Incidental Mutation 'R6299:Trmt1'
| ID |
508976 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Trmt1
|
| Ensembl Gene |
ENSMUSG00000001909 |
| Gene Name |
tRNA methyltransferase 1 |
| Synonyms |
6720406L13Rik, D8Ertd812e |
| MMRRC Submission |
044465-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.737)
|
| Stock # |
R6299 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
85412953-85426437 bp(+) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
T to A
at 85423919 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Stop codon
at position 36
(C36*)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001974]
[ENSMUST00000037165]
[ENSMUST00000109767]
[ENSMUST00000109768]
[ENSMUST00000125370]
[ENSMUST00000131700]
[ENSMUST00000152301]
[ENSMUST00000177084]
[ENSMUST00000143427]
[ENSMUST00000175784]
[ENSMUST00000177423]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
Transcript: ENSMUST00000001974
AA Change: C375*
|
| SMART Domains |
Protein: ENSMUSP00000001974
Gene: ENSMUSG00000001909
AA Change: C375*
| 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 null
Transcript: ENSMUST00000109767
AA Change: C375*
|
| SMART Domains |
Protein: ENSMUSP00000105389
Gene: ENSMUSG00000001909
AA Change: C375*
| 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 null
Transcript: ENSMUST00000109768
AA Change: C368*
|
| SMART Domains |
Protein: ENSMUSP00000105390
Gene: ENSMUSG00000001909
AA Change: C368*
| 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 null
Transcript: ENSMUST00000125370
AA Change: C346*
|
| SMART Domains |
Protein: ENSMUSP00000135510
Gene: ENSMUSG00000001909
AA Change: C346*
| 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 |
probably null
Transcript: ENSMUST00000175884
AA Change: C36*
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138300
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137953
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148118
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000136423
|
| SMART Domains |
Protein: ENSMUSP00000134723
Gene: ENSMUSG00000001909
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
190 |
203 |
N/A |
INTRINSIC |
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000175767
|
| 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: ENSMUST00000177286
|
| 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: ENSMUST00000175704
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177260
|
| 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 |
0.9714 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 98.2%
|
| Validation Efficiency |
100% (61/61) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bms1 |
G |
A |
6: 118,395,476 (GRCm39) |
R24W |
probably damaging |
Het |
| C130050O18Rik |
A |
T |
5: 139,400,126 (GRCm39) |
S60C |
probably damaging |
Het |
| Cabcoco1 |
A |
G |
10: 68,272,720 (GRCm39) |
Y222H |
probably damaging |
Het |
| Cc2d1b |
T |
C |
4: 108,485,335 (GRCm39) |
V559A |
probably benign |
Het |
| Cgrrf1 |
T |
A |
14: 47,077,647 (GRCm39) |
N46K |
probably damaging |
Het |
| Clca3a1 |
T |
C |
3: 144,464,275 (GRCm39) |
D114G |
probably damaging |
Het |
| Clcnkb |
T |
A |
4: 141,138,034 (GRCm39) |
L279F |
probably damaging |
Het |
| Cr2 |
T |
C |
1: 194,850,954 (GRCm39) |
T151A |
probably damaging |
Het |
| Creb3l3 |
C |
T |
10: 80,924,447 (GRCm39) |
E236K |
probably damaging |
Het |
| Dcstamp |
T |
A |
15: 39,618,599 (GRCm39) |
V336D |
probably damaging |
Het |
| Dop1a |
T |
G |
9: 86,386,265 (GRCm39) |
F379V |
probably damaging |
Het |
| Esf1 |
T |
C |
2: 139,965,554 (GRCm39) |
K714R |
possibly damaging |
Het |
| Exoc3l4 |
A |
T |
12: 111,388,513 (GRCm39) |
M1L |
possibly damaging |
Het |
| Extl3 |
T |
C |
14: 65,314,121 (GRCm39) |
R354G |
probably benign |
Het |
| Fastkd3 |
T |
C |
13: 68,735,855 (GRCm39) |
L535P |
probably damaging |
Het |
| Gab2 |
A |
G |
7: 96,731,066 (GRCm39) |
T12A |
probably benign |
Het |
| Gm10549 |
C |
A |
18: 33,597,358 (GRCm39) |
|
probably benign |
Het |
| Golga4 |
T |
A |
9: 118,386,438 (GRCm39) |
S1187T |
probably benign |
Het |
| Haus3 |
A |
G |
5: 34,325,140 (GRCm39) |
V173A |
probably benign |
Het |
| Herc2 |
T |
A |
7: 55,784,803 (GRCm39) |
Y1416N |
possibly damaging |
Het |
| Hspg2 |
A |
G |
4: 137,272,016 (GRCm39) |
Y2566C |
probably damaging |
Het |
| Inpp5f |
A |
T |
7: 128,237,884 (GRCm39) |
T34S |
possibly damaging |
Het |
| Iqck |
G |
A |
7: 118,475,485 (GRCm39) |
G70S |
unknown |
Het |
| Jade1 |
T |
C |
3: 41,568,160 (GRCm39) |
F743L |
probably damaging |
Het |
| Kif5a |
T |
C |
10: 127,069,690 (GRCm39) |
K845R |
probably damaging |
Het |
| Klhl30 |
A |
G |
1: 91,285,636 (GRCm39) |
|
probably null |
Het |
| Map2k1 |
T |
C |
9: 64,121,772 (GRCm39) |
D67G |
possibly damaging |
Het |
| Mcm9 |
A |
C |
10: 53,413,777 (GRCm39) |
C434W |
probably damaging |
Het |
| Muc4 |
T |
G |
16: 32,570,853 (GRCm39) |
S638A |
possibly damaging |
Het |
| Nectin3 |
A |
G |
16: 46,284,345 (GRCm39) |
V113A |
probably damaging |
Het |
| Nfya |
T |
C |
17: 48,699,938 (GRCm39) |
|
probably benign |
Het |
| Nup155 |
G |
T |
15: 8,157,922 (GRCm39) |
A460S |
possibly damaging |
Het |
| Nup210 |
T |
C |
6: 91,051,270 (GRCm39) |
E371G |
possibly damaging |
Het |
| Olfm3 |
T |
C |
3: 114,914,632 (GRCm39) |
S228P |
probably damaging |
Het |
| Or52n20 |
C |
A |
7: 104,320,075 (GRCm39) |
D55E |
probably benign |
Het |
| Or8b51 |
A |
T |
9: 38,569,073 (GRCm39) |
I205N |
possibly damaging |
Het |
| Plin1 |
A |
C |
7: 79,371,224 (GRCm39) |
V500G |
probably benign |
Het |
| Ppfia1 |
A |
C |
7: 144,064,049 (GRCm39) |
M513R |
probably benign |
Het |
| Ppp1cb |
T |
A |
5: 32,640,798 (GRCm39) |
C27* |
probably null |
Het |
| Prss22 |
T |
A |
17: 24,215,408 (GRCm39) |
I123F |
probably damaging |
Het |
| Rbm24 |
G |
T |
13: 46,572,549 (GRCm39) |
V15L |
probably damaging |
Het |
| Reln |
T |
C |
5: 22,491,942 (GRCm39) |
T97A |
possibly damaging |
Het |
| Sipa1l2 |
T |
C |
8: 126,180,203 (GRCm39) |
T1065A |
possibly damaging |
Het |
| Sipa1l3 |
A |
C |
7: 29,065,974 (GRCm39) |
|
probably null |
Het |
| Snrnp200 |
T |
A |
2: 127,064,081 (GRCm39) |
Y689* |
probably null |
Het |
| Srcap |
T |
C |
7: 127,129,626 (GRCm39) |
|
probably benign |
Het |
| Sv2a |
T |
C |
3: 96,095,565 (GRCm39) |
|
probably null |
Het |
| Tcf12 |
A |
T |
9: 71,766,211 (GRCm39) |
V474D |
probably damaging |
Het |
| Tpcn2 |
A |
T |
7: 144,815,980 (GRCm39) |
S403T |
probably damaging |
Het |
| Trim65 |
C |
A |
11: 116,017,377 (GRCm39) |
A362S |
probably benign |
Het |
| Trpm8 |
T |
A |
1: 88,282,201 (GRCm39) |
L699Q |
probably damaging |
Het |
| Ube2m |
A |
C |
7: 12,769,797 (GRCm39) |
I116R |
probably damaging |
Het |
| Ulk1 |
T |
C |
5: 110,938,963 (GRCm39) |
K492E |
possibly damaging |
Het |
| Usp40 |
T |
A |
1: 87,925,649 (GRCm39) |
K193N |
probably damaging |
Het |
| Vmn1r3 |
A |
G |
4: 3,185,098 (GRCm39) |
S70P |
possibly damaging |
Het |
| Vmn2r2 |
T |
A |
3: 64,024,074 (GRCm39) |
K836* |
probably null |
Het |
| Vmn2r75 |
T |
A |
7: 85,814,482 (GRCm39) |
H337L |
probably benign |
Het |
| Wars1 |
G |
A |
12: 108,827,309 (GRCm39) |
T437M |
probably benign |
Het |
| Zdhhc5 |
T |
C |
2: 84,520,825 (GRCm39) |
T451A |
probably benign |
Het |
| Zfp788 |
T |
G |
7: 41,297,965 (GRCm39) |
H180Q |
possibly damaging |
Het |
| Zkscan7 |
A |
G |
9: 122,717,782 (GRCm39) |
E59G |
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 |
|
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'- GTAGTGACCATATCAGGGACTC -3'
(R):5'- CCCACAAAGTCCAGGTCATG -3'
Sequencing Primer
(F):5'- GTGACCATATCAGGGACTCATGATC -3'
(R):5'- CAGGTCATGGATGGGCTC -3'
|
| Posted On |
2018-04-02 |
Incidental Mutation