Incidental Mutation 'R8497:Tsen54'
| ID |
658331 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
067939-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R8497 (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 115713410 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 438
(F438L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000102090
(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: F477L
PolyPhen 2
Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: F477L
| 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: F438L
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: F438L
| 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
AA Change: V153A
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: V153A
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.8%
|
| Validation Efficiency |
100% (51/51) |
| 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 |
|---|
| A1cf |
C |
T |
19: 31,923,250 (GRCm39) |
H509Y |
probably benign |
Het |
| Afm |
A |
T |
5: 90,699,202 (GRCm39) |
|
probably null |
Het |
| Apc |
G |
A |
18: 34,446,083 (GRCm39) |
C975Y |
possibly damaging |
Het |
| Ash1l |
G |
T |
3: 88,914,951 (GRCm39) |
M1860I |
probably benign |
Het |
| Bdkrb1 |
C |
T |
12: 105,570,463 (GRCm39) |
Q10* |
probably null |
Het |
| Bphl |
A |
G |
13: 34,221,706 (GRCm39) |
K21E |
possibly damaging |
Het |
| Cadps2 |
T |
C |
6: 23,355,918 (GRCm39) |
N837D |
probably benign |
Het |
| Cat |
C |
G |
2: 103,287,221 (GRCm39) |
A470P |
probably damaging |
Het |
| Cdc34 |
G |
T |
10: 79,520,845 (GRCm39) |
D11Y |
probably damaging |
Het |
| Cep290 |
A |
G |
10: 100,387,320 (GRCm39) |
E1936G |
probably damaging |
Het |
| Cnot6 |
A |
T |
11: 49,566,191 (GRCm39) |
N501K |
possibly damaging |
Het |
| Cyth3 |
A |
C |
5: 143,678,328 (GRCm39) |
D44A |
probably benign |
Het |
| Dchs1 |
C |
T |
7: 105,408,168 (GRCm39) |
G1888D |
probably damaging |
Het |
| Ffar1 |
T |
G |
7: 30,560,334 (GRCm39) |
I188L |
probably benign |
Het |
| Fhip1b |
G |
T |
7: 105,030,396 (GRCm39) |
D820E |
probably damaging |
Het |
| Gpr17 |
A |
G |
18: 32,080,173 (GRCm39) |
Y297H |
probably damaging |
Het |
| H2-M10.5 |
A |
C |
17: 37,084,729 (GRCm39) |
E151A |
probably damaging |
Het |
| Hmcn1 |
C |
T |
1: 150,455,990 (GRCm39) |
R5310K |
probably benign |
Het |
| Hmcn2 |
T |
C |
2: 31,313,357 (GRCm39) |
L3522P |
possibly damaging |
Het |
| Hs2st1 |
T |
G |
3: 144,140,452 (GRCm39) |
T290P |
probably damaging |
Het |
| Il5ra |
G |
A |
6: 106,715,066 (GRCm39) |
L231F |
probably benign |
Het |
| Itgav |
T |
A |
2: 83,615,805 (GRCm39) |
C529S |
probably damaging |
Het |
| Itprid1 |
A |
T |
6: 55,875,179 (GRCm39) |
R376S |
probably benign |
Het |
| Lrrcc1 |
A |
G |
3: 14,605,044 (GRCm39) |
D138G |
possibly damaging |
Het |
| Mat1a |
C |
T |
14: 40,843,851 (GRCm39) |
R357W |
probably damaging |
Het |
| Mmp1a |
TG |
TGG |
9: 7,465,083 (GRCm38) |
|
probably null |
Het |
| Mtss2 |
T |
C |
8: 111,465,222 (GRCm39) |
V492A |
possibly damaging |
Het |
| Nalcn |
A |
G |
14: 123,752,771 (GRCm39) |
V330A |
probably damaging |
Het |
| Neu3 |
A |
T |
7: 99,472,342 (GRCm39) |
|
probably null |
Het |
| Nfx1 |
A |
G |
4: 40,976,968 (GRCm39) |
D214G |
possibly damaging |
Het |
| Or2a14 |
T |
C |
6: 43,130,818 (GRCm39) |
L193P |
probably damaging |
Het |
| Or2y17 |
G |
A |
11: 49,231,721 (GRCm39) |
D121N |
probably damaging |
Het |
| Or4f14 |
T |
A |
2: 111,742,964 (GRCm39) |
I104F |
possibly damaging |
Het |
| Or5b104 |
T |
C |
19: 13,072,707 (GRCm39) |
T102A |
probably benign |
Het |
| Pcdhb14 |
A |
T |
18: 37,582,349 (GRCm39) |
H485L |
probably benign |
Het |
| Pdss2 |
A |
C |
10: 43,289,521 (GRCm39) |
K342T |
possibly damaging |
Het |
| Ppargc1a |
A |
G |
5: 51,647,570 (GRCm39) |
S254P |
probably damaging |
Het |
| Prelid1 |
A |
G |
13: 55,470,833 (GRCm39) |
D87G |
probably damaging |
Het |
| Prkg1 |
C |
A |
19: 31,279,709 (GRCm39) |
C190F |
probably damaging |
Het |
| Psmb5 |
A |
G |
14: 54,851,837 (GRCm39) |
S116P |
possibly damaging |
Het |
| Rassf6 |
A |
G |
5: 90,779,391 (GRCm39) |
V14A |
possibly damaging |
Het |
| Ripk1 |
T |
C |
13: 34,211,934 (GRCm39) |
S415P |
probably damaging |
Het |
| Rnft1 |
A |
T |
11: 86,386,132 (GRCm39) |
K344* |
probably null |
Het |
| Sacs |
G |
A |
14: 61,429,702 (GRCm39) |
R587Q |
probably benign |
Het |
| Skp2 |
A |
T |
15: 9,127,971 (GRCm39) |
|
probably null |
Het |
| Spata31d1a |
T |
C |
13: 59,848,988 (GRCm39) |
K1047E |
possibly damaging |
Het |
| Spopfm2 |
T |
A |
3: 94,083,119 (GRCm39) |
I231F |
possibly damaging |
Het |
| Szt2 |
G |
A |
4: 118,245,518 (GRCm39) |
T1098I |
possibly damaging |
Het |
| Tcf20 |
A |
G |
15: 82,740,152 (GRCm39) |
M433T |
probably benign |
Het |
| Utp23 |
C |
T |
15: 51,745,614 (GRCm39) |
T144I |
probably damaging |
Het |
| Vmn2r105 |
T |
C |
17: 20,455,134 (GRCm39) |
M1V |
probably null |
Het |
| Wdfy4 |
C |
T |
14: 32,688,356 (GRCm39) |
V2926M |
probably damaging |
Het |
| Zfp407 |
T |
C |
18: 84,578,021 (GRCm39) |
K1031E |
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 |
|
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 |
|
|
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'- CCAGGTGAGTCCTATATGAGAGAC -3'
Sequencing Primer
(F):5'- GGGCTCTCCTGAAGCACTCATC -3'
(R):5'- TCCTATATGAGAGACAGCTGGCAC -3'
|
| Posted On |
2021-01-18 |
Incidental Mutation