Mutagenetix > Incidental Mutation

Incidental Mutation 'R8110:Tsen54'

630822

Institutional Source

Beutler Lab

Gene Symbol

Tsen54

Ensembl Gene

ENSMUSG00000020781

Gene Name

tRNA splicing endonuclease subunit 54

Synonyms

0610034P02Rik

MMRRC Submission

067539-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R8110 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115705550-115713920 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 115705760 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 26 (A26S)

Ref Sequence

ENSEMBL: ENSMUSP00000021134 (fasta)

Gene Model

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

AlphaFold

Q8C2A2

Predicted Effect

unknown
Transcript: ENSMUST00000021134
AA Change: A26S

SMART Domains

Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: A26S

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

unknown
Transcript: ENSMUST00000106481
AA Change: A26S

SMART Domains

Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: A26S

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: 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: 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: 99.9%
3x: 99.7%
10x: 98.6%
20x: 93.1%

Validation Efficiency

99% (73/74)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd45	T	C	1: 160,978,889 (GRCm39)		probably null	Het
Appl1	C	A	14: 26,649,751 (GRCm39)	G592*	probably null	Het
Arfgef2	T	A	2: 166,720,464 (GRCm39)	M1501K	probably benign	Het
Calcrl	C	T	2: 84,169,683 (GRCm39)	A333T	probably damaging	Het
Cd200r3	T	A	16: 44,771,835 (GRCm39)	I33N	probably benign	Het
Ceacam15	A	G	7: 16,407,334 (GRCm39)	L61P	probably benign	Het
Cfap69	T	A	5: 5,632,515 (GRCm39)	H827L	possibly damaging	Het
Csmd3	T	A	15: 47,507,666 (GRCm39)	E2780V	probably damaging	Het
Cyp2u1	G	A	3: 131,087,303 (GRCm39)	T426I	probably damaging	Het
Eefsec	A	C	6: 88,353,312 (GRCm39)	I119S	probably damaging	Het
Fem1b	T	C	9: 62,703,550 (GRCm39)	N570S	probably damaging	Het
Fmo9	A	G	1: 166,491,095 (GRCm39)	M461T	probably benign	Het
Fryl	A	G	5: 73,290,620 (GRCm39)	Y95H	probably benign	Het
Fsip2	T	C	2: 82,789,017 (GRCm39)	I346T	probably benign	Het
Fto	T	C	8: 92,211,818 (GRCm39)	F381S	probably damaging	Het
Gabbr1	G	C	17: 37,359,475 (GRCm39)	S150T	probably benign	Het
Galnt9	G	T	5: 110,763,339 (GRCm39)	W448L	probably damaging	Het
Gcnt2	G	T	13: 41,071,198 (GRCm39)		probably benign	Het
Gm10800	CAAGAAAACTGAAAATCAAAGAAAACTGAAAATCA	CAAGAAAACTGAAAATCA	2: 98,497,361 (GRCm39)		probably null	Het
Gmcl1	G	T	6: 86,698,408 (GRCm39)	A163E	probably damaging	Het
Hectd4	A	G	5: 121,471,012 (GRCm39)	Y2633C	possibly damaging	Het
Hsd11b2	A	G	8: 106,249,266 (GRCm39)	I214V	probably damaging	Het
Hspa12a	T	A	19: 58,809,445 (GRCm39)	E217V	possibly damaging	Het
Itih2	A	G	2: 10,101,948 (GRCm39)	F845L	probably damaging	Het
Kcnn3	T	A	3: 89,568,540 (GRCm39)	L606H	probably damaging	Het
Krt6b	G	A	15: 101,588,577 (GRCm39)	R28C	probably damaging	Het
Lama2	T	A	10: 26,866,866 (GRCm39)	D2876V	probably damaging	Het
Lmbrd2	T	C	15: 9,175,279 (GRCm39)	S397P	probably damaging	Het
Lmf2	C	T	15: 89,236,561 (GRCm39)		probably null	Het
Lrp2	A	G	2: 69,336,797 (GRCm39)	I1325T	probably benign	Het
Ltbp2	A	T	12: 84,850,676 (GRCm39)	C879*	probably null	Het
Map3k1	A	G	13: 111,891,847 (GRCm39)	V1136A	probably damaging	Het
Mettl3	G	T	14: 52,537,709 (GRCm39)	H84N	probably benign	Het
Mia2	A	G	12: 59,155,873 (GRCm39)		probably null	Het
Mlip	G	T	9: 77,146,861 (GRCm39)	T92K	probably damaging	Het
Nalcn	T	A	14: 123,702,113 (GRCm39)	Y466F	probably benign	Het
Nav2	T	A	7: 49,201,698 (GRCm39)	L235*	probably null	Het
Nbn	T	C	4: 15,981,588 (GRCm39)	V560A	probably benign	Het
Ncln	A	T	10: 81,328,987 (GRCm39)	Y144N	possibly damaging	Het
Nfe2l2	A	C	2: 75,509,765 (GRCm39)	D18E	probably benign	Het
Or10aa3	G	A	1: 173,878,091 (GRCm39)	A51T	probably benign	Het
Or12d2	A	G	17: 37,624,604 (GRCm39)	F224L	probably benign	Het
Or1ak2	T	C	2: 36,827,721 (GRCm39)	C197R	possibly damaging	Het
Or5w11	T	C	2: 87,458,951 (GRCm39)	I48T	possibly damaging	Het
Otop3	A	T	11: 115,230,221 (GRCm39)	M33L	probably benign	Het
Pate7	T	C	9: 35,689,329 (GRCm39)	*84W	probably null	Het
Pdzd2	G	A	15: 12,373,592 (GRCm39)	S2181L	probably benign	Het
Phf14	T	C	6: 11,953,422 (GRCm39)	I387T	possibly damaging	Het
Prb1c	C	T	6: 132,338,531 (GRCm39)	G229D	unknown	Het
Prdm9	T	A	17: 15,774,960 (GRCm39)	N318Y	probably damaging	Het
Proca1	A	G	11: 78,095,737 (GRCm39)	D123G	probably damaging	Het
Prune2	G	A	19: 17,098,083 (GRCm39)	G1196S	probably benign	Het
Psd3	T	A	8: 68,573,708 (GRCm39)	S158C	probably damaging	Het
Rps18	A	G	17: 34,174,110 (GRCm39)	V15A	probably benign	Het
Sanbr	G	T	11: 23,526,764 (GRCm39)	T696N	probably benign	Het
Sharpin	C	A	15: 76,231,965 (GRCm39)	R271L	possibly damaging	Het
Smad5	C	A	13: 56,871,701 (GRCm39)	Q99K	probably damaging	Het
Sox5	T	C	6: 144,062,200 (GRCm39)	M151V	possibly damaging	Het
Sphkap	A	T	1: 83,256,492 (GRCm39)	F419Y	possibly damaging	Het
Tbx20	T	A	9: 24,636,821 (GRCm39)	Y422F	probably damaging	Het
Tcirg1	A	C	19: 3,949,099 (GRCm39)	F397V	probably damaging	Het
Tex36	G	A	7: 133,197,012 (GRCm39)	S35F	possibly damaging	Het
Usp50	T	A	2: 126,622,250 (GRCm39)		probably null	Het
Vmn2r5	A	T	3: 64,398,709 (GRCm39)	F757I	probably benign	Het
Zbbx	T	C	3: 75,062,749 (GRCm39)	T3A	possibly damaging	Het
Zfp28	T	A	7: 6,392,828 (GRCm39)	M168K	probably benign	Het
Zfp568	G	T	7: 29,722,551 (GRCm39)	G499W	probably damaging	Het
Zfp7	C	G	15: 76,775,131 (GRCm39)	P391R	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
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
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'- CTTTATGATCCCGAGGAGCG -3'
(R):5'- TCCACAAAGCCCTCTTCTGG -3'

Sequencing Primer
(F):5'- TAGGACCGCGCGGAATG -3'
(R):5'- TGGTTTCCACTCCGCGG -3'

Posted On

2020-06-30