Incidental Mutation 'R2300:Tsen54'
| ID |
245307 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
040299-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.959)
|
| Stock # |
R2300 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 115712904 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Cysteine
at position 464
(S464C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021134
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021134]
[ENSMUST00000103032]
[ENSMUST00000106481]
[ENSMUST00000133250]
[ENSMUST00000136343]
[ENSMUST00000154304]
[ENSMUST00000177736]
|
| AlphaFold |
Q8C2A2 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021134
AA Change: S464C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: S464C
| 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: ENSMUST00000103032
|
| SMART Domains |
Protein: ENSMUSP00000099321
Gene: ENSMUSG00000020782
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
24 |
60 |
9.17e1 |
SMART |
|
WD40
|
62 |
101 |
7.96e0 |
SMART |
|
Blast:WD40
|
112 |
157 |
6e-20 |
BLAST |
|
WD40
|
181 |
217 |
3.96e1 |
SMART |
|
WD40
|
221 |
258 |
5.7e1 |
SMART |
|
Pfam:LLGL
|
268 |
372 |
3.2e-47 |
PFAM |
|
WD40
|
411 |
451 |
1.38e0 |
SMART |
|
Blast:WD40
|
489 |
532 |
3e-12 |
BLAST |
|
low complexity region
|
536 |
547 |
N/A |
INTRINSIC |
|
Blast:WD40
|
576 |
615 |
2e-10 |
BLAST |
|
low complexity region
|
649 |
668 |
N/A |
INTRINSIC |
|
Blast:WD40
|
830 |
879 |
2e-10 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106481
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
| 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 |
probably benign
Transcript: ENSMUST00000133250
|
| SMART Domains |
Protein: ENSMUSP00000118344
Gene: ENSMUSG00000020782
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:WD40
|
13 |
60 |
2e-20 |
BLAST |
|
SCOP:d1gxra_
|
19 |
118 |
5e-8 |
SMART |
|
Blast:WD40
|
62 |
101 |
4e-22 |
BLAST |
|
Blast:WD40
|
112 |
146 |
1e-15 |
BLAST |
|
| 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 |
possibly damaging
Transcript: ENSMUST00000154304
AA Change: S147C
PolyPhen 2
Score 0.949 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: S147C
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
21 |
43 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000157061
AA Change: S101C
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177736
|
| SMART Domains |
Protein: ENSMUSP00000136054
Gene: ENSMUSG00000020782
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
24 |
60 |
5.9e-1 |
SMART |
|
WD40
|
62 |
101 |
5.2e-2 |
SMART |
|
Blast:WD40
|
112 |
157 |
6e-20 |
BLAST |
|
WD40
|
181 |
217 |
2.5e-1 |
SMART |
|
WD40
|
221 |
258 |
3.6e-1 |
SMART |
|
Pfam:LLGL
|
271 |
372 |
6.2e-41 |
PFAM |
|
WD40
|
411 |
451 |
8.8e-3 |
SMART |
|
Blast:WD40
|
489 |
532 |
3e-12 |
BLAST |
|
low complexity region
|
536 |
547 |
N/A |
INTRINSIC |
|
Blast:WD40
|
576 |
615 |
2e-10 |
BLAST |
|
low complexity region
|
649 |
668 |
N/A |
INTRINSIC |
|
Blast:WD40
|
854 |
903 |
2e-10 |
BLAST |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.5%
|
| Validation Efficiency |
|
| 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: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrl1 |
G |
T |
8: 84,656,746 (GRCm39) |
E355* |
probably null |
Het |
| Aldh6a1 |
G |
T |
12: 84,486,303 (GRCm39) |
T205N |
probably damaging |
Het |
| Arhgap24 |
A |
G |
5: 103,008,291 (GRCm39) |
I71V |
probably damaging |
Het |
| Arid2 |
A |
T |
15: 96,299,887 (GRCm39) |
E1800V |
probably damaging |
Het |
| Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
| Cd53 |
T |
C |
3: 106,670,572 (GRCm39) |
T154A |
probably benign |
Het |
| Chd7 |
G |
A |
4: 8,855,241 (GRCm39) |
A2157T |
probably benign |
Het |
| Clca4b |
A |
T |
3: 144,622,432 (GRCm39) |
N544K |
probably benign |
Het |
| Cntrl |
A |
G |
2: 35,017,525 (GRCm39) |
E444G |
probably benign |
Het |
| Crygs |
C |
T |
16: 22,624,301 (GRCm39) |
G102D |
possibly damaging |
Het |
| Gabrr1 |
A |
G |
4: 33,152,449 (GRCm39) |
K130E |
probably benign |
Het |
| H3f3a |
C |
T |
1: 180,630,703 (GRCm39) |
R117H |
probably benign |
Het |
| Jag1 |
T |
C |
2: 136,938,235 (GRCm39) |
Y255C |
probably damaging |
Het |
| Kif11 |
A |
G |
19: 37,399,987 (GRCm39) |
T825A |
probably benign |
Het |
| Lama4 |
T |
A |
10: 38,963,316 (GRCm39) |
M1296K |
probably benign |
Het |
| Lrp1 |
G |
T |
10: 127,392,784 (GRCm39) |
C2760* |
probably null |
Het |
| Mrc2 |
G |
A |
11: 105,239,257 (GRCm39) |
|
probably null |
Het |
| Nolc1 |
CAG |
CAGAAG |
19: 46,069,798 (GRCm39) |
|
probably benign |
Het |
| Nolc1 |
CAG |
CAGTAG |
19: 46,069,807 (GRCm39) |
|
probably benign |
Het |
| Nop16 |
A |
G |
13: 54,733,679 (GRCm39) |
|
probably null |
Het |
| Or2n1 |
T |
A |
17: 38,486,441 (GRCm39) |
Y155* |
probably null |
Het |
| Or5ak22 |
T |
C |
2: 85,230,476 (GRCm39) |
I134V |
probably benign |
Het |
| Ostf1 |
T |
C |
19: 18,558,644 (GRCm39) |
D213G |
probably damaging |
Het |
| Slc28a2 |
C |
T |
2: 122,272,259 (GRCm39) |
Q34* |
probably null |
Het |
| St18 |
A |
G |
1: 6,925,626 (GRCm39) |
D928G |
probably damaging |
Het |
| Stag1 |
T |
C |
9: 100,594,553 (GRCm39) |
V31A |
possibly damaging |
Het |
| Tcl1b1 |
G |
A |
12: 105,130,783 (GRCm39) |
A89T |
probably benign |
Het |
| Ttn |
A |
G |
2: 76,737,792 (GRCm39) |
F4249S |
probably benign |
Het |
| Xdh |
A |
G |
17: 74,198,260 (GRCm39) |
F1209S |
probably damaging |
Het |
| Ylpm1 |
G |
A |
12: 85,107,093 (GRCm39) |
|
probably null |
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 |
|
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 |
|
|
R5485:Tsen54
|
UTSW |
11 |
115,706,048 (GRCm39) |
missense |
probably benign |
0.15 |
|
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'- CCCTGTGACACTGCTTTGTAG -3'
(R):5'- GCCCAGGACTTAGGTGAAAG -3'
Sequencing Primer
(F):5'- GGAGAGGAGAGTCCTTATCTT -3'
(R):5'- GATCTTGGGTTCCCATGGCAC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation