Incidental Mutation 'R7520:Tsen54'
| ID |
582638 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
045592-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R7520 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 115711797 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 405
(T405A)
|
| 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: T405A
PolyPhen 2
Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: T405A
| 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 |
possibly damaging
Transcript: ENSMUST00000106481
AA Change: T405A
PolyPhen 2
Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: T405A
| 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 |
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: T249A
PolyPhen 2
Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
AA Change: T249A
| 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 |
probably damaging
Transcript: ENSMUST00000154304
AA Change: T88A
PolyPhen 2
Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: T88A
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
21 |
43 |
N/A |
INTRINSIC |
|
| Predicted Effect |
|
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.6%
|
| Validation Efficiency |
100% (50/50) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl4fm2 |
T |
C |
4: 144,281,859 (GRCm39) |
Y311C |
probably damaging |
Het |
| Abca1 |
A |
T |
4: 53,078,114 (GRCm39) |
I886N |
probably benign |
Het |
| Adamts6 |
A |
G |
13: 104,433,694 (GRCm39) |
H41R |
probably benign |
Het |
| Adck1 |
T |
C |
12: 88,425,975 (GRCm39) |
|
probably null |
Het |
| Atat1 |
G |
T |
17: 36,208,706 (GRCm39) |
T398K |
probably benign |
Het |
| Bahcc1 |
A |
G |
11: 120,167,031 (GRCm39) |
E1144G |
possibly damaging |
Het |
| Cand2 |
G |
T |
6: 115,762,212 (GRCm39) |
E213* |
probably null |
Het |
| Cep350 |
A |
G |
1: 155,791,375 (GRCm39) |
S1250P |
probably benign |
Het |
| Cln3 |
A |
G |
7: 126,180,852 (GRCm39) |
L63P |
probably damaging |
Het |
| Col4a4 |
A |
T |
1: 82,484,808 (GRCm39) |
C486* |
probably null |
Het |
| Ctnnal1 |
A |
T |
4: 56,837,838 (GRCm39) |
M264K |
probably damaging |
Het |
| Ddr2 |
T |
A |
1: 169,812,008 (GRCm39) |
D738V |
probably damaging |
Het |
| Dnah6 |
T |
C |
6: 73,104,887 (GRCm39) |
M1901V |
probably benign |
Het |
| Dnhd1 |
A |
G |
7: 105,345,255 (GRCm39) |
T2200A |
probably benign |
Het |
| Dolk |
A |
G |
2: 30,174,555 (GRCm39) |
Y497H |
probably benign |
Het |
| Drd5 |
T |
C |
5: 38,478,195 (GRCm39) |
V396A |
probably benign |
Het |
| Epsti1 |
A |
T |
14: 78,200,883 (GRCm39) |
|
probably null |
Het |
| Erich3 |
A |
G |
3: 154,468,763 (GRCm39) |
T1072A |
unknown |
Het |
| Ero1a |
A |
T |
14: 45,544,032 (GRCm39) |
N57K |
probably damaging |
Het |
| Exph5 |
T |
C |
9: 53,278,514 (GRCm39) |
|
probably null |
Het |
| Frmd5 |
C |
T |
2: 121,384,745 (GRCm39) |
|
probably null |
Het |
| H2-Q7 |
A |
G |
17: 35,661,686 (GRCm39) |
T310A |
probably benign |
Het |
| Hecw2 |
G |
T |
1: 53,965,215 (GRCm39) |
A537E |
probably benign |
Het |
| Itga4 |
A |
T |
2: 79,131,333 (GRCm39) |
D567V |
probably damaging |
Het |
| Kcnu1 |
A |
T |
8: 26,375,368 (GRCm39) |
N361Y |
probably damaging |
Het |
| Keap1 |
A |
G |
9: 21,144,787 (GRCm39) |
S408P |
probably benign |
Het |
| Mamdc4 |
T |
A |
2: 25,455,360 (GRCm39) |
I928F |
possibly damaging |
Het |
| Mboat4 |
T |
C |
8: 34,591,028 (GRCm39) |
F155S |
probably benign |
Het |
| Mtbp |
A |
G |
15: 55,440,742 (GRCm39) |
|
probably benign |
Het |
| Nmi |
T |
G |
2: 51,842,492 (GRCm39) |
K200T |
probably benign |
Het |
| Or2n1e |
G |
A |
17: 38,586,331 (GRCm39) |
C223Y |
probably benign |
Het |
| Or8g19 |
G |
T |
9: 39,055,414 (GRCm39) |
R6L |
probably benign |
Het |
| Pcdha7 |
G |
A |
18: 37,108,366 (GRCm39) |
V464M |
probably damaging |
Het |
| Peg10 |
T |
A |
6: 4,756,796 (GRCm39) |
N457K |
unknown |
Het |
| Plekha7 |
A |
T |
7: 115,736,519 (GRCm39) |
I944N |
possibly damaging |
Het |
| Plpp1 |
T |
A |
13: 112,937,781 (GRCm39) |
D13E |
possibly damaging |
Het |
| Pnpla6 |
G |
T |
8: 3,587,508 (GRCm39) |
V1070F |
probably damaging |
Het |
| Riox1 |
T |
A |
12: 83,998,545 (GRCm39) |
Y360* |
probably null |
Het |
| Sdhb |
A |
G |
4: 140,693,882 (GRCm39) |
D50G |
possibly damaging |
Het |
| Slc35f2 |
T |
A |
9: 53,708,385 (GRCm39) |
V126D |
possibly damaging |
Het |
| Slmap |
A |
G |
14: 26,148,575 (GRCm39) |
V612A |
probably benign |
Het |
| Snap91 |
T |
A |
9: 86,721,702 (GRCm39) |
I46F |
probably damaging |
Het |
| Sp110 |
G |
A |
1: 85,506,813 (GRCm39) |
R417C |
probably benign |
Het |
| Taar7b |
T |
C |
10: 23,876,381 (GRCm39) |
L182P |
probably damaging |
Het |
| Tmc1 |
T |
A |
19: 20,776,542 (GRCm39) |
M606L |
probably damaging |
Het |
| Trpm8 |
T |
A |
1: 88,271,043 (GRCm39) |
D444E |
probably benign |
Het |
| Ttll5 |
T |
C |
12: 85,946,245 (GRCm39) |
W492R |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,728,123 (GRCm39) |
T5566S |
unknown |
Het |
| Utp20 |
A |
T |
10: 88,654,457 (GRCm39) |
M210K |
probably damaging |
Het |
| Zfand1 |
A |
G |
3: 10,411,009 (GRCm39) |
V115A |
probably 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 |
|
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 |
|
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'- ACAGATGCTGAGTCCTGGTG -3'
(R):5'- CCCACGGAACAGCCTATATAGG -3'
Sequencing Primer
(F):5'- GTCCTGGTGCCAAAAGCTGAAC -3'
(R):5'- GGAACAGCCTATATAGGTCCCAC -3'
|
| Posted On |
2019-10-17 |
Incidental Mutation