Incidental Mutation 'R5485:Tsen54'
| ID |
432533 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
043046-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.959)
|
| Stock # |
R5485 (G1)
|
| Quality Score |
214 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 115706048 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 90
(E90G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000102090
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021134]
[ENSMUST00000041684]
[ENSMUST00000106481]
[ENSMUST00000136343]
[ENSMUST00000156812]
|
| AlphaFold |
Q8C2A2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021134
AA Change: E90G
PolyPhen 2
Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: E90G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
16 |
30 |
N/A |
INTRINSIC |
|
Pfam:tRNA_int_end_N2
|
63 |
130 |
1.4e-21 |
PFAM |
|
low complexity region
|
196 |
208 |
N/A |
INTRINSIC |
|
low complexity region
|
219 |
232 |
N/A |
INTRINSIC |
|
low complexity region
|
314 |
324 |
N/A |
INTRINSIC |
|
coiled coil region
|
338 |
360 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000041684
|
| SMART Domains |
Protein: ENSMUSP00000041328
Gene: ENSMUSG00000034471
| Domain | Start | End | E-Value | Type |
|---|
|
ANK
|
2 |
32 |
1.27e3 |
SMART |
|
ANK
|
48 |
77 |
3.01e-4 |
SMART |
|
ANK
|
81 |
110 |
3.41e-3 |
SMART |
|
ANK
|
114 |
143 |
1.4e-4 |
SMART |
|
ANK
|
147 |
176 |
3.26e0 |
SMART |
|
ANK
|
188 |
217 |
3.33e-6 |
SMART |
|
ANK
|
220 |
249 |
4.82e-3 |
SMART |
|
SH3
|
284 |
346 |
1.13e-6 |
SMART |
|
SAM
|
485 |
551 |
8.53e-12 |
SMART |
|
SAM
|
554 |
621 |
1.41e-12 |
SMART |
|
low complexity region
|
762 |
774 |
N/A |
INTRINSIC |
|
Pfam:Caskin-Pro-rich
|
793 |
883 |
1.4e-32 |
PFAM |
|
low complexity region
|
904 |
921 |
N/A |
INTRINSIC |
|
low complexity region
|
925 |
944 |
N/A |
INTRINSIC |
|
low complexity region
|
961 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1042 |
1069 |
N/A |
INTRINSIC |
|
low complexity region
|
1084 |
1090 |
N/A |
INTRINSIC |
|
low complexity region
|
1120 |
1132 |
N/A |
INTRINSIC |
|
Pfam:Caskin-tail
|
1144 |
1201 |
4.5e-28 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106481
AA Change: E90G
PolyPhen 2
Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: E90G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
16 |
30 |
N/A |
INTRINSIC |
|
Pfam:tRNA_int_end_N2
|
62 |
132 |
1.9e-23 |
PFAM |
|
low complexity region
|
196 |
208 |
N/A |
INTRINSIC |
|
low complexity region
|
219 |
232 |
N/A |
INTRINSIC |
|
low complexity region
|
314 |
324 |
N/A |
INTRINSIC |
|
coiled coil region
|
338 |
360 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128266
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129765
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000136343
|
| SMART Domains |
Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
63 |
76 |
N/A |
INTRINSIC |
|
low complexity region
|
158 |
168 |
N/A |
INTRINSIC |
|
coiled coil region
|
182 |
204 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141748
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000156812
|
| SMART Domains |
Protein: ENSMUSP00000114310
Gene: ENSMUSG00000034471
| Domain | Start | End | E-Value | Type |
|---|
|
ANK
|
2 |
32 |
1.27e3 |
SMART |
|
ANK
|
48 |
77 |
3.01e-4 |
SMART |
|
ANK
|
81 |
110 |
3.41e-3 |
SMART |
|
| Meta Mutation Damage Score |
0.1689 |
| Coding Region Coverage |
- 1x: 98.2%
- 3x: 97.3%
- 10x: 95.1%
- 20x: 90.6%
|
| Validation Efficiency |
98% (59/60) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700093K21Rik |
A |
T |
11: 23,467,378 (GRCm39) |
V85D |
probably benign |
Het |
| Abcb8 |
A |
G |
5: 24,605,159 (GRCm39) |
N115S |
probably benign |
Het |
| Appl1 |
C |
A |
14: 26,684,823 (GRCm39) |
L75F |
probably damaging |
Het |
| Atp13a5 |
A |
G |
16: 29,100,760 (GRCm39) |
|
probably null |
Het |
| Atp2c2 |
T |
A |
8: 120,479,801 (GRCm39) |
|
probably null |
Het |
| Cfap54 |
T |
A |
10: 92,864,979 (GRCm39) |
I94F |
probably damaging |
Het |
| Clasp1 |
A |
G |
1: 118,395,643 (GRCm39) |
I194V |
possibly damaging |
Het |
| Crebbp |
A |
C |
16: 3,932,777 (GRCm39) |
D1000E |
probably benign |
Het |
| Ctdnep1 |
C |
T |
11: 69,872,316 (GRCm39) |
R3W |
possibly damaging |
Het |
| Dgkb |
T |
C |
12: 38,177,363 (GRCm39) |
V230A |
probably damaging |
Het |
| Duoxa2 |
T |
C |
2: 122,129,633 (GRCm39) |
F38L |
possibly damaging |
Het |
| Ecd |
T |
C |
14: 20,388,273 (GRCm39) |
S172G |
probably benign |
Het |
| Endog |
G |
T |
2: 30,061,663 (GRCm39) |
|
probably benign |
Het |
| Eqtn |
G |
A |
4: 94,813,193 (GRCm39) |
P131L |
possibly damaging |
Het |
| Gabbr1 |
T |
A |
17: 37,367,767 (GRCm39) |
S290T |
possibly damaging |
Het |
| Glt8d2 |
T |
A |
10: 82,487,282 (GRCm39) |
R319S |
possibly damaging |
Het |
| Gm16686 |
A |
G |
4: 88,673,641 (GRCm39) |
|
probably benign |
Het |
| Gm5709 |
A |
T |
3: 59,542,983 (GRCm39) |
|
noncoding transcript |
Het |
| Gm7381 |
T |
C |
8: 3,892,161 (GRCm39) |
|
noncoding transcript |
Het |
| Gorab |
T |
G |
1: 163,213,871 (GRCm39) |
D353A |
possibly damaging |
Het |
| Gstm1 |
A |
G |
3: 107,924,720 (GRCm39) |
L20P |
probably damaging |
Het |
| Hexim2 |
A |
G |
11: 103,029,884 (GRCm39) |
D312G |
probably benign |
Het |
| Hfm1 |
A |
G |
5: 106,995,528 (GRCm39) |
|
probably null |
Het |
| Mbd4 |
C |
A |
6: 115,827,679 (GRCm39) |
A66S |
probably benign |
Het |
| Mmp27 |
T |
A |
9: 7,573,363 (GRCm39) |
W152R |
probably damaging |
Het |
| Mogat1 |
A |
G |
1: 78,500,307 (GRCm39) |
T124A |
probably benign |
Het |
| Mrps18b |
A |
T |
17: 36,225,236 (GRCm39) |
V102D |
probably damaging |
Het |
| Or10g3b |
A |
T |
14: 52,586,776 (GRCm39) |
C242* |
probably null |
Het |
| Peg10 |
T |
A |
6: 4,755,565 (GRCm39) |
M47K |
probably benign |
Het |
| Plxnc1 |
T |
G |
10: 94,758,604 (GRCm39) |
Q364P |
probably benign |
Het |
| Psd |
A |
T |
19: 46,304,528 (GRCm39) |
|
probably null |
Het |
| Rims1 |
T |
G |
1: 22,522,289 (GRCm39) |
I470L |
possibly damaging |
Het |
| Sbsn |
T |
C |
7: 30,452,542 (GRCm39) |
V519A |
possibly damaging |
Het |
| Senp1 |
A |
G |
15: 97,964,377 (GRCm39) |
V279A |
probably benign |
Het |
| Sfxn5 |
T |
A |
6: 85,309,582 (GRCm39) |
|
probably benign |
Het |
| Slc6a13 |
T |
A |
6: 121,313,032 (GRCm39) |
M483K |
probably damaging |
Het |
| Slc6a21 |
G |
A |
7: 44,931,966 (GRCm39) |
|
probably null |
Het |
| Slco6c1 |
T |
C |
1: 97,053,481 (GRCm39) |
Y140C |
probably damaging |
Het |
| Spata32 |
A |
G |
11: 103,100,122 (GRCm39) |
S128P |
probably damaging |
Het |
| Spty2d1 |
G |
T |
7: 46,647,633 (GRCm39) |
T432K |
possibly damaging |
Het |
| Stx8 |
A |
G |
11: 67,911,792 (GRCm39) |
Q170R |
probably benign |
Het |
| Sytl3 |
G |
A |
17: 6,982,879 (GRCm39) |
V112I |
probably benign |
Het |
| Tdrkh |
A |
G |
3: 94,336,019 (GRCm39) |
I420V |
probably benign |
Het |
| Tmem117 |
T |
C |
15: 94,992,711 (GRCm39) |
V457A |
probably benign |
Het |
| Tpk1 |
T |
C |
6: 43,642,746 (GRCm39) |
|
probably benign |
Het |
| Trpc2 |
GTGTCCTA |
GTGTCCTATGTCCTA |
7: 101,744,420 (GRCm39) |
|
probably null |
Het |
| Ugt1a2 |
A |
T |
1: 88,128,968 (GRCm39) |
M204L |
probably damaging |
Het |
| Vmn2r17 |
A |
T |
5: 109,567,972 (GRCm39) |
I32F |
probably benign |
Het |
| Xkr6 |
T |
C |
14: 64,056,833 (GRCm39) |
V248A |
unknown |
Het |
| Zfhx4 |
C |
A |
3: 5,308,067 (GRCm39) |
S431Y |
probably damaging |
Het |
| Zfp318 |
T |
A |
17: 46,723,180 (GRCm39) |
S1728T |
possibly damaging |
Het |
| Zfp563 |
T |
C |
17: 33,308,540 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Tsen54 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01327:Tsen54
|
APN |
11 |
115,712,538 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
PIT4486001:Tsen54
|
UTSW |
11 |
115,713,422 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0179:Tsen54
|
UTSW |
11 |
115,712,856 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0255:Tsen54
|
UTSW |
11 |
115,706,234 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0380:Tsen54
|
UTSW |
11 |
115,713,423 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0619:Tsen54
|
UTSW |
11 |
115,705,890 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0653:Tsen54
|
UTSW |
11 |
115,705,887 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1120:Tsen54
|
UTSW |
11 |
115,705,839 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2109:Tsen54
|
UTSW |
11 |
115,706,549 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2248:Tsen54
|
UTSW |
11 |
115,706,232 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2300:Tsen54
|
UTSW |
11 |
115,712,904 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3081:Tsen54
|
UTSW |
11 |
115,710,990 (GRCm39) |
missense |
probably benign |
0.08 |
|
R3763:Tsen54
|
UTSW |
11 |
115,711,237 (GRCm39) |
missense |
probably benign |
0.22 |
|
R4179:Tsen54
|
UTSW |
11 |
115,711,678 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4521:Tsen54
|
UTSW |
11 |
115,707,932 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4618:Tsen54
|
UTSW |
11 |
115,706,247 (GRCm39) |
unclassified |
probably benign |
|
|
R6111:Tsen54
|
UTSW |
11 |
115,710,956 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R6238:Tsen54
|
UTSW |
11 |
115,711,513 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6459:Tsen54
|
UTSW |
11 |
115,712,506 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6555:Tsen54
|
UTSW |
11 |
115,711,519 (GRCm39) |
missense |
probably benign |
0.43 |
|
R7378:Tsen54
|
UTSW |
11 |
115,712,531 (GRCm39) |
missense |
probably benign |
0.19 |
|
R7520:Tsen54
|
UTSW |
11 |
115,711,797 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7922:Tsen54
|
UTSW |
11 |
115,711,608 (GRCm39) |
nonsense |
probably null |
|
|
R8110:Tsen54
|
UTSW |
11 |
115,705,760 (GRCm39) |
missense |
unknown |
|
|
R8159:Tsen54
|
UTSW |
11 |
115,711,804 (GRCm39) |
nonsense |
probably null |
|
|
R8497:Tsen54
|
UTSW |
11 |
115,713,410 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8529:Tsen54
|
UTSW |
11 |
115,711,386 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R8786:Tsen54
|
UTSW |
11 |
115,711,498 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9365:Tsen54
|
UTSW |
11 |
115,713,410 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9571:Tsen54
|
UTSW |
11 |
115,707,933 (GRCm39) |
critical splice donor site |
probably null |
|
|
X0028:Tsen54
|
UTSW |
11 |
115,707,925 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
Z1176:Tsen54
|
UTSW |
11 |
115,711,404 (GRCm39) |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCTTTATGATCCCGAGGAGC -3'
(R):5'- TACAAAGCCTCTTCGGGGTG -3'
Sequencing Primer
(F):5'- TGTCGCCAAGAGCTGTG -3'
(R):5'- GAAGTCGCTGCCGTCCTTC -3'
|
| Posted On |
2016-10-05 |
Incidental Mutation