Mutagenetix > Incidental Mutation

Incidental Mutation 'R4455:Tsen34'

329141

Institutional Source

Beutler Lab

Gene Symbol

Tsen34

Ensembl Gene

ENSMUSG00000035585

Gene Name

tRNA splicing endonuclease subunit 34

Synonyms

Leng5, 0610027F08Rik

MMRRC Submission

041715-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.858) question?

Stock #

R4455 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

3696086-3704034 bp(+) (GRCm39)

Type of Mutation

splice site (5 bp from exon)

DNA Base Change (assembly)

G to A at 3698097 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000120403 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038521] [ENSMUST00000038608] [ENSMUST00000108627] [ENSMUST00000108629] [ENSMUST00000108630] [ENSMUST00000118710] [ENSMUST00000123088] [ENSMUST00000137204] [ENSMUST00000142713] [ENSMUST00000155060] [ENSMUST00000205287] [ENSMUST00000206343] [ENSMUST00000205734] [ENSMUST00000128364] [ENSMUST00000127106] [ENSMUST00000206571] [ENSMUST00000206379]

AlphaFold

Q8BMZ5

Predicted Effect

probably benign
Transcript: ENSMUST00000038521
AA Change: A122T

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000046911
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC
Pfam:tRNA_int_endo	219	303	2.9e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000038608

SMART Domains

Protein: ENSMUSP00000037107
Gene: ENSMUSG00000035596

Domain	Start	End	E-Value	Type
transmembrane domain	5	22	N/A	INTRINSIC
Pfam:MBOAT	57	420	2.4e-37	PFAM
transmembrane domain	425	447	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108627
AA Change: A122T

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000104267
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC
Pfam:tRNA_int_endo	223	307	4.8e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108629
AA Change: A122T

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000104269
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC
Pfam:tRNA_int_endo	223	256	3.7e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108630
AA Change: A122T

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000104270
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC
Pfam:tRNA_int_endo	223	307	7.9e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118710

SMART Domains

Protein: ENSMUSP00000112710
Gene: ENSMUSG00000035596

Domain	Start	End	E-Value	Type
transmembrane domain	5	22	N/A	INTRINSIC
transmembrane domain	35	57	N/A	INTRINSIC
Pfam:MBOAT	86	343	1.5e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123088
AA Change: A122T

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000123614
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139396

Predicted Effect

probably null
Transcript: ENSMUST00000137204

SMART Domains

Protein: ENSMUSP00000120403
Gene: ENSMUSG00000035585

Domain	Start	End	E-Value	Type
low complexity region	69	85	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000142713
AA Change: A122T

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000118440
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000155060
AA Change: A122T

PolyPhen 2 Score 0.135 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000118816
Gene: ENSMUSG00000035585
AA Change: A122T

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000205287
AA Change: A122T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

Predicted Effect

probably benign
Transcript: ENSMUST00000206343

Predicted Effect

probably benign
Transcript: ENSMUST00000147288

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205644

Predicted Effect

probably benign
Transcript: ENSMUST00000205734

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150785

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131688

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150684

Predicted Effect

probably benign
Transcript: ENSMUST00000128364

SMART Domains

Protein: ENSMUSP00000120521
Gene: ENSMUSG00000035596

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
low complexity region	32	46	N/A	INTRINSIC
low complexity region	58	67	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000127106

SMART Domains

Protein: ENSMUSP00000116446
Gene: ENSMUSG00000035596

Domain	Start	End	E-Value	Type
transmembrane domain	5	22	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206448

Predicted Effect

probably benign
Transcript: ENSMUST00000206571

Predicted Effect

probably benign
Transcript: ENSMUST00000206379

Meta Mutation Damage Score

0.0711

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 95.0%

Validation Efficiency

100% (61/61)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a catalytic subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from precursor tRNAs. The endonuclease complex is also associated with a pre-mRNA 3-prime end processing factor. A mutation in this gene results in the neurological disorder pontocerebellar hypoplasia type 2. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Oct 2009]

Allele List at MGI

Other mutations in this stock

Total: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700102P08Rik	A	G	9: 108,274,395 (GRCm39)	H166R	possibly damaging	Het
Aktip	T	C	8: 91,851,479 (GRCm39)	E248G	probably benign	Het
Ankk1	A	G	9: 49,329,366 (GRCm39)	V336A	probably benign	Het
Aoc1	T	A	6: 48,882,401 (GRCm39)	D92E	probably damaging	Het
Aoc1l3	A	T	6: 48,964,394 (GRCm39)	N134I	possibly damaging	Het
Arfgef2	T	C	2: 166,736,635 (GRCm39)	I1769T	probably benign	Het
Arfgef3	A	T	10: 18,483,423 (GRCm39)	S1434T	probably benign	Het
Baz1a	C	A	12: 54,958,153 (GRCm39)	V1033L	probably benign	Het
Bbs12	T	C	3: 37,374,461 (GRCm39)	V418A	probably damaging	Het
Cacnb4	A	G	2: 52,355,665 (GRCm39)	V214A	probably damaging	Het
Calhm6	A	T	10: 34,002,531 (GRCm39)	I184N	probably damaging	Het
Camk2d	T	C	3: 126,574,052 (GRCm39)	V153A	probably damaging	Het
Ccdc18	C	T	5: 108,309,395 (GRCm39)	S330L	possibly damaging	Het
Cdh11	T	C	8: 103,374,455 (GRCm39)	D500G	probably benign	Het
Cdkn2d	C	G	9: 21,202,185 (GRCm39)	V21L	probably benign	Het
Clca4a	G	A	3: 144,663,020 (GRCm39)	P610S	probably damaging	Het
Dctn1	T	C	6: 83,172,031 (GRCm39)	L807P	probably damaging	Het
Dop1b	T	C	16: 93,563,103 (GRCm39)	L869P	probably damaging	Het
Egr2	GAA	GA	10: 67,375,733 (GRCm39)		probably null	Het
Eya1	C	T	1: 14,253,420 (GRCm39)	V519M	probably damaging	Het
Fam227b	T	A	2: 125,988,188 (GRCm39)		probably benign	Het
Fsip2	G	T	2: 82,821,120 (GRCm39)	A5618S	possibly damaging	Het
Grb10	T	G	11: 11,917,665 (GRCm39)	Q72P	possibly damaging	Het
H3f3a	G	T	1: 180,630,668 (GRCm39)	R129S	probably benign	Het
Hfm1	T	C	5: 107,034,374 (GRCm39)		probably null	Het
Kansl1	T	C	11: 104,315,184 (GRCm39)	T285A	possibly damaging	Het
Krtap16-1	A	T	11: 99,876,559 (GRCm39)	C282S	probably benign	Het
Magi1	A	G	6: 93,762,438 (GRCm39)	V89A	probably damaging	Het
Mllt1	A	G	17: 57,226,965 (GRCm39)	Y71H	probably damaging	Het
Ms4a14	T	A	19: 11,280,990 (GRCm39)	T523S	possibly damaging	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Muc5b	T	C	7: 141,412,555 (GRCm39)	S1834P	unknown	Het
Necap1	C	T	6: 122,864,328 (GRCm39)	S270F	possibly damaging	Het
Piwil2	T	C	14: 70,628,014 (GRCm39)	M752V	probably benign	Het
Prune1	G	A	3: 95,189,207 (GRCm39)		probably null	Het
Ptpro	A	G	6: 137,370,657 (GRCm39)	E586G	probably damaging	Het
Rela	T	A	19: 5,697,290 (GRCm39)	I499K	probably damaging	Het
Rpl31-ps17	C	T	12: 54,748,397 (GRCm39)		noncoding transcript	Het
Scara5	T	A	14: 66,000,196 (GRCm39)	D455E	probably benign	Het
Slc2a4	G	A	11: 69,834,148 (GRCm39)		probably benign	Het
Sntb2	G	A	8: 107,718,239 (GRCm39)		probably null	Het
Sspo	C	T	6: 48,442,450 (GRCm39)	R1982C	probably damaging	Het
Ttc28	AC	A	5: 111,371,924 (GRCm39)		probably null	Het
Ttn	T	C	2: 76,777,257 (GRCm39)	M1382V	probably benign	Het
Utp18	G	A	11: 93,776,273 (GRCm39)	R71C	probably benign	Het
Xrn1	T	A	9: 95,855,698 (GRCm39)		probably benign	Het
Yeats2	A	G	16: 19,980,743 (GRCm39)	K187R	possibly damaging	Het

Other mutations in Tsen34

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00324:Tsen34	APN	7	3,703,530 (GRCm39)	makesense	probably null
R1612:Tsen34	UTSW	7	3,698,395 (GRCm39)	missense	probably damaging	0.99
R2441:Tsen34	UTSW	7	3,697,994 (GRCm39)	missense	possibly damaging	0.92
R4702:Tsen34	UTSW	7	3,703,632 (GRCm39)	missense	probably damaging	1.00
R4870:Tsen34	UTSW	7	3,697,380 (GRCm39)	unclassified	probably benign
R5950:Tsen34	UTSW	7	3,697,787 (GRCm39)	missense	probably null	0.97
R6221:Tsen34	UTSW	7	3,698,543 (GRCm39)	missense	probably damaging	0.99
R6266:Tsen34	UTSW	7	3,696,984 (GRCm39)	unclassified	probably benign
R7121:Tsen34	UTSW	7	3,697,986 (GRCm39)	missense	probably benign	0.18
R7134:Tsen34	UTSW	7	3,703,640 (GRCm39)	missense	probably damaging	0.98
R7190:Tsen34	UTSW	7	3,697,806 (GRCm39)	missense	possibly damaging	0.94
R7345:Tsen34	UTSW	7	3,698,614 (GRCm39)	missense	probably damaging	1.00
R7448:Tsen34	UTSW	7	3,698,834 (GRCm39)	critical splice donor site	probably null
R7743:Tsen34	UTSW	7	3,697,601 (GRCm39)	missense	possibly damaging	0.54
R7887:Tsen34	UTSW	7	3,697,707 (GRCm39)	missense	probably damaging	1.00
R8723:Tsen34	UTSW	7	3,698,149 (GRCm39)	missense	probably benign	0.00
R8916:Tsen34	UTSW	7	3,697,340 (GRCm39)	unclassified	probably benign
RF020:Tsen34	UTSW	7	3,698,795 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- AAGGGACTGCAGGATGTGTC -3'
(R):5'- TGAGTCCACAAGGTCTCCTTAG -3'

Sequencing Primer
(F):5'- CTTGGGGTTCCAGTTAAGTTTAC -3'
(R):5'- ACAAGGTCTCCTTAGCGCCAG -3'

Posted On

2015-07-21