Incidental Mutation 'R7952:Trmt1'
| ID |
649620 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Trmt1
|
| Ensembl Gene |
ENSMUSG00000001909 |
| Gene Name |
tRNA methyltransferase 1 |
| Synonyms |
6720406L13Rik, D8Ertd812e |
| MMRRC Submission |
045996-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.737)
|
| Stock # |
R7952 (G1)
|
| Quality Score |
198.009 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
85412953-85426437 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 85415969 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 9
(R9H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105390
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001974]
[ENSMUST00000001975]
[ENSMUST00000109767]
[ENSMUST00000109768]
[ENSMUST00000125370]
[ENSMUST00000131700]
[ENSMUST00000143427]
[ENSMUST00000152301]
[ENSMUST00000175784]
[ENSMUST00000177084]
[ENSMUST00000177423]
[ENSMUST00000177531]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001974
|
| SMART Domains |
Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
| 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: ENSMUST00000001975
|
| SMART Domains |
Protein: ENSMUSP00000001975
Gene: ENSMUSG00000001910
| Domain | Start | End | E-Value | Type |
|---|
|
BTB
|
30 |
124 |
4.05e-25 |
SMART |
|
low complexity region
|
135 |
146 |
N/A |
INTRINSIC |
|
low complexity region
|
224 |
235 |
N/A |
INTRINSIC |
|
low complexity region
|
252 |
264 |
N/A |
INTRINSIC |
|
low complexity region
|
267 |
281 |
N/A |
INTRINSIC |
|
BEN
|
382 |
457 |
6.4e-18 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000109767
|
| SMART Domains |
Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
| 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 |
possibly damaging
Transcript: ENSMUST00000109768
AA Change: R9H
PolyPhen 2
Score 0.498 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: R9H
| 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 benign
Transcript: ENSMUST00000125370
|
| SMART Domains |
Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
| 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 |
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 |
possibly damaging
Transcript: ENSMUST00000143427
AA Change: R9H
PolyPhen 2
Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000117140
Gene: ENSMUSG00000001909
AA Change: R9H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
47 |
98 |
3.2e-12 |
PFAM |
|
| 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: 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 |
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 |
probably benign
Transcript: ENSMUST00000177423
AA Change: R9H
PolyPhen 2
Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
|
| SMART Domains |
Protein: ENSMUSP00000135327
Gene: ENSMUSG00000001909
AA Change: R9H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
47 |
262 |
1.4e-66 |
PFAM |
|
Pfam:Met_10
|
138 |
252 |
5.6e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177531
|
| SMART Domains |
Protein: ENSMUSP00000135540
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
54 |
174 |
1.8e-21 |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
98% (47/48) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acbd3 |
T |
C |
1: 180,579,903 (GRCm39) |
S516P |
possibly damaging |
Het |
| Adora1 |
A |
G |
1: 134,131,024 (GRCm39) |
S216P |
possibly damaging |
Het |
| Arhgap17 |
G |
T |
7: 122,885,914 (GRCm39) |
S739R |
probably benign |
Het |
| Bphl |
A |
G |
13: 34,230,780 (GRCm39) |
T75A |
probably benign |
Het |
| Ccdc73 |
G |
A |
2: 104,775,801 (GRCm39) |
|
probably null |
Het |
| Cela3b |
T |
C |
4: 137,149,219 (GRCm39) |
I262V |
probably benign |
Het |
| Chpf |
T |
C |
1: 75,455,586 (GRCm39) |
N55S |
probably benign |
Het |
| Chst8 |
A |
G |
7: 34,374,919 (GRCm39) |
Y307H |
probably damaging |
Het |
| Cmtm2b |
G |
T |
8: 105,057,203 (GRCm39) |
E188* |
probably null |
Het |
| Cmya5 |
TTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAG |
TTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAGGCGCATGCTCCTCCTCTCTGTGGACTATGGGCTCAG |
13: 93,233,512 (GRCm39) |
|
probably benign |
Het |
| Cxadr |
C |
T |
16: 78,131,123 (GRCm39) |
T213M |
possibly damaging |
Het |
| D3Ertd751e |
T |
A |
3: 41,703,096 (GRCm39) |
|
probably null |
Het |
| Dhx32 |
T |
C |
7: 133,350,725 (GRCm39) |
Y115C |
probably benign |
Het |
| Dop1b |
C |
A |
16: 93,546,848 (GRCm39) |
T284K |
possibly damaging |
Het |
| Dync2h1 |
A |
G |
9: 7,129,802 (GRCm39) |
V1732A |
possibly damaging |
Het |
| Egf |
C |
T |
3: 129,533,645 (GRCm39) |
R65Q |
probably damaging |
Het |
| Fat4 |
T |
G |
3: 38,945,870 (GRCm39) |
S1588A |
probably damaging |
Het |
| Fmnl3 |
A |
G |
15: 99,220,518 (GRCm39) |
V588A |
probably damaging |
Het |
| Galnt3 |
C |
T |
2: 65,928,186 (GRCm39) |
E237K |
probably benign |
Het |
| Grik2 |
T |
C |
10: 49,298,633 (GRCm39) |
I363V |
probably benign |
Het |
| Grik3 |
C |
T |
4: 125,598,340 (GRCm39) |
T769I |
probably damaging |
Het |
| Hpd |
A |
T |
5: 123,316,327 (GRCm39) |
D141E |
possibly damaging |
Het |
| Hrc |
A |
T |
7: 44,985,692 (GRCm39) |
D281V |
probably damaging |
Het |
| Igfn1 |
A |
T |
1: 135,891,693 (GRCm39) |
I2274K |
probably damaging |
Het |
| Iqgap3 |
A |
G |
3: 88,005,677 (GRCm39) |
I502V |
probably benign |
Het |
| Kcnh8 |
A |
T |
17: 53,266,493 (GRCm39) |
Q835L |
probably benign |
Het |
| Kmt2d |
C |
T |
15: 98,748,649 (GRCm39) |
G2892R |
unknown |
Het |
| Lama4 |
T |
G |
10: 38,906,486 (GRCm39) |
I284S |
probably benign |
Het |
| Madd |
C |
A |
2: 90,992,886 (GRCm39) |
G1011V |
probably damaging |
Het |
| Mroh2b |
T |
C |
15: 4,980,693 (GRCm39) |
F1421L |
probably damaging |
Het |
| Nadk |
G |
T |
4: 155,661,524 (GRCm39) |
D17Y |
probably benign |
Het |
| Nedd9 |
C |
A |
13: 41,470,431 (GRCm39) |
D241Y |
probably damaging |
Het |
| Notch2 |
T |
C |
3: 98,007,552 (GRCm39) |
V434A |
probably benign |
Het |
| Ofcc1 |
C |
T |
13: 40,433,781 (GRCm39) |
R108Q |
probably benign |
Het |
| Or10al2 |
T |
C |
17: 37,983,708 (GRCm39) |
Y265H |
probably damaging |
Het |
| Or51g1 |
A |
G |
7: 102,633,721 (GRCm39) |
F217L |
probably benign |
Het |
| Pkd1l3 |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
8: 110,350,827 (GRCm39) |
|
probably benign |
Het |
| Pramel41 |
T |
C |
5: 94,594,902 (GRCm39) |
V254A |
probably benign |
Het |
| Prss55 |
A |
G |
14: 64,313,132 (GRCm39) |
Y251H |
probably damaging |
Het |
| Rec8 |
T |
C |
14: 55,862,760 (GRCm39) |
V573A |
possibly damaging |
Het |
| Ryr2 |
T |
C |
13: 11,661,313 (GRCm39) |
|
probably null |
Het |
| Sec31b |
A |
G |
19: 44,508,979 (GRCm39) |
S667P |
probably benign |
Het |
| Smim17 |
A |
G |
7: 6,427,849 (GRCm39) |
D45G |
possibly damaging |
Het |
| Sspo |
A |
G |
6: 48,464,263 (GRCm39) |
T3906A |
probably damaging |
Het |
| Tanc2 |
G |
T |
11: 105,787,423 (GRCm39) |
G908W |
probably damaging |
Het |
| Tcf7l2 |
A |
T |
19: 55,886,989 (GRCm39) |
M1L |
probably benign |
Het |
| Tpx2 |
C |
T |
2: 152,735,514 (GRCm39) |
A714V |
probably damaging |
Het |
| Trgc4 |
T |
A |
13: 19,533,740 (GRCm39) |
S121R |
|
Het |
| Unc13a |
A |
T |
8: 72,111,131 (GRCm39) |
V360E |
possibly damaging |
Het |
| Vmn1r225 |
T |
A |
17: 20,722,589 (GRCm39) |
I10N |
probably damaging |
Het |
| Xkr4 |
A |
G |
1: 3,740,842 (GRCm39) |
S244P |
possibly damaging |
Het |
| Zkscan14 |
G |
T |
5: 145,132,708 (GRCm39) |
H274Q |
probably damaging |
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 |
|
|
R6666:Trmt1
|
UTSW |
8 |
85,425,083 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7669:Trmt1
|
UTSW |
8 |
85,424,180 (GRCm39) |
missense |
probably benign |
0.05 |
|
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'- AGTGAAACTCCCTTGTAGAAGAG -3'
(R):5'- GTGGCCTCCATAACATCCTG -3'
Sequencing Primer
(F):5'- AGAAGAGTCTTGACCCTG -3'
(R):5'- ATAACATCCTGCGTTCTCGAGGG -3'
|
| Posted On |
2020-09-15 |
Incidental Mutation