Incidental Mutation 'PIT4486001:Tsen54'
| ID |
556120 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.959)
|
| Stock # |
PIT4486001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 115713422 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Phenylalanine
at position 481
(V481F)
|
| 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: V481F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: V481F
| 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: V442F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: V442F
| 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 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 |
probably benign
Transcript: ENSMUST00000154304
|
| SMART Domains |
Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
21 |
43 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000157061
|
| 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: 93.0%
- 3x: 90.5%
- 10x: 84.1%
- 20x: 70.1%
|
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700018F24Rik |
T |
C |
5: 144,980,914 (GRCm39) |
S108P |
probably damaging |
Het |
| Abhd16b |
A |
T |
2: 181,135,752 (GRCm39) |
Q218L |
probably benign |
Het |
| Abhd3 |
T |
A |
18: 10,645,233 (GRCm39) |
I354F |
probably benign |
Het |
| Abt1 |
T |
C |
13: 23,607,851 (GRCm39) |
Y51C |
possibly damaging |
Het |
| Actl9 |
T |
A |
17: 33,653,172 (GRCm39) |
Y411N |
possibly damaging |
Het |
| Ano4 |
A |
G |
10: 88,828,891 (GRCm39) |
V516A |
probably damaging |
Het |
| Bptf |
A |
T |
11: 106,945,614 (GRCm39) |
S2542T |
probably damaging |
Het |
| Card11 |
C |
T |
5: 140,862,163 (GRCm39) |
V1045M |
probably damaging |
Het |
| Ccdc121 |
T |
A |
5: 31,645,087 (GRCm39) |
I280K |
probably damaging |
Het |
| Cd300ld2 |
CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG |
CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG |
11: 114,903,257 (GRCm39) |
|
probably benign |
Het |
| Cdh3 |
A |
G |
8: 107,268,122 (GRCm39) |
K386E |
possibly damaging |
Het |
| Cks1b |
C |
A |
3: 89,323,621 (GRCm39) |
Q49H |
probably damaging |
Het |
| Clpb |
A |
T |
7: 101,313,139 (GRCm39) |
D41V |
probably benign |
Het |
| Cyp3a11 |
A |
T |
5: 145,797,302 (GRCm39) |
M359K |
probably damaging |
Het |
| Cyp3a13 |
A |
T |
5: 137,908,228 (GRCm39) |
I207N |
probably benign |
Het |
| Dennd4c |
T |
A |
4: 86,717,701 (GRCm39) |
L566* |
probably null |
Het |
| Dhtkd1 |
A |
T |
2: 5,904,806 (GRCm39) |
D859E |
probably benign |
Het |
| Efcab6 |
T |
C |
15: 83,857,514 (GRCm39) |
D295G |
probably benign |
Het |
| Fcgbp |
A |
G |
7: 27,774,698 (GRCm39) |
T91A |
possibly damaging |
Het |
| Gm11569 |
GCAGCTGGGCCTGCAGCAGCTGGAAATGCAGCAGCTAGGACGGCAACA |
GCA |
11: 99,689,491 (GRCm39) |
|
probably benign |
Het |
| Gsdma3 |
A |
G |
11: 98,528,880 (GRCm39) |
K454E |
unknown |
Het |
| Herc1 |
T |
A |
9: 66,279,671 (GRCm39) |
I193N |
probably damaging |
Het |
| Kdm5b |
T |
A |
1: 134,556,423 (GRCm39) |
L1370Q |
probably damaging |
Het |
| Lrrc37 |
A |
T |
11: 103,509,027 (GRCm39) |
H980Q |
unknown |
Het |
| Map4 |
T |
G |
9: 109,901,682 (GRCm39) |
V965G |
probably damaging |
Het |
| Mkrn2os |
T |
C |
6: 115,562,444 (GRCm39) |
D173G |
probably benign |
Het |
| Ndfip2 |
A |
G |
14: 105,532,300 (GRCm39) |
D232G |
probably damaging |
Het |
| Nipal2 |
C |
T |
15: 34,584,875 (GRCm39) |
G231D |
probably damaging |
Het |
| Notch3 |
A |
T |
17: 32,373,737 (GRCm39) |
N490K |
probably damaging |
Het |
| Or5p68 |
A |
G |
7: 107,945,529 (GRCm39) |
S220P |
possibly damaging |
Het |
| Or8g50 |
T |
A |
9: 39,648,535 (GRCm39) |
C141* |
probably null |
Het |
| Prkar2a |
T |
C |
9: 108,610,326 (GRCm39) |
L185S |
probably damaging |
Het |
| Ptpn9 |
T |
G |
9: 56,968,287 (GRCm39) |
N542K |
probably damaging |
Het |
| Pus10 |
G |
A |
11: 23,662,326 (GRCm39) |
|
probably null |
Het |
| Pyroxd2 |
A |
G |
19: 42,728,828 (GRCm39) |
S191P |
probably benign |
Het |
| Rab15 |
T |
A |
12: 76,848,716 (GRCm39) |
K122* |
probably null |
Het |
| Rara |
A |
G |
11: 98,864,321 (GRCm39) |
N416S |
possibly damaging |
Het |
| Rims2 |
T |
C |
15: 39,339,916 (GRCm39) |
V870A |
possibly damaging |
Het |
| Sec16a |
T |
C |
2: 26,315,785 (GRCm39) |
T293A |
|
Het |
| Slc26a3 |
G |
A |
12: 31,520,949 (GRCm39) |
D718N |
probably benign |
Het |
| Slc44a5 |
G |
A |
3: 153,964,659 (GRCm39) |
V520I |
possibly damaging |
Het |
| Spata31e2 |
G |
A |
1: 26,724,410 (GRCm39) |
P257S |
probably damaging |
Het |
| Tgfb2 |
A |
T |
1: 186,422,924 (GRCm39) |
Y142N |
probably benign |
Het |
| Tgfbi |
A |
T |
13: 56,777,607 (GRCm39) |
I364F |
probably damaging |
Het |
| Tmem144 |
A |
C |
3: 79,734,174 (GRCm39) |
D176E |
probably benign |
Het |
| Tns4 |
A |
T |
11: 98,962,161 (GRCm39) |
L612Q |
probably damaging |
Het |
| Toe1 |
A |
G |
4: 116,663,692 (GRCm39) |
L76S |
probably damaging |
Het |
| Trank1 |
T |
C |
9: 111,219,175 (GRCm39) |
F1971L |
probably damaging |
Het |
| Uimc1 |
A |
G |
13: 55,223,381 (GRCm39) |
L297P |
probably damaging |
Het |
| Wnt8a |
T |
C |
18: 34,680,636 (GRCm39) |
Y334H |
probably damaging |
Het |
| Zfp281 |
A |
G |
1: 136,554,741 (GRCm39) |
D573G |
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 |
|
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 |
|
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'- TCTACTCTGGGCTCTCCTGAAG -3'
(R):5'- TCCAGGTGAGTCCTATATGAGAGAC -3'
Sequencing Primer
(F):5'- GGGCTCTCCTGAAGCACTCATC -3'
(R):5'- TCCTATATGAGAGACAGCTGGCAC -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation