:Trmt1
|
UTSW |
8 |
85,417,487 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2979:Trmt1
|
UTSW |
8 |
85,423,511 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3813:Trmt1
|
UTSW |
8 |
85,421,846 (GRCm39) |
unclassified |
probably benign |
|
|
R4407:Trmt1
|
UTSW |
8 |
85,424,384 (GRCm39) |
unclassified |
probably benign |
|
|
R4461:Trmt1
|
UTSW |
8 |
85,425,778 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4588:Trmt1
|
UTSW |
8 |
85,417,382 (GRCm39) |
intron |
probably benign |
|
|
R5170:Trmt1
|
UTSW |
8 |
85,421,861 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6299:Trmt1
|
UTSW |
8 |
85,423,919 (GRCm39) |
nonsense |
probably null |
|
|
R6614:Trmt1
|
UTSW |
8 |
85,415,962 (GRCm39) |
missense |
probably benign |
|
|
R7669:Trmt1
|
UTSW |
8 |
85,424,180 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7952:Trmt1
|
UTSW |
8 |
85,415,969 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R9784:Trmt1
|
UTSW |
8 |
85,424,330 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Z1176:Trmt1
|
UTSW |
8 |
85,425,827 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
Z1176:Trmt1
|
UTSW |
8 |
85,424,869 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGTGAAGACAGATGCTCCCC -3'
(R):5'- CTGACTCAGATACTCACACGTATG -3'
Sequencing Primer
(F):5'- CCTCTGGGACATCATGCGTTG -3'
(R):5'- CACGTATGTGTGACTCAAGAAC -3'
|
| Posted On |
2018-07-23 |
Incidental Mutation