Mutagenetix > Incidental Mutation

Incidental Mutation 'R9492:Trmt13'

716976

Institutional Source

Beutler Lab

Gene Symbol

Trmt13

Ensembl Gene

ENSMUSG00000033439

Gene Name

tRNA methyltransferase 13

Synonyms

A930028L21Rik, Ccdc76, 4631408H19Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.151) question?

Stock #

R9492 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

116374742-116408236 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 116388281 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 52 (Y52H)

Ref Sequence

ENSEMBL: ENSMUSP00000142410 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029571] [ENSMUST00000041524] [ENSMUST00000134761] [ENSMUST00000183638] [ENSMUST00000184963] [ENSMUST00000197190] [ENSMUST00000197335] [ENSMUST00000198454] [ENSMUST00000198311] [ENSMUST00000198386]

AlphaFold

Q8BYH3

Predicted Effect

probably benign
Transcript: ENSMUST00000029571

SMART Domains

Protein: ENSMUSP00000029571
Gene: ENSMUSG00000027959

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
Pfam:SAS-6_N	44	141	1.7e-29	PFAM
low complexity region	223	235	N/A	INTRINSIC
coiled coil region	415	471	N/A	INTRINSIC
low complexity region	632	644	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000041524

SMART Domains

Protein: ENSMUSP00000047320
Gene: ENSMUSG00000033439

Domain	Start	End	E-Value	Type
Pfam:zf-TRM13_CCCH	17	45	7.2e-17	PFAM
Pfam:zf-U11-48K	56	80	3.4e-12	PFAM
Pfam:TRM13	165	469	7e-96	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000134761

SMART Domains

Protein: ENSMUSP00000138761
Gene: ENSMUSG00000033439

Domain	Start	End	E-Value	Type
Pfam:zf-U11-48K	16	42	1.6e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000183638

SMART Domains

Protein: ENSMUSP00000139223
Gene: ENSMUSG00000033439

Domain	Start	End	E-Value	Type
Pfam:zf-TRM13_CCCH	16	46	1.4e-17	PFAM
Pfam:zf-U11-48K	55	81	1.2e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000184963

SMART Domains

Protein: ENSMUSP00000138868
Gene: ENSMUSG00000033439

Domain	Start	End	E-Value	Type
Pfam:zf-TRM13_CCCH	16	46	2.9e-17	PFAM
Pfam:zf-U11-48K	55	81	2.3e-12	PFAM
Pfam:TRM13	165	285	3.4e-42	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000197190

SMART Domains

Protein: ENSMUSP00000143637
Gene: ENSMUSG00000033439

Domain	Start	End	E-Value	Type
Pfam:TRM13	116	179	5.2e-19	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000197335

SMART Domains

Protein: ENSMUSP00000143123
Gene: ENSMUSG00000027959

Domain	Start	End	E-Value	Type
PDB:2Y3W\|C	7	136	3e-48	PDB
low complexity region	188	200	N/A	INTRINSIC
coiled coil region	380	436	N/A	INTRINSIC
low complexity region	597	609	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000198454
AA Change: Y52H

PolyPhen 2 Score 0.100 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000142410
Gene: ENSMUSG00000033439
AA Change: Y52H

Domain	Start	End	E-Value	Type
Pfam:zf-TRM13_CCCH	16	46	1.9e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000198311

SMART Domains

Protein: ENSMUSP00000143233
Gene: ENSMUSG00000027959

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
PDB:2Y3W\|C	15	171	9e-62	PDB
low complexity region	223	235	N/A	INTRINSIC
coiled coil region	415	471	N/A	INTRINSIC
low complexity region	632	644	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000198386

SMART Domains

Protein: ENSMUSP00000143175
Gene: ENSMUSG00000027959

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
PDB:2Y3W\|C	15	171	1e-62	PDB
low complexity region	223	235	N/A	INTRINSIC
coiled coil region	415	471	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	A	C	1: 120,078,472 (GRCm39)	K43T	probably damaging	Het
Abca12	A	G	1: 71,297,380 (GRCm39)	V2370A	possibly damaging	Het
Abca13	T	A	11: 9,243,667 (GRCm39)	C1843*	probably null	Het
Abr	C	T	11: 76,399,751 (GRCm39)	S82N	probably benign	Het
Acot2	T	C	12: 84,039,384 (GRCm39)	S298P	probably benign	Het
Acrbp	A	G	6: 125,038,062 (GRCm39)	D421G	probably benign	Het
Adam25	A	T	8: 41,206,736 (GRCm39)	M1L	probably benign	Het
Ano8	A	G	8: 71,934,784 (GRCm39)	V441A	possibly damaging	Het
Aoc1l1	T	C	6: 48,955,540 (GRCm39)	S717P	probably benign	Het
Atg2b	T	C	12: 105,624,549 (GRCm39)	H650R	probably benign	Het
Atp11a	C	T	8: 12,894,490 (GRCm39)	T695I	probably damaging	Het
AU018091	A	G	7: 3,214,023 (GRCm39)	S74P	probably benign	Het
Cadps2	A	G	6: 23,427,238 (GRCm39)	Y597H	probably benign	Het
Ccdc15	C	T	9: 37,215,665 (GRCm39)	E619K	probably damaging	Het
Ceacam11	G	T	7: 17,709,468 (GRCm39)	C222F	probably benign	Het
Cmya5	T	C	13: 93,177,822 (GRCm39)	*3677W	probably null	Het
Col11a1	G	C	3: 114,005,752 (GRCm39)	C1628S	probably benign	Het
Dhx8	T	C	11: 101,654,808 (GRCm39)	I1032T	possibly damaging	Het
Dpp10	T	C	1: 123,281,159 (GRCm39)	D630G	probably damaging	Het
Eci3	C	T	13: 35,143,976 (GRCm39)	G50R	probably benign	Het
Eif2a	A	G	3: 58,448,475 (GRCm39)	T103A	probably benign	Het
Frem1	T	C	4: 82,920,057 (GRCm39)	E432G	probably damaging	Het
Gdnf	C	T	15: 7,840,423 (GRCm39)		probably benign	Het
Hace1	T	A	10: 45,547,230 (GRCm39)	M471K	probably benign	Het
Hydin	A	G	8: 111,326,877 (GRCm39)	T4739A	possibly damaging	Het
Ilf2	A	G	3: 90,394,570 (GRCm39)	I320V	probably benign	Het
Iqgap3	C	A	3: 88,016,176 (GRCm39)	F986L	probably damaging	Het
Klhl21	T	C	4: 152,093,419 (GRCm39)	L7S	probably benign	Het
Lrrc61	G	T	6: 48,545,761 (GRCm39)	E195*	probably null	Het
Maz	G	T	7: 126,622,292 (GRCm39)	A443E	possibly damaging	Het
Mcm5	C	T	8: 75,844,168 (GRCm39)	S313F	probably benign	Het
Mtor	T	A	4: 148,568,801 (GRCm39)	L1107Q	probably damaging	Het
Nectin3	T	C	16: 46,215,511 (GRCm39)	H494R	probably benign	Het
Nlgn1	G	T	3: 25,488,480 (GRCm39)	Y618*	probably null	Het
Nup98	C	T	7: 101,778,252 (GRCm39)	E1372K	probably benign	Het
Or12e9	A	G	2: 87,201,960 (GRCm39)	N28S	probably benign	Het
Or5af1	T	C	11: 58,722,610 (GRCm39)	V210A	probably benign	Het
Otud6b	A	G	4: 14,818,349 (GRCm39)	I184T	probably damaging	Het
Pcsk6	A	G	7: 65,697,346 (GRCm39)	N891S	probably benign	Het
Pde4a	T	A	9: 21,106,096 (GRCm39)	L237Q	probably damaging	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Perm1	TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT	TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT	4: 156,302,525 (GRCm39)		probably benign	Het
Pou3f1	A	G	4: 124,552,179 (GRCm39)	H227R	possibly damaging	Het
Prss53	G	A	7: 127,488,802 (GRCm39)	R31C	probably damaging	Het
Psmb8	T	A	17: 34,417,435 (GRCm39)	D21E	probably benign	Het
Ptprq	A	G	10: 107,478,813 (GRCm39)	Y1277H	probably damaging	Het
Rexo2	T	C	9: 48,380,176 (GRCm39)	T219A	probably benign	Het
Rfc3	A	G	5: 151,566,411 (GRCm39)	F346S	probably damaging	Het
Rhoq	A	T	17: 87,304,373 (GRCm39)	Q168L		Het
Sgk1	A	G	10: 21,874,096 (GRCm39)	N452S	probably damaging	Het
Slc35f3	A	G	8: 127,048,026 (GRCm39)	K122R	probably damaging	Het
Slc4a2	T	A	5: 24,644,761 (GRCm39)	M1021K	probably benign	Het
Sorcs2	A	G	5: 36,186,484 (GRCm39)	V886A	probably benign	Het
Spata20	T	A	11: 94,374,444 (GRCm39)	M308L	probably damaging	Het
Spen	A	T	4: 141,199,098 (GRCm39)	H3176Q	probably benign	Het
Stat5b	T	A	11: 100,692,361 (GRCm39)	H141L	probably benign	Het
Syne2	T	A	12: 75,995,839 (GRCm39)	H2126Q	possibly damaging	Het
Traj46	A	G	14: 54,409,851 (GRCm39)	T20A		Het
Trim30a	G	T	7: 104,078,330 (GRCm39)	Q249K	probably damaging	Het
Trpv3	A	G	11: 73,187,267 (GRCm39)	I700V	probably damaging	Het
Tyr	G	A	7: 87,121,704 (GRCm39)	H363Y	probably damaging	Het
Tyr	C	G	7: 87,121,705 (GRCm39)	M362I	possibly damaging	Het
Ubb	G	A	11: 62,442,984 (GRCm39)	V5M	probably damaging	Het
Unc5a	T	C	13: 55,150,288 (GRCm39)	L519P	probably damaging	Het
Uso1	A	G	5: 92,315,191 (GRCm39)	D185G	possibly damaging	Het
Vmn1r228	C	T	17: 20,996,862 (GRCm39)	E219K	probably damaging	Het
Wdr49	A	G	3: 75,240,669 (GRCm39)	V400A	probably damaging	Het
Zfp292	A	G	4: 34,810,794 (GRCm39)	M755T	probably benign	Het

Other mutations in Trmt13

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00926:Trmt13	APN	3	116,383,884 (GRCm39)	nonsense	probably null
IGL01516:Trmt13	APN	3	116,383,459 (GRCm39)	unclassified	probably benign
IGL01732:Trmt13	APN	3	116,375,113 (GRCm39)	missense	probably damaging	1.00
IGL01783:Trmt13	APN	3	116,376,561 (GRCm39)	nonsense	probably null
IGL02470:Trmt13	APN	3	116,383,877 (GRCm39)	critical splice donor site	probably null
IGL02492:Trmt13	APN	3	116,376,192 (GRCm39)	missense	possibly damaging	0.53
IGL02531:Trmt13	APN	3	116,385,840 (GRCm39)	critical splice donor site	probably null
IGL03156:Trmt13	APN	3	116,379,451 (GRCm39)	missense	probably benign	0.00
R0394:Trmt13	UTSW	3	116,376,299 (GRCm39)	missense	probably damaging	1.00
R0446:Trmt13	UTSW	3	116,376,275 (GRCm39)	missense	probably damaging	1.00
R2211:Trmt13	UTSW	3	116,388,403 (GRCm39)	missense	probably benign	0.00
R2942:Trmt13	UTSW	3	116,379,421 (GRCm39)	missense	probably damaging	1.00
R3124:Trmt13	UTSW	3	116,383,893 (GRCm39)	missense	probably benign	0.00
R3945:Trmt13	UTSW	3	116,375,167 (GRCm39)	missense	probably damaging	1.00
R3946:Trmt13	UTSW	3	116,375,167 (GRCm39)	missense	probably damaging	1.00
R4255:Trmt13	UTSW	3	116,376,337 (GRCm39)	nonsense	probably null
R4520:Trmt13	UTSW	3	116,375,262 (GRCm39)	splice site	probably null
R4609:Trmt13	UTSW	3	116,388,476 (GRCm39)	utr 5 prime	probably benign
R4678:Trmt13	UTSW	3	116,383,404 (GRCm39)	missense	probably damaging	1.00
R4679:Trmt13	UTSW	3	116,383,404 (GRCm39)	missense	probably damaging	1.00
R4703:Trmt13	UTSW	3	116,388,247 (GRCm39)	missense	probably benign	0.00
R6526:Trmt13	UTSW	3	116,385,864 (GRCm39)	missense	probably damaging	1.00
R7064:Trmt13	UTSW	3	116,376,346 (GRCm39)	missense	probably damaging	1.00
R7079:Trmt13	UTSW	3	116,376,480 (GRCm39)	missense	probably benign	0.00
R7308:Trmt13	UTSW	3	116,388,388 (GRCm39)	missense	probably benign	0.09
R8347:Trmt13	UTSW	3	116,376,417 (GRCm39)	missense	probably benign	0.00
R8491:Trmt13	UTSW	3	116,376,228 (GRCm39)	missense	probably benign
R8544:Trmt13	UTSW	3	116,386,094 (GRCm39)	splice site	probably null
R9108:Trmt13	UTSW	3	116,375,129 (GRCm39)	missense	probably damaging	1.00
R9208:Trmt13	UTSW	3	116,376,356 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- ATCACTTCCCCTGAGGATGG -3'
(R):5'- AAGGACCCAGCGTTATGGAG -3'

Sequencing Primer
(F):5'- ATGAGTGTAAGGGTCTCTGAGAC -3'
(R):5'- AGCGTTATGGAGGCTCCG -3'

Posted On

2022-07-18