Incidental Mutation 'R2197:Trmt1'
| ID |
238420 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Trmt1
|
| Ensembl Gene |
ENSMUSG00000001909 |
| Gene Name |
tRNA methyltransferase 1 |
| Synonyms |
6720406L13Rik, D8Ertd812e |
| MMRRC Submission |
040199-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.686)
|
| Stock # |
R2197 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
8 |
| Chromosomal Location |
85412953-85426437 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 85417487 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 121
(S121T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135540
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001974]
[ENSMUST00000001975]
[ENSMUST00000109767]
[ENSMUST00000109768]
[ENSMUST00000125370]
[ENSMUST00000175784]
[ENSMUST00000152301]
[ENSMUST00000177084]
[ENSMUST00000131700]
[ENSMUST00000143427]
[ENSMUST00000177423]
[ENSMUST00000177531]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001974
AA Change: S121T
PolyPhen 2
Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
AA Change: S121T
| 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 |
noncoding transcript
Transcript: ENSMUST00000077990
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000109767
AA Change: S121T
PolyPhen 2
Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
AA Change: S121T
| 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 benign
Transcript: ENSMUST00000109768
AA Change: S114T
PolyPhen 2
Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: S114T
| 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
AA Change: S121T
PolyPhen 2
Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
AA Change: S121T
| 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: ENSMUST00000127915
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000175784
AA Change: S124T
PolyPhen 2
Score 0.704 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000135273
Gene: ENSMUSG00000001909
AA Change: S124T
| 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 |
possibly damaging
Transcript: ENSMUST00000152301
AA Change: S124T
PolyPhen 2
Score 0.507 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000116712
Gene: ENSMUSG00000001909
AA Change: S124T
| 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: ENSMUST00000177084
AA Change: S96T
PolyPhen 2
Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000135675
Gene: ENSMUSG00000001909
AA Change: S96T
| 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: ENSMUST00000137953
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128022
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175980
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176053
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150085
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148118
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128537
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175870
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176914
|
| 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 |
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 |
possibly damaging
Transcript: ENSMUST00000177423
AA Change: S117T
PolyPhen 2
Score 0.683 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000135327
Gene: ENSMUSG00000001909
AA Change: S117T
| 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 damaging
Transcript: ENSMUST00000177531
AA Change: S121T
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000135540
Gene: ENSMUSG00000001909
AA Change: S121T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TRM
|
54 |
174 |
1.8e-21 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177286
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177364
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.2%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam11 |
A |
T |
11: 102,660,750 (GRCm39) |
I94F |
possibly damaging |
Het |
| Ankrd50 |
A |
T |
3: 38,509,741 (GRCm39) |
D875E |
probably damaging |
Het |
| Arf3 |
T |
C |
15: 98,639,285 (GRCm39) |
N60S |
probably benign |
Het |
| Atxn2 |
T |
G |
5: 121,944,280 (GRCm39) |
|
probably null |
Het |
| B3gnt8 |
A |
T |
7: 25,328,373 (GRCm39) |
I268F |
probably benign |
Het |
| Bmp1 |
T |
A |
14: 70,723,712 (GRCm39) |
D708V |
possibly damaging |
Het |
| C1s2 |
A |
G |
6: 124,609,069 (GRCm39) |
S163P |
probably damaging |
Het |
| C3 |
A |
G |
17: 57,526,623 (GRCm39) |
I786T |
probably benign |
Het |
| Cacna2d2 |
T |
A |
9: 107,404,602 (GRCm39) |
L1138Q |
probably damaging |
Het |
| Cage1 |
T |
A |
13: 38,207,029 (GRCm39) |
Y272F |
probably damaging |
Het |
| Cd300ld |
A |
T |
11: 114,875,058 (GRCm39) |
M192K |
possibly damaging |
Het |
| Cdc5l |
A |
T |
17: 45,718,745 (GRCm39) |
F624I |
probably benign |
Het |
| Cdh8 |
T |
A |
8: 99,922,897 (GRCm39) |
Q333L |
probably damaging |
Het |
| Ciapin1 |
T |
A |
8: 95,555,787 (GRCm39) |
K128* |
probably null |
Het |
| Col6a3 |
T |
A |
1: 90,731,467 (GRCm39) |
E988D |
probably benign |
Het |
| Crip3 |
A |
G |
17: 46,740,338 (GRCm39) |
E46G |
probably damaging |
Het |
| D5Ertd579e |
A |
G |
5: 36,772,137 (GRCm39) |
S753P |
possibly damaging |
Het |
| Dock6 |
T |
A |
9: 21,744,177 (GRCm39) |
D126V |
probably damaging |
Het |
| Duxf4 |
T |
A |
10: 58,072,158 (GRCm39) |
I19F |
possibly damaging |
Het |
| Dvl3 |
A |
G |
16: 20,342,506 (GRCm39) |
E153G |
probably damaging |
Het |
| Epas1 |
A |
T |
17: 87,136,471 (GRCm39) |
M748L |
probably benign |
Het |
| Exoc8 |
A |
G |
8: 125,622,477 (GRCm39) |
L630P |
probably damaging |
Het |
| Fam227a |
G |
A |
15: 79,507,668 (GRCm39) |
T454M |
probably damaging |
Het |
| Flnc |
A |
T |
6: 29,459,134 (GRCm39) |
D2472V |
probably damaging |
Het |
| Galnt4 |
G |
A |
10: 98,944,509 (GRCm39) |
G78E |
probably damaging |
Het |
| Ghr |
A |
T |
15: 3,362,956 (GRCm39) |
L172* |
probably null |
Het |
| Gjb5 |
A |
T |
4: 127,250,063 (GRCm39) |
|
probably null |
Het |
| Hdac5 |
T |
C |
11: 102,095,340 (GRCm39) |
D427G |
probably damaging |
Het |
| Hsd17b4 |
G |
A |
18: 50,316,369 (GRCm39) |
|
probably null |
Het |
| Kcnab1 |
T |
C |
3: 65,017,368 (GRCm39) |
I59T |
probably benign |
Het |
| Kcnh7 |
A |
G |
2: 62,607,950 (GRCm39) |
Y544H |
probably damaging |
Het |
| Kdm7a |
A |
G |
6: 39,123,870 (GRCm39) |
S765P |
probably damaging |
Het |
| Lama1 |
A |
T |
17: 68,059,936 (GRCm39) |
H675L |
probably benign |
Het |
| Lemd3 |
CCCTCCTCCTCCTCCTCCTCC |
CCCTCCTCCTCCTCCTCC |
10: 120,814,432 (GRCm39) |
|
probably benign |
Het |
| Llgl1 |
T |
C |
11: 60,600,865 (GRCm39) |
S654P |
possibly damaging |
Het |
| Lvrn |
G |
T |
18: 47,011,409 (GRCm39) |
M455I |
probably benign |
Het |
| Mfsd12 |
T |
A |
10: 81,193,568 (GRCm39) |
L46Q |
probably damaging |
Het |
| Mtcl1 |
A |
T |
17: 66,673,427 (GRCm39) |
M783K |
probably benign |
Het |
| Mthfd1l |
A |
T |
10: 3,978,399 (GRCm39) |
T420S |
probably damaging |
Het |
| Mybphl |
T |
A |
3: 108,284,635 (GRCm39) |
I294N |
probably damaging |
Het |
| Or4c52 |
G |
A |
2: 89,845,768 (GRCm39) |
G165S |
probably damaging |
Het |
| Or4f14b |
T |
C |
2: 111,775,658 (GRCm39) |
T48A |
possibly damaging |
Het |
| Or52ab7 |
T |
A |
7: 102,977,831 (GRCm39) |
L46* |
probably null |
Het |
| Oxa1l |
A |
T |
14: 54,598,924 (GRCm39) |
Q70L |
probably benign |
Het |
| Pcdhac2 |
A |
T |
18: 37,279,185 (GRCm39) |
I722F |
probably damaging |
Het |
| Pde4d |
A |
G |
13: 110,084,924 (GRCm39) |
D460G |
probably damaging |
Het |
| Pth1r |
CGGG |
CGGGGGG |
9: 110,556,058 (GRCm39) |
|
probably benign |
Het |
| Rab11fip3 |
A |
G |
17: 26,287,152 (GRCm39) |
S334P |
probably benign |
Het |
| Ror2 |
C |
T |
13: 53,439,816 (GRCm39) |
|
probably null |
Het |
| Scnn1g |
G |
C |
7: 121,366,519 (GRCm39) |
W572S |
probably damaging |
Het |
| Skint5 |
G |
A |
4: 113,798,046 (GRCm39) |
S179L |
probably damaging |
Het |
| Slc22a2 |
G |
T |
17: 12,817,949 (GRCm39) |
G175V |
probably damaging |
Het |
| Spaca6 |
G |
A |
17: 18,056,416 (GRCm39) |
|
probably null |
Het |
| Tbc1d30 |
C |
T |
10: 121,140,312 (GRCm39) |
R207H |
probably damaging |
Het |
| Tdrd5 |
A |
G |
1: 156,087,435 (GRCm39) |
I829T |
probably benign |
Het |
| Tmcc3 |
T |
C |
10: 94,414,780 (GRCm39) |
S161P |
probably damaging |
Het |
| Tmem150b |
A |
G |
7: 4,719,353 (GRCm39) |
V189A |
probably benign |
Het |
| Tmem248 |
A |
G |
5: 130,260,597 (GRCm39) |
D54G |
probably benign |
Het |
| Tyk2 |
C |
T |
9: 21,026,503 (GRCm39) |
V698M |
probably damaging |
Het |
| Usp17la |
A |
G |
7: 104,509,919 (GRCm39) |
R175G |
probably damaging |
Het |
| Vav1 |
A |
G |
17: 57,610,140 (GRCm39) |
N464S |
probably benign |
Het |
| Vmn2r57 |
T |
G |
7: 41,078,249 (GRCm39) |
|
probably null |
Het |
| Vmn2r78 |
A |
G |
7: 86,570,535 (GRCm39) |
Y351C |
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 |
|
|
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 |
|
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'- GGTTCCTGAAAGCTCTAGGC -3'
(R):5'- TGCTTTCCCAGGGAGCTATC -3'
Sequencing Primer
(F):5'- CTTTCTGCCTTTCTCCTGGGGG -3'
(R):5'- GGAGCTATCCCTCTGACTGATG -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation