Mutagenetix > Incidental Mutation

Incidental Mutation 'R2109:Tsen54'

232397

Institutional Source

Beutler Lab

Gene Symbol

Tsen54

Ensembl Gene

ENSMUSG00000020781

Gene Name

tRNA splicing endonuclease subunit 54

Synonyms

0610034P02Rik

MMRRC Submission

040113-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R2109 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

115705550-115713920 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 115706549 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 9 (D9G)

Ref Sequence

ENSEMBL: ENSMUSP00000120506 (fasta)

Gene Model

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

AlphaFold

Q8C2A2

Predicted Effect

probably damaging
Transcript: ENSMUST00000021134
AA Change: D132G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: D132G

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 damaging
Transcript: ENSMUST00000106481
AA Change: D132G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: D132G

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 damaging
Transcript: ENSMUST00000136343
AA Change: D9G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
AA Change: D9G

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410002F23Rik	G	T	7: 43,900,435 (GRCm39)	R113S	probably benign	Het
Ackr2	A	T	9: 121,738,026 (GRCm39)	I134F	probably damaging	Het
Actr3b	T	A	5: 26,036,709 (GRCm39)	I174N	possibly damaging	Het
Akap9	T	A	5: 4,094,847 (GRCm39)	S2214T	possibly damaging	Het
Arhgef12	C	A	9: 42,890,768 (GRCm39)	R986L	possibly damaging	Het
Brap	G	T	5: 121,801,422 (GRCm39)	S59I	possibly damaging	Het
Btnl1	C	T	17: 34,598,578 (GRCm39)	H65Y	probably damaging	Het
C1s2	T	C	6: 124,612,004 (GRCm39)	T121A	probably damaging	Het
Capn1	T	A	19: 6,064,388 (GRCm39)	Y37F	probably benign	Het
Ccdc39	T	C	3: 33,869,650 (GRCm39)	K726E	probably damaging	Het
Cd300lb	G	A	11: 114,816,865 (GRCm39)	S195F	probably damaging	Het
Cenpf	T	C	1: 189,411,264 (GRCm39)	K307E	probably damaging	Het
Chodl	A	C	16: 78,738,251 (GRCm39)	N73T	possibly damaging	Het
Cimip2c	G	A	5: 30,637,851 (GRCm39)	G66E	probably damaging	Het
Crnn	A	T	3: 93,055,747 (GRCm39)	M178L	probably benign	Het
Cyp4a12b	A	G	4: 115,290,110 (GRCm39)	D221G	probably damaging	Het
Dipk2a	A	T	9: 94,406,498 (GRCm39)	I303N	probably damaging	Het
Dmxl2	A	G	9: 54,301,097 (GRCm39)	V2338A	probably benign	Het
Dnah9	G	T	11: 65,928,411 (GRCm39)	P2086Q	probably damaging	Het
Dsg2	A	G	18: 20,725,346 (GRCm39)	I486V	probably benign	Het
E2f8	A	G	7: 48,524,855 (GRCm39)	S265P	probably damaging	Het
Eif1b	A	G	9: 120,323,296 (GRCm39)	D52G	probably benign	Het
Etl4	A	T	2: 20,790,153 (GRCm39)	T602S	probably benign	Het
Exoc3l2	A	T	7: 19,223,059 (GRCm39)		probably benign	Het
Fbxl6	C	A	15: 76,421,173 (GRCm39)	V297F	probably damaging	Het
Fgr	T	A	4: 132,725,786 (GRCm39)	N398K	probably benign	Het
G3bp1	A	G	11: 55,379,986 (GRCm39)	R107G	probably damaging	Het
Gp2	A	T	7: 119,052,155 (GRCm39)	N186K	probably benign	Het
Hbs1l	T	A	10: 21,217,831 (GRCm39)	L249*	probably null	Het
Hmgcs2	T	A	3: 98,204,337 (GRCm39)	L246*	probably null	Het
Hsp90ab1	G	T	17: 45,880,254 (GRCm39)	H96Q	probably benign	Het
Ibtk	C	T	9: 85,588,603 (GRCm39)	V1078I	probably benign	Het
Ltn1	T	C	16: 87,212,530 (GRCm39)	D677G	probably benign	Het
Lyst	C	T	13: 13,887,405 (GRCm39)	T3078I	possibly damaging	Het
Mamdc4	A	G	2: 25,459,402 (GRCm39)	F199S	probably damaging	Het
Megf6	G	T	4: 154,261,578 (GRCm39)	V68L	probably benign	Het
Mki67	G	A	7: 135,299,592 (GRCm39)	T1814I	probably damaging	Het
Msantd5l	T	A	11: 51,145,264 (GRCm39)	I108F	possibly damaging	Het
Mttp	A	T	3: 137,800,763 (GRCm39)	F766I	probably benign	Het
Nbl1	T	A	4: 138,810,915 (GRCm39)		probably null	Het
Nmrk1	T	A	19: 18,618,802 (GRCm39)	L118Q	probably damaging	Het
Nopchap1	C	T	10: 83,201,656 (GRCm39)	S143L	probably damaging	Het
Oog3	A	T	4: 143,886,082 (GRCm39)	L172H	probably damaging	Het
Or2y11	T	G	11: 49,443,260 (GRCm39)	S229A	probably damaging	Het
Osbpl1a	T	G	18: 12,892,457 (GRCm39)	Q332P	probably damaging	Het
Pik3cg	A	G	12: 32,243,709 (GRCm39)	F921L	possibly damaging	Het
Plch2	T	C	4: 155,069,054 (GRCm39)	S1086G	possibly damaging	Het
Plekha5	A	G	6: 140,369,942 (GRCm39)	T18A	possibly damaging	Het
Pogz	T	A	3: 94,786,276 (GRCm39)	S955T	probably benign	Het
Pot1b	A	T	17: 55,960,413 (GRCm39)	I639N	probably benign	Het
Prkdc	T	C	16: 15,505,254 (GRCm39)	I852T	probably benign	Het
Prps1l1	A	G	12: 35,035,521 (GRCm39)	K212R	probably benign	Het
Ptpn5	A	G	7: 46,735,807 (GRCm39)	Y304H	probably damaging	Het
Ralgapa1	A	G	12: 55,822,973 (GRCm39)	I281T	possibly damaging	Het
Rgs22	A	T	15: 36,099,880 (GRCm39)	Y278*	probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf213	T	A	11: 119,333,489 (GRCm39)	Y2899*	probably null	Het
Rttn	C	T	18: 89,004,197 (GRCm39)	T397I	possibly damaging	Het
Sacs	G	T	14: 61,410,902 (GRCm39)		probably null	Het
Sbf2	G	T	7: 110,060,419 (GRCm39)	Q182K	probably damaging	Het
Sec14l5	C	T	16: 4,984,968 (GRCm39)	R105*	probably null	Het
Sh2b1	A	T	7: 126,071,536 (GRCm39)	D216E	possibly damaging	Het
Sh3gl3	A	G	7: 81,920,008 (GRCm39)	N72S	possibly damaging	Het
Slc12a1	A	T	2: 125,015,619 (GRCm39)	I391F	probably damaging	Het
Slc36a2	G	A	11: 55,072,381 (GRCm39)	A77V	probably damaging	Het
Smc2	A	T	4: 52,474,987 (GRCm39)	I888L	probably benign	Het
Smoc1	C	T	12: 81,197,450 (GRCm39)	T194M	probably damaging	Het
Sorcs1	C	T	19: 50,666,630 (GRCm39)	G93R	probably benign	Het
Sox30	T	G	11: 45,882,595 (GRCm39)	F542V	probably damaging	Het
Svep1	A	G	4: 58,206,030 (GRCm39)	V116A	possibly damaging	Het
Synj2	A	G	17: 6,063,966 (GRCm39)	D330G	probably benign	Het
Tenm3	A	C	8: 48,796,384 (GRCm39)	S202A	possibly damaging	Het
Tg	C	T	15: 66,601,443 (GRCm39)	T151I	probably benign	Het
Tnfaip2	A	G	12: 111,414,527 (GRCm39)	E361G	probably damaging	Het
Tnk1	A	T	11: 69,746,009 (GRCm39)	D305E	probably damaging	Het
Tpp1	A	G	7: 105,399,177 (GRCm39)	L133P	probably damaging	Het
Trappc1	T	A	11: 69,215,243 (GRCm39)	M41K	probably damaging	Het
Ttn	T	A	2: 76,804,598 (GRCm39)	I225F	probably damaging	Het
Ube4b	T	C	4: 149,457,298 (GRCm39)	K313R	probably benign	Het
Vps50	T	C	6: 3,555,379 (GRCm39)	V425A	probably damaging	Het
Wbp2	A	T	11: 115,971,445 (GRCm39)	Y153*	probably null	Het
Xrn1	A	G	9: 95,861,273 (GRCm39)	S478G	probably benign	Het
Zfp354c	T	C	11: 50,707,969 (GRCm39)	E77G	probably benign	Het
Zfp462	T	C	4: 55,008,496 (GRCm39)	M154T	probably benign	Het
Zfp704	A	G	3: 9,539,585 (GRCm39)	V255A	probably damaging	Het
Zfp763	G	T	17: 33,238,752 (GRCm39)	A131E	probably benign	Het
Zfp931	A	T	2: 177,711,651 (GRCm39)	V32E	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
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'- TGGTGGACCAGGAGGAATTC -3'
(R):5'- ACAGGCTGTCTCACCTACAG -3'

Sequencing Primer
(F):5'- AAGTTATGTGTGGACTTTGAGAACAG -3'
(R):5'- GTCTCACCTACAGCCCTGG -3'

Posted On

2014-09-18