Incidental Mutation 'R3763:Tsen54'
| ID |
270603 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tsen54
|
| Ensembl Gene |
ENSMUSG00000020781 |
| Gene Name |
tRNA splicing endonuclease subunit 54 |
| Synonyms |
0610034P02Rik |
| MMRRC Submission |
040873-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R3763 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
115705550-115713920 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 115711237 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 62
(N62S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000120506
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021134]
[ENSMUST00000103032]
[ENSMUST00000106481]
[ENSMUST00000133250]
[ENSMUST00000136343]
[ENSMUST00000177736]
[ENSMUST00000154304]
|
| AlphaFold |
Q8C2A2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021134
AA Change: N218S
PolyPhen 2
Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: N218S
| 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 benign
Transcript: ENSMUST00000106481
AA Change: N218S
PolyPhen 2
Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: N218S
| 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: 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
AA Change: N62S
PolyPhen 2
Score 0.220 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
AA Change: N62S
| 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: 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 |
|
| 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
|
| Meta Mutation Damage Score |
0.0579 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.5%
|
| Validation Efficiency |
100% (37/37) |
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acvr2a |
A |
G |
2: 48,760,331 (GRCm39) |
E29G |
possibly damaging |
Het |
| Aff3 |
A |
G |
1: 38,291,770 (GRCm39) |
|
probably benign |
Het |
| AW146154 |
A |
G |
7: 41,129,794 (GRCm39) |
C441R |
probably damaging |
Het |
| Cacna1a |
T |
C |
8: 85,310,271 (GRCm39) |
V1443A |
possibly damaging |
Het |
| Commd1 |
T |
A |
11: 22,924,102 (GRCm39) |
F292Y |
probably benign |
Het |
| Ct45a |
C |
T |
X: 55,590,568 (GRCm39) |
V78I |
probably benign |
Het |
| Ddx18 |
A |
G |
1: 121,489,106 (GRCm39) |
Y314H |
probably damaging |
Het |
| Dna2 |
C |
T |
10: 62,802,576 (GRCm39) |
T898I |
probably damaging |
Het |
| Epc1 |
C |
A |
18: 6,440,091 (GRCm39) |
V59L |
possibly damaging |
Het |
| Etv6 |
C |
A |
6: 134,239,975 (GRCm39) |
|
probably benign |
Het |
| Fam118a |
A |
G |
15: 84,937,998 (GRCm39) |
D293G |
possibly damaging |
Het |
| Gzmn |
A |
C |
14: 56,404,361 (GRCm39) |
S159A |
probably benign |
Het |
| Insc |
A |
G |
7: 114,390,207 (GRCm39) |
D26G |
probably damaging |
Het |
| L1td1 |
A |
G |
4: 98,626,072 (GRCm39) |
R756G |
probably damaging |
Het |
| Ltk |
A |
G |
2: 119,582,318 (GRCm39) |
L499P |
probably benign |
Het |
| Mast4 |
A |
T |
13: 102,923,927 (GRCm39) |
L291M |
probably damaging |
Het |
| Nefm |
G |
T |
14: 68,361,797 (GRCm39) |
R156S |
probably damaging |
Het |
| Nppc |
T |
A |
1: 86,597,580 (GRCm39) |
N63Y |
probably damaging |
Het |
| Or5p79 |
A |
T |
7: 108,221,924 (GRCm39) |
I302F |
probably damaging |
Het |
| Or6c69 |
A |
G |
10: 129,747,314 (GRCm39) |
S278P |
probably damaging |
Het |
| Pcdhb7 |
T |
C |
18: 37,474,936 (GRCm39) |
V24A |
probably benign |
Het |
| Pcm1 |
C |
A |
8: 41,733,114 (GRCm39) |
Q787K |
probably damaging |
Het |
| Prg3 |
A |
G |
2: 84,823,334 (GRCm39) |
K170E |
possibly damaging |
Het |
| Slc25a54 |
T |
C |
3: 109,019,370 (GRCm39) |
S325P |
probably damaging |
Het |
| Slc44a1 |
T |
C |
4: 53,563,286 (GRCm39) |
V671A |
probably benign |
Het |
| Spock3 |
T |
A |
8: 63,597,049 (GRCm39) |
|
probably null |
Het |
| Stk-ps2 |
G |
A |
1: 46,069,081 (GRCm39) |
|
noncoding transcript |
Het |
| Svep1 |
T |
G |
4: 58,084,833 (GRCm39) |
D1835A |
possibly damaging |
Het |
| Tmcc3 |
A |
G |
10: 94,415,179 (GRCm39) |
T294A |
probably benign |
Het |
| Ulk1 |
C |
T |
5: 110,937,223 (GRCm39) |
R691Q |
probably benign |
Het |
| Vmn2r18 |
G |
A |
5: 151,508,644 (GRCm39) |
A160V |
probably damaging |
Het |
| Wnk4 |
T |
C |
11: 101,160,114 (GRCm39) |
V661A |
probably benign |
Het |
| Zfhx4 |
A |
G |
3: 5,468,404 (GRCm39) |
Y2854C |
probably damaging |
Het |
| Zfp563 |
G |
T |
17: 33,323,902 (GRCm39) |
E166* |
probably null |
Het |
| Zfp687 |
T |
A |
3: 94,919,391 (GRCm39) |
N127I |
probably damaging |
Het |
| Zfp958 |
T |
A |
8: 4,676,226 (GRCm39) |
|
probably null |
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 |
|
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'- AGCTGTCGGTAATCCACCTG -3'
(R):5'- TCTGCTCAAAGTTCCAGCG -3'
Sequencing Primer
(F):5'- GGTAATCCACCTGCTGCTG -3'
(R):5'- GTGACTCTCTCGGTCACAC -3'
|
| Posted On |
2015-03-18 |
Incidental Mutation