Incidental Mutation 'R6459:Tsen54'
| ID |
517530 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
044594-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R6459 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115712506 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 269
(V269A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000120506
(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: V425A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: V425A
| 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 damaging
Transcript: ENSMUST00000106481
AA Change: V425A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: V425A
| 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 damaging
Transcript: ENSMUST00000136343
AA Change: V269A
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
AA Change: V269A
| 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 damaging
Transcript: ENSMUST00000154304
AA Change: V108A
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: V108A
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
21 |
43 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000157061
AA Change: V62A
|
| 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: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 93.6%
|
| Validation Efficiency |
98% (52/53) |
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abr |
C |
A |
11: 76,315,815 (GRCm39) |
R583L |
probably damaging |
Het |
| Acss1 |
A |
G |
2: 150,509,840 (GRCm39) |
I93T |
probably damaging |
Het |
| Ank3 |
C |
T |
10: 69,827,577 (GRCm39) |
|
probably benign |
Het |
| Aoah |
A |
G |
13: 21,184,112 (GRCm39) |
Y392C |
probably damaging |
Het |
| Atl3 |
A |
T |
19: 7,498,163 (GRCm39) |
E186D |
probably benign |
Het |
| Atp4a |
A |
G |
7: 30,411,887 (GRCm39) |
K41E |
probably benign |
Het |
| Atp9a |
G |
A |
2: 168,509,933 (GRCm39) |
P500L |
probably damaging |
Het |
| Ccdc88b |
A |
T |
19: 6,832,246 (GRCm39) |
V363D |
possibly damaging |
Het |
| Cftr |
T |
C |
6: 18,258,235 (GRCm39) |
V532A |
probably damaging |
Het |
| Cldn13 |
T |
C |
5: 134,943,769 (GRCm39) |
T139A |
possibly damaging |
Het |
| Cnksr3 |
T |
C |
10: 7,076,820 (GRCm39) |
Y124C |
probably benign |
Het |
| Cyb5r2 |
T |
C |
7: 107,352,462 (GRCm39) |
K161E |
possibly damaging |
Het |
| Epop |
T |
C |
11: 97,519,333 (GRCm39) |
S259G |
possibly damaging |
Het |
| Fhl2 |
G |
A |
1: 43,162,813 (GRCm39) |
T234I |
possibly damaging |
Het |
| Fnip2 |
T |
C |
3: 79,388,941 (GRCm39) |
T567A |
possibly damaging |
Het |
| Frmd4b |
A |
G |
6: 97,464,601 (GRCm39) |
C39R |
probably damaging |
Het |
| Grhl3 |
T |
C |
4: 135,284,744 (GRCm39) |
N116S |
possibly damaging |
Het |
| Igkv14-111 |
A |
T |
6: 68,233,725 (GRCm39) |
R75S |
probably benign |
Het |
| Il16 |
A |
T |
7: 83,371,529 (GRCm39) |
D92E |
probably damaging |
Het |
| Il16 |
C |
A |
7: 83,371,536 (GRCm39) |
G90V |
probably damaging |
Het |
| Ipo11 |
T |
C |
13: 107,002,277 (GRCm39) |
|
probably null |
Het |
| Kng2 |
A |
G |
16: 22,830,865 (GRCm39) |
I148T |
probably damaging |
Het |
| Lrrc41 |
T |
C |
4: 115,945,977 (GRCm39) |
S231P |
possibly damaging |
Het |
| Maneal |
C |
T |
4: 124,750,635 (GRCm39) |
V374I |
possibly damaging |
Het |
| Mgat4c |
T |
A |
10: 102,220,988 (GRCm39) |
L90Q |
probably damaging |
Het |
| Mrps28 |
A |
G |
3: 8,965,040 (GRCm39) |
|
probably null |
Het |
| Ncapd3 |
A |
G |
9: 26,963,051 (GRCm39) |
D452G |
probably benign |
Het |
| Nefh |
T |
C |
11: 4,889,551 (GRCm39) |
T1023A |
unknown |
Het |
| Nipa1 |
A |
G |
7: 55,629,354 (GRCm39) |
V253A |
probably benign |
Het |
| Or5ac17 |
C |
T |
16: 59,036,383 (GRCm39) |
V198M |
probably benign |
Het |
| Or5b97 |
G |
T |
19: 12,878,369 (GRCm39) |
F258L |
possibly damaging |
Het |
| Or5m11 |
G |
T |
2: 85,781,862 (GRCm39) |
G152C |
probably damaging |
Het |
| Or8d23 |
A |
G |
9: 38,841,961 (GRCm39) |
S165G |
probably benign |
Het |
| Or8k41 |
T |
A |
2: 86,313,573 (GRCm39) |
H171L |
probably benign |
Het |
| Pak1 |
A |
G |
7: 97,557,088 (GRCm39) |
D495G |
probably benign |
Het |
| Pcm1 |
G |
A |
8: 41,714,073 (GRCm39) |
R213H |
probably damaging |
Het |
| Prg4 |
T |
C |
1: 150,330,052 (GRCm39) |
|
probably benign |
Het |
| Proser1 |
C |
T |
3: 53,385,750 (GRCm39) |
T544M |
possibly damaging |
Het |
| Rftn1 |
T |
C |
17: 50,354,334 (GRCm39) |
M343V |
probably benign |
Het |
| Ryr1 |
T |
C |
7: 28,715,079 (GRCm39) |
I4656V |
probably benign |
Het |
| Scg2 |
T |
A |
1: 79,414,007 (GRCm39) |
N239Y |
probably damaging |
Het |
| Sec16a |
C |
A |
2: 26,313,512 (GRCm39) |
M1949I |
probably benign |
Het |
| Sipa1l2 |
A |
G |
8: 126,171,223 (GRCm39) |
|
probably null |
Het |
| Slc10a2 |
A |
C |
8: 5,148,581 (GRCm39) |
|
probably null |
Het |
| Slc25a16 |
C |
T |
10: 62,773,256 (GRCm39) |
Q164* |
probably null |
Het |
| Specc1l |
T |
C |
10: 75,082,001 (GRCm39) |
Y483H |
probably damaging |
Het |
| Ston1 |
T |
C |
17: 88,943,896 (GRCm39) |
V434A |
probably benign |
Het |
| Tarbp2 |
A |
G |
15: 102,426,914 (GRCm39) |
|
probably benign |
Het |
| Trappc8 |
C |
T |
18: 20,969,925 (GRCm39) |
V1022M |
probably benign |
Het |
| Vps13a |
A |
T |
19: 16,641,382 (GRCm39) |
M78K |
possibly damaging |
Het |
| Vwa5b2 |
A |
G |
16: 20,413,429 (GRCm39) |
T215A |
probably damaging |
Het |
| Zc3h7a |
A |
G |
16: 10,971,025 (GRCm39) |
Y335H |
probably damaging |
Het |
| Zfp994 |
T |
A |
17: 22,419,527 (GRCm39) |
Q474L |
possibly damaging |
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 |
|
|
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 |
|
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'- GACGCAGAACTCTGTAAGGC -3'
(R):5'- GCACTGGGAGCTAAGTATATAGGC -3'
Sequencing Primer
(F):5'- CTCTGTAAGGCATCATAGGAACATG -3'
(R):5'- CTAAGTATATAGGCAGGTGTCCC -3'
|
| Posted On |
2018-05-21 |
Incidental Mutation