Incidental Mutation 'R1120:Tsen54'
ID |
95534 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Tsen54
|
Ensembl Gene |
ENSMUSG00000020781 |
Gene Name |
tRNA splicing endonuclease subunit 54 |
Synonyms |
0610034P02Rik |
MMRRC Submission |
039193-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.959)
|
Stock # |
R1120 (G1)
|
Quality Score |
92 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 115705839 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Alanine to Valine
at position 52
(A52V)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000102090
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021134]
[ENSMUST00000041684]
[ENSMUST00000106481]
[ENSMUST00000136343]
[ENSMUST00000156812]
|
AlphaFold |
Q8C2A2 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000021134
AA Change: A52V
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000021134 Gene: ENSMUSG00000020781 AA Change: A52V
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 damaging
Transcript: ENSMUST00000106481
AA Change: A52V
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000102090 Gene: ENSMUSG00000020781 AA Change: A52V
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 |
0.0790 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
Validation Efficiency |
100% (40/40) |
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: 40 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb8 |
T |
G |
5: 24,613,818 (GRCm39) |
|
probably null |
Het |
Akp3 |
A |
T |
1: 87,053,159 (GRCm39) |
Q77L |
probably damaging |
Het |
Blm |
A |
G |
7: 80,131,214 (GRCm39) |
L878S |
probably damaging |
Het |
Cabin1 |
A |
G |
10: 75,561,550 (GRCm39) |
Y984H |
probably damaging |
Het |
Cadps2 |
T |
C |
6: 23,838,793 (GRCm39) |
Q86R |
probably damaging |
Het |
Cd2 |
C |
T |
3: 101,194,804 (GRCm39) |
D95N |
probably damaging |
Het |
Cd36 |
A |
G |
5: 17,990,826 (GRCm39) |
I438T |
possibly damaging |
Het |
Crhbp |
G |
T |
13: 95,578,593 (GRCm39) |
T176K |
probably benign |
Het |
D630045J12Rik |
G |
T |
6: 38,171,705 (GRCm39) |
T821K |
probably damaging |
Het |
Disp1 |
T |
C |
1: 182,880,139 (GRCm39) |
D288G |
probably benign |
Het |
Dsc3 |
A |
G |
18: 20,120,034 (GRCm39) |
V208A |
probably benign |
Het |
Eef1e1 |
A |
T |
13: 38,842,910 (GRCm39) |
N20K |
probably damaging |
Het |
Ercc5 |
A |
G |
1: 44,201,001 (GRCm39) |
D187G |
probably damaging |
Het |
Etl4 |
T |
A |
2: 20,811,514 (GRCm39) |
M1199K |
probably benign |
Het |
Fnbp1 |
A |
T |
2: 30,926,606 (GRCm39) |
Y433N |
probably damaging |
Het |
Fxyd3 |
A |
G |
7: 30,770,803 (GRCm39) |
|
probably benign |
Het |
Hfm1 |
A |
T |
5: 107,052,084 (GRCm39) |
|
probably benign |
Het |
Irak2 |
T |
A |
6: 113,652,720 (GRCm39) |
|
probably benign |
Het |
Jpt2 |
T |
C |
17: 25,179,585 (GRCm39) |
M1V |
probably null |
Het |
Knl1 |
A |
G |
2: 118,892,856 (GRCm39) |
R51G |
probably damaging |
Het |
Krtap8-1 |
A |
G |
16: 89,284,753 (GRCm39) |
Y15H |
probably benign |
Het |
Lrba |
A |
T |
3: 86,202,499 (GRCm39) |
D250V |
probably damaging |
Het |
Mgat4a |
A |
G |
1: 37,491,662 (GRCm39) |
S357P |
probably damaging |
Het |
Nup98 |
T |
A |
7: 101,809,923 (GRCm39) |
T536S |
probably damaging |
Het |
Or4a27 |
A |
G |
2: 88,559,281 (GRCm39) |
Y221H |
probably damaging |
Het |
Or4c109 |
A |
G |
2: 88,818,423 (GRCm39) |
M41T |
possibly damaging |
Het |
Or9k2 |
A |
G |
10: 129,998,406 (GRCm39) |
L263P |
probably damaging |
Het |
Parp14 |
G |
A |
16: 35,677,130 (GRCm39) |
A946V |
probably benign |
Het |
Pnpla8 |
A |
G |
12: 44,351,730 (GRCm39) |
T568A |
possibly damaging |
Het |
Ptprn |
A |
G |
1: 75,234,825 (GRCm39) |
I254T |
probably benign |
Het |
Rab5b |
A |
C |
10: 128,515,483 (GRCm39) |
N188K |
probably benign |
Het |
Samd5 |
A |
G |
10: 9,504,792 (GRCm39) |
V154A |
possibly damaging |
Het |
Smarcb1 |
A |
G |
10: 75,757,157 (GRCm39) |
F25L |
probably benign |
Het |
Smchd1 |
A |
T |
17: 71,665,141 (GRCm39) |
Y1847* |
probably null |
Het |
Smpd4 |
T |
C |
16: 17,456,350 (GRCm39) |
|
probably benign |
Het |
Tex14 |
T |
A |
11: 87,429,502 (GRCm39) |
|
probably benign |
Het |
Tnfrsf26 |
G |
A |
7: 143,171,651 (GRCm39) |
R101C |
probably damaging |
Het |
Trmu |
A |
G |
15: 85,774,486 (GRCm39) |
K37E |
possibly damaging |
Het |
Ubb |
T |
C |
11: 62,443,009 (GRCm39) |
I13T |
possibly damaging |
Het |
Vmn2r101 |
A |
T |
17: 19,797,723 (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 |
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 |
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'- ACATCTGGAAACCTGCACATCGAG -3'
(R):5'- TGTCACAAAGCAGCTAAGCGGAC -3'
Sequencing Primer
(F):5'- CTTTATGATCCCGAGGAGCGAG -3'
(R):5'- CCACAAAGCCCTCTTCTGG -3'
|
Posted On |
2014-01-05 |