Mutagenetix > Incidental Mutation

Incidental Mutation 'R4521:Tsen54'

334233

Institutional Source

Beutler Lab

Gene Symbol

Tsen54

Ensembl Gene

ENSMUSG00000020781

Gene Name

tRNA splicing endonuclease subunit 54

Synonyms

MMRRC Submission

041764-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R4521 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

115814724-115823094 bp(+) (GRCm38)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 115817106 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000120506 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021134] [ENSMUST00000041684] [ENSMUST00000106481] [ENSMUST00000136343] [ENSMUST00000136343] [ENSMUST00000154304] [ENSMUST00000156812]

AlphaFold

Q8C2A2

Predicted Effect

probably null
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 null
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 null
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 null
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: 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: 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

Predicted Effect

probably benign
Transcript: ENSMUST00000157061

Meta Mutation Damage Score

0.9502

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

100% (49/49)

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: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ascc3	A	G	10: 50,660,670	N700D	probably benign	Het
Bora	G	T	14: 99,068,548	S451I	probably damaging	Het
Cadm3	A	T	1: 173,345,063		probably null	Het
Car14	A	G	3: 95,904,378		probably benign	Het
Ccdc88c	G	T	12: 100,913,332	S1843R	possibly damaging	Het
Cdc20b	A	G	13: 113,081,191	I381M	probably damaging	Het
Col12a1	C	T	9: 79,633,357	V2449I	probably benign	Het
Crb2	T	C	2: 37,795,337		probably benign	Het
Dcaf6	A	T	1: 165,390,490	D347E	probably damaging	Het
Dlgap2	G	A	8: 14,727,871	R372H	probably damaging	Het
Fat3	T	C	9: 15,922,942	N4118S	probably null	Het
Fbxo41	A	G	6: 85,484,042	I228T	probably damaging	Het
Fpr2	A	C	17: 17,893,247	R168S	probably benign	Het
Ghr	A	G	15: 3,325,958	I281T	probably damaging	Het
Glmp	C	A	3: 88,328,039	N259K	possibly damaging	Het
Grhl3	T	C	4: 135,546,250	K564E	probably damaging	Het
Helz2	T	C	2: 181,228,833	H2875R	probably benign	Het
Lcp1	A	G	14: 75,215,168	D438G	possibly damaging	Het
Lrfn2	T	A	17: 49,069,894	M1K	probably null	Het
Lrp6	A	G	6: 134,485,862	C612R	probably damaging	Het
Map3k13	T	C	16: 21,905,775	V341A	possibly damaging	Het
Megf8	T	A	7: 25,342,701	C1315S	probably benign	Het
Mrgpra9	A	T	7: 47,235,190	L243H	probably damaging	Het
Mrgprx1	T	C	7: 48,021,699	D100G	probably benign	Het
Nop2	G	T	6: 125,133,552	R47L	probably damaging	Het
Nup93	T	C	8: 94,314,636	Y801H	probably damaging	Het
Olfr623	C	T	7: 103,660,332	R306H	probably benign	Het
Olfr810	T	A	10: 129,791,181	N136I	possibly damaging	Het
Orc4	G	A	2: 48,937,489	P31S	probably benign	Het
Plce1	T	C	19: 38,524,319	S21P	possibly damaging	Het
Plpp2	A	G	10: 79,530,625	Y118H	probably damaging	Het
Ppwd1	A	G	13: 104,209,659	V496A	probably benign	Het
Rbm20	A	G	19: 53,817,202	N466S	probably benign	Het
Rpl10l	T	C	12: 66,283,738	D207G	probably benign	Het
Skida1	T	C	2: 18,045,872		probably benign	Het
Stk17b	A	G	1: 53,764,038	Y73H	probably damaging	Het
Tapbpl	A	G	6: 125,228,122	I287T	probably damaging	Het
Tmem38a	C	T	8: 72,572,161	P20S	possibly damaging	Het
Topbp1	T	C	9: 103,334,202		probably benign	Het
Ttn	G	A	2: 76,725,216	R28736*	probably null	Het
Wdr36	G	A	18: 32,841,148		probably null	Het

Other mutations in Tsen54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01327:Tsen54	APN	11	115821712	missense	possibly damaging	0.90
PIT4486001:Tsen54	UTSW	11	115822596	missense	probably damaging	1.00
R0179:Tsen54	UTSW	11	115822030	missense	probably damaging	1.00
R0255:Tsen54	UTSW	11	115815408	missense	probably damaging	1.00
R0380:Tsen54	UTSW	11	115822597	missense	probably damaging	1.00
R0619:Tsen54	UTSW	11	115815064	missense	probably damaging	1.00
R0653:Tsen54	UTSW	11	115815061	missense	probably damaging	1.00
R1120:Tsen54	UTSW	11	115815013	missense	probably damaging	0.98
R2109:Tsen54	UTSW	11	115815723	missense	probably damaging	1.00
R2248:Tsen54	UTSW	11	115815406	missense	probably damaging	1.00
R2300:Tsen54	UTSW	11	115822078	missense	probably damaging	1.00
R3081:Tsen54	UTSW	11	115820164	missense	probably benign	0.08
R3763:Tsen54	UTSW	11	115820411	missense	probably benign	0.22
R4179:Tsen54	UTSW	11	115820852	missense	probably damaging	0.99
R4618:Tsen54	UTSW	11	115815421	unclassified	probably benign
R5485:Tsen54	UTSW	11	115815222	missense	probably benign	0.15
R6111:Tsen54	UTSW	11	115820130	missense	possibly damaging	0.82
R6238:Tsen54	UTSW	11	115820687	missense	probably benign	0.02
R6459:Tsen54	UTSW	11	115821680	missense	probably damaging	1.00
R6555:Tsen54	UTSW	11	115820693	missense	probably benign	0.43
R7378:Tsen54	UTSW	11	115821705	missense	probably benign	0.19
R7520:Tsen54	UTSW	11	115820971	missense	probably damaging	0.99
R7922:Tsen54	UTSW	11	115820782	nonsense	probably null
R8110:Tsen54	UTSW	11	115814934	missense	unknown
R8159:Tsen54	UTSW	11	115820978	nonsense	probably null
R8497:Tsen54	UTSW	11	115822584	missense	probably damaging	1.00
R8529:Tsen54	UTSW	11	115820560	missense	possibly damaging	0.95
R8786:Tsen54	UTSW	11	115820672	missense	probably damaging	0.98
R9365:Tsen54	UTSW	11	115822584	missense	probably damaging	1.00
R9571:Tsen54	UTSW	11	115817107	critical splice donor site	probably null
X0028:Tsen54	UTSW	11	115817099	missense	possibly damaging	0.50
Z1176:Tsen54	UTSW	11	115820578	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- GTAGCTTGAGGCCAATCTGATG -3'
(R):5'- CCACAAGATGACTATTGCGGTTC -3'

Sequencing Primer
(F):5'- ATGTGCATATCTCCAGGACG -3'
(R):5'- ACAAGATGACTATTGCGGTTCTTTGC -3'

Posted On

2015-08-18