Mutagenetix > Incidental Mutation

Incidental Mutation 'R0179:Tsen54'

23059

Institutional Source

Beutler Lab

Gene Symbol

Tsen54

Ensembl Gene

ENSMUSG00000020781

Gene Name

tRNA splicing endonuclease subunit 54

Synonyms

0610034P02Rik

MMRRC Submission

038447-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R0179 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

115705550-115713920 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 115712856 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Cysteine at position 131 (S131C)

Ref Sequence

ENSEMBL: ENSMUSP00000116955 (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: S448C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: S448C

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

SMART Domains

Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781

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

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

noncoding transcript
Transcript: ENSMUST00000141748

Predicted Effect

probably damaging
Transcript: ENSMUST00000154304
AA Change: S131C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: S131C

Domain	Start	End	E-Value	Type
coiled coil region	21	43	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000157061
AA Change: S85C

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

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 94.1%

Validation Efficiency

98% (81/83)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts1	C	T	16: 85,592,353 (GRCm39)	S948N	probably benign	Het
Adck1	A	T	12: 88,425,942 (GRCm39)	M457L	possibly damaging	Het
Adprm	A	T	11: 66,929,051 (GRCm39)	H313Q	possibly damaging	Het
Adss1	T	C	12: 112,598,703 (GRCm39)	I104T	probably benign	Het
Agxt2	A	C	15: 10,399,134 (GRCm39)	Q435P	possibly damaging	Het
Amotl1	G	A	9: 14,460,069 (GRCm39)	A890V	probably benign	Het
Ankrd50	A	G	3: 38,509,463 (GRCm39)	V968A	possibly damaging	Het
Brf2	T	C	8: 27,615,896 (GRCm39)	D163G	possibly damaging	Het
Cd226	C	A	18: 89,225,263 (GRCm39)	N53K	probably benign	Het
Cdc42ep2	T	C	19: 5,968,636 (GRCm39)	D23G	probably benign	Het
Cdc7	T	C	5: 107,112,905 (GRCm39)	S8P	probably benign	Het
Cdh8	C	T	8: 99,838,344 (GRCm39)	E499K	possibly damaging	Het
Chd7	T	A	4: 8,862,516 (GRCm39)	F2534L	probably benign	Het
Ckb	T	C	12: 111,636,610 (GRCm39)	T255A	probably benign	Het
Cntnap5c	G	T	17: 58,076,620 (GRCm39)	W19L	probably benign	Het
Cntrl	A	G	2: 35,057,871 (GRCm39)	E1854G	probably benign	Het
Colec12	C	T	18: 9,858,921 (GRCm39)	P568L	unknown	Het
Cop1	A	G	1: 159,077,636 (GRCm39)	D157G	probably benign	Het
Csf2rb	A	C	15: 78,220,572 (GRCm39)	Q38P	possibly damaging	Het
Ctla2b	T	C	13: 61,044,107 (GRCm39)	D52G	possibly damaging	Het
Dcaf7	A	T	11: 105,942,623 (GRCm39)	D190V	probably damaging	Het
Depdc5	T	A	5: 33,058,918 (GRCm39)		probably benign	Het
Dgkq	A	G	5: 108,806,066 (GRCm39)		probably benign	Het
Dhrs2	A	G	14: 55,477,933 (GRCm39)	T222A	probably damaging	Het
Dock1	G	A	7: 134,700,566 (GRCm39)	D1109N	probably damaging	Het
E4f1	G	C	17: 24,670,411 (GRCm39)	T92S	possibly damaging	Het
Ep400	A	T	5: 110,816,515 (GRCm39)	S2669T	probably damaging	Het
Eprs1	T	G	1: 185,145,744 (GRCm39)	D1184E	probably benign	Het
Fpr-rs4	A	T	17: 18,242,289 (GRCm39)	K99*	probably null	Het
Fzr1	A	T	10: 81,204,904 (GRCm39)		probably benign	Het
Gcc2	C	T	10: 58,112,472 (GRCm39)	R1001C	probably benign	Het
Gm4884	A	G	7: 40,693,252 (GRCm39)	D407G	probably benign	Het
Golga4	A	T	9: 118,389,808 (GRCm39)		probably null	Het
Gp2	T	G	7: 119,051,540 (GRCm39)	D225A	possibly damaging	Het
Gramd1a	T	A	7: 30,841,843 (GRCm39)	T120S	probably damaging	Het
Hbb-bh2	T	A	7: 103,488,434 (GRCm39)	N121I	probably benign	Het
Htr6	A	T	4: 138,789,437 (GRCm39)	L276Q	probably damaging	Het
Itga9	A	T	9: 118,490,454 (GRCm39)	I262F	probably benign	Het
Lamc3	A	G	2: 31,805,096 (GRCm39)		probably benign	Het
Large1	T	C	8: 73,825,474 (GRCm39)	N200S	probably benign	Het
Lct	C	T	1: 128,255,422 (GRCm39)	V207I	probably benign	Het
Marf1	C	A	16: 13,969,040 (GRCm39)	L144F	probably damaging	Het
Morc2b	A	T	17: 33,355,956 (GRCm39)	Y605*	probably null	Het
Mtus1	G	T	8: 41,455,398 (GRCm39)	L87I	possibly damaging	Het
Muc2	A	G	7: 141,302,708 (GRCm39)	Y17C	probably damaging	Het
Myf5	T	C	10: 107,321,779 (GRCm39)	D5G	possibly damaging	Het
Nasp	C	T	4: 116,459,354 (GRCm39)	V375M	probably damaging	Het
Nr1h2	A	T	7: 44,201,689 (GRCm39)		probably null	Het
Nrg2	T	C	18: 36,155,468 (GRCm39)	Q447R	probably benign	Het
Ntn5	G	A	7: 45,335,737 (GRCm39)	G56D	probably damaging	Het
Oasl2	A	G	5: 115,048,973 (GRCm39)	R138G	probably benign	Het
Or4c29	A	T	2: 88,740,237 (GRCm39)	C167S	possibly damaging	Het
Or5b124	T	A	19: 13,610,504 (GRCm39)	F10I	probably damaging	Het
Or9k7	T	C	10: 130,046,207 (GRCm39)	Y264C	probably damaging	Het
Pcdhb5	G	A	18: 37,455,612 (GRCm39)	G664D	probably damaging	Het
Ppp1r15a	T	C	7: 45,174,424 (GRCm39)	E128G	probably damaging	Het
Prpf19	T	C	19: 10,875,172 (GRCm39)		probably benign	Het
Ptpn3	T	A	4: 57,270,118 (GRCm39)	T15S	probably benign	Het
R3hdm2	G	A	10: 127,330,975 (GRCm39)	C818Y	probably damaging	Het
Rad51d	A	G	11: 82,780,824 (GRCm39)	V39A	possibly damaging	Het
Rptor	A	T	11: 119,763,193 (GRCm39)	T926S	probably benign	Het
Rwdd4a	G	A	8: 47,995,742 (GRCm39)	D41N	probably damaging	Het
Sephs1	A	G	2: 4,904,371 (GRCm39)	T250A	probably benign	Het
Spata31g1	T	C	4: 42,972,214 (GRCm39)	S516P	probably benign	Het
Ssbp3	T	C	4: 106,903,585 (GRCm39)	S334P	probably damaging	Het
Suco	A	G	1: 161,703,874 (GRCm39)		probably benign	Het
Synj1	T	C	16: 90,761,519 (GRCm39)	K649R	possibly damaging	Het
Tdp2	C	T	13: 25,024,431 (GRCm39)	H243Y	possibly damaging	Het
Tinag	A	G	9: 76,904,164 (GRCm39)		probably benign	Het
Trerf1	T	C	17: 47,627,588 (GRCm39)		noncoding transcript	Het
Trip10	T	C	17: 57,569,349 (GRCm39)		probably benign	Het
Unc5c	A	T	3: 141,523,828 (GRCm39)	R794*	probably null	Het
Vmn2r59	A	T	7: 41,696,432 (GRCm39)	Y103*	probably null	Het
Washc5	A	G	15: 59,224,379 (GRCm39)	V460A	probably benign	Het
Wdr87-ps	A	G	7: 29,235,365 (GRCm39)		noncoding transcript	Het
Whamm	A	G	7: 81,243,763 (GRCm39)	T358A	probably benign	Het
Xlr4b	C	T	X: 72,262,277 (GRCm39)		probably benign	Het
Zbbx	C	T	3: 74,992,869 (GRCm39)		probably benign	Het
Zdhhc23	G	A	16: 43,794,066 (GRCm39)	P203S	probably benign	Het
Zfp27	T	A	7: 29,595,850 (GRCm39)	E38D	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
PIT4486001:Tsen54	UTSW	11	115,713,422 (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'- AGAAGGCTGACTCCCTTCCTCAAC -3'
(R):5'- TTCAGGGTCTGGCAAACTGGTG -3'

Sequencing Primer
(F):5'- GGGACACCTGCCTATATACTTAG -3'
(R):5'- ACTGGTGGCAGGGTTCAAG -3'

Posted On

2013-04-16