Mutagenetix > Incidental Mutation

Incidental Mutation 'R4618:Tsen54'

345115

Institutional Source

Beutler Lab

Gene Symbol

Tsen54

Ensembl Gene

ENSMUSG00000020781

Gene Name

tRNA splicing endonuclease subunit 54

Synonyms

0610034P02Rik

MMRRC Submission

041884-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R4618 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

115705550-115713920 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to A at 115706247 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000114310 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021134] [ENSMUST00000041684] [ENSMUST00000106481] [ENSMUST00000136343] [ENSMUST00000156812]

AlphaFold

Q8C2A2

Predicted Effect

probably benign
Transcript: ENSMUST00000021134

SMART Domains

Protein: ENSMUSP00000021134
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	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: ENSMUST00000041684

SMART Domains

Protein: ENSMUSP00000041328
Gene: ENSMUSG00000034471

Domain	Start	End	E-Value	Type
ANK	2	32	1.27e3	SMART
ANK	48	77	3.01e-4	SMART
ANK	81	110	3.41e-3	SMART
ANK	114	143	1.4e-4	SMART
ANK	147	176	3.26e0	SMART
ANK	188	217	3.33e-6	SMART
ANK	220	249	4.82e-3	SMART
SH3	284	346	1.13e-6	SMART
SAM	485	551	8.53e-12	SMART
SAM	554	621	1.41e-12	SMART
low complexity region	762	774	N/A	INTRINSIC
Pfam:Caskin-Pro-rich	793	883	1.4e-32	PFAM
low complexity region	904	921	N/A	INTRINSIC
low complexity region	925	944	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC
low complexity region	1042	1069	N/A	INTRINSIC
low complexity region	1084	1090	N/A	INTRINSIC
low complexity region	1120	1132	N/A	INTRINSIC
Pfam:Caskin-tail	1144	1201	4.5e-28	PFAM

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

noncoding transcript
Transcript: ENSMUST00000129765

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 benign
Transcript: ENSMUST00000156812

SMART Domains

Protein: ENSMUSP00000114310
Gene: ENSMUSG00000034471

Domain	Start	End	E-Value	Type
ANK	2	32	1.27e3	SMART
ANK	48	77	3.01e-4	SMART
ANK	81	110	3.41e-3	SMART

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

98% (89/91)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930432M17Rik	A	T	3: 121,473,095 (GRCm39)	K83N	unknown	Het
Adamtsl3	T	A	7: 82,255,728 (GRCm39)	M1580K	probably benign	Het
Adprhl1	A	G	8: 13,292,250 (GRCm39)		probably null	Het
Akap3	G	T	6: 126,843,406 (GRCm39)	C675F	probably benign	Het
Asap1	A	T	15: 64,024,744 (GRCm39)	H318Q	probably damaging	Het
Atf7ip	G	T	6: 136,542,104 (GRCm39)	A18S	probably damaging	Het
Bcl2a1a	A	C	9: 88,839,357 (GRCm39)	N85T	probably damaging	Het
Btnl6	G	A	17: 34,733,120 (GRCm39)	P248S	probably damaging	Het
C9	A	G	15: 6,520,944 (GRCm39)	D51G	probably damaging	Het
Ccdc14	T	A	16: 34,526,865 (GRCm39)	C257S	probably benign	Het
Cd5l	A	G	3: 87,275,926 (GRCm39)	T299A	probably benign	Het
Cstdc3	T	A	16: 36,132,952 (GRCm39)	D76E	possibly damaging	Het
Endou	C	T	15: 97,611,763 (GRCm39)	V292M	possibly damaging	Het
Fbxo36	T	C	1: 84,877,749 (GRCm39)	I137T	probably damaging	Het
Fcer1a	T	C	1: 173,050,208 (GRCm39)	I161V	possibly damaging	Het
Fsip2	A	G	2: 82,818,103 (GRCm39)	Y4612C	probably benign	Het
Gcnt2	T	A	13: 41,111,670 (GRCm39)	L353*	probably null	Het
Ghrhr	T	C	6: 55,358,739 (GRCm39)	F172S	probably damaging	Het
Gins1	T	A	2: 150,759,781 (GRCm39)		probably null	Het
Gm16519	T	G	17: 71,236,237 (GRCm39)	L62R	probably damaging	Het
Gpr20	T	C	15: 73,567,585 (GRCm39)	N268S	probably benign	Het
Greb1l	A	G	18: 10,498,965 (GRCm39)	T283A	probably benign	Het
Grin2c	T	A	11: 115,143,573 (GRCm39)	D729V	probably damaging	Het
Heatr4	T	G	12: 84,024,841 (GRCm39)	T327P	probably damaging	Het
Hes2	A	C	4: 152,244,845 (GRCm39)	S105R	probably benign	Het
Hsph1	A	G	5: 149,542,308 (GRCm39)	V705A	probably benign	Het
Ighv1-82	T	C	12: 115,916,280 (GRCm39)	T77A	probably benign	Het
Itih1	A	T	14: 30,651,788 (GRCm39)	D851E	probably benign	Het
Klhdc7b	A	G	15: 89,271,472 (GRCm39)	T785A	probably benign	Het
Lmbr1	G	T	5: 29,551,863 (GRCm39)	A74E	probably damaging	Het
Lonp1	A	C	17: 56,929,511 (GRCm39)	H175Q	probably benign	Het
Maml2	T	C	9: 13,531,371 (GRCm39)	F195S	probably damaging	Het
Man2b2	G	T	5: 36,974,983 (GRCm39)	T436K	probably benign	Het
Man2c1	T	C	9: 57,049,439 (GRCm39)		probably null	Het
Mrps15	G	A	4: 125,940,837 (GRCm39)		probably benign	Het
Mtrf1l	C	A	10: 5,767,586 (GRCm39)	V177F	probably benign	Het
Naxd	A	T	8: 11,559,489 (GRCm39)	I213F	probably damaging	Het
Nbeal1	T	A	1: 60,267,890 (GRCm39)		probably benign	Het
Nfatc1	T	C	18: 80,741,047 (GRCm39)	I318V	probably damaging	Het
Nid2	T	A	14: 19,858,078 (GRCm39)	I1297N	probably damaging	Het
Nol10	T	C	12: 17,398,562 (GRCm39)	V3A	probably damaging	Het
Nop14	G	T	5: 34,796,562 (GRCm39)	P765Q	probably damaging	Het
Noxa1	C	T	2: 24,981,761 (GRCm39)	G114D	probably damaging	Het
Ntmt2	A	T	1: 163,552,597 (GRCm39)	F10I	probably damaging	Het
Opa1	T	C	16: 29,405,857 (GRCm39)	W141R	probably damaging	Het
Or10a2	G	A	7: 106,673,761 (GRCm39)	C242Y	probably damaging	Het
Or13p4	A	T	4: 118,546,667 (GRCm39)		probably benign	Het
Or5d18	A	G	2: 87,864,898 (GRCm39)	V195A	probably benign	Het
Or8h10	A	G	2: 86,808,618 (GRCm39)	I174T	possibly damaging	Het
Pde4d	A	T	13: 110,070,411 (GRCm39)	M7L	probably benign	Het
Phykpl	G	A	11: 51,483,056 (GRCm39)	A188T	probably damaging	Het
Pkd2l1	C	A	19: 44,142,573 (GRCm39)	A490S	probably damaging	Het
Pkhd1l1	T	A	15: 44,403,078 (GRCm39)	V2260D	probably damaging	Het
Ptprt	T	C	2: 161,395,765 (GRCm39)	E1136G	probably damaging	Het
Rad21	A	T	15: 51,833,420 (GRCm39)	L353Q	probably damaging	Het
Rfx4	G	T	10: 84,716,760 (GRCm39)	A425S	probably benign	Het
Rnf38	A	G	4: 44,142,450 (GRCm39)	S169P	probably damaging	Het
Samd9l	C	A	6: 3,376,347 (GRCm39)	V305F	probably damaging	Het
Serpini1	A	G	3: 75,523,883 (GRCm39)	K164E	probably benign	Het
Sirt6	A	G	10: 81,462,408 (GRCm39)	L37P	probably damaging	Het
Sorbs1	T	C	19: 40,361,962 (GRCm39)	T141A	probably damaging	Het
Tacc2	A	T	7: 130,227,946 (GRCm39)	T1563S	probably benign	Het
Tbc1d14	A	C	5: 36,687,725 (GRCm39)		probably benign	Het
Tbrg4	G	A	11: 6,570,185 (GRCm39)		probably benign	Het
Tox2	T	C	2: 163,162,567 (GRCm39)	L479P	probably damaging	Het
Tpp1	A	T	7: 105,400,913 (GRCm39)	L38Q	probably benign	Het
Trhr	A	G	15: 44,061,037 (GRCm39)	N186D	probably benign	Het
Trmt1l	C	T	1: 151,329,799 (GRCm39)	Q581*	probably null	Het
Tsg101	A	G	7: 46,542,257 (GRCm39)	I138T	possibly damaging	Het
Usp22	A	G	11: 61,052,269 (GRCm39)	S237P	probably damaging	Het
Vmn1r209	A	G	13: 22,990,619 (GRCm39)	S24P	possibly damaging	Het
Vmn2r18	A	T	5: 151,508,424 (GRCm39)	H233Q	possibly damaging	Het
Vmn2r45	A	T	7: 8,486,436 (GRCm39)	I284N	probably benign	Het
Vmn2r66	T	C	7: 84,644,296 (GRCm39)	I705V	possibly damaging	Het
Vsig1	G	T	X: 139,827,135 (GRCm39)	A95S	probably benign	Het
Zdhhc11	T	A	13: 74,127,349 (GRCm39)	M242K	probably benign	Het
Zfp352	A	G	4: 90,113,318 (GRCm39)	K486R	probably benign	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
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'- ACCAGAAGAGGGCTTTGTGG -3'
(R):5'- CATCACTGCATGACCAGGAC -3'

Sequencing Primer
(F):5'- AGTTGACGTCTCCTGCGG -3'
(R):5'- TGCATGACCAGGACAAACAATG -3'

Posted On

2015-09-25