Mutagenetix > Incidental Mutation

Incidental Mutation 'R5399:Trmt10a'

429842

Institutional Source

Beutler Lab

Gene Symbol

Trmt10a

Ensembl Gene

ENSMUSG00000004127

Gene Name

tRNA methyltransferase 10A

Synonyms

3110023L08Rik, Rg9mtd2

MMRRC Submission

042970-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5399 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

137849214-137865582 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 137853265 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 42 (I42K)

Ref Sequence

ENSEMBL: ENSMUSP00000124465 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040321] [ENSMUST00000098580] [ENSMUST00000159481] [ENSMUST00000159622] [ENSMUST00000161141] [ENSMUST00000162864]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000040321
AA Change: I42K

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000042082
Gene: ENSMUSG00000004127
AA Change: I42K

Domain	Start	End	E-Value	Type
low complexity region	44	82	N/A	INTRINSIC
Pfam:tRNA_m1G_MT	111	277	3.7e-52	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000098580

SMART Domains

Protein: ENSMUSP00000096179
Gene: ENSMUSG00000028158

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LPD_N	43	594	8.87e-165	SMART
Blast:LPD_N	597	710	6e-58	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000159481
AA Change: I42K

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000124465
Gene: ENSMUSG00000004127
AA Change: I42K

Domain	Start	End	E-Value	Type
coiled coil region	44	85	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000159622
AA Change: I42K

SMART Domains

Protein: ENSMUSP00000130478
Gene: ENSMUSG00000004127
AA Change: I42K

Domain	Start	End	E-Value	Type
low complexity region	44	67	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000161141
AA Change: I42K

PolyPhen 2 Score 0.917 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000125681
Gene: ENSMUSG00000004127
AA Change: I42K

Domain	Start	End	E-Value	Type
low complexity region	44	82	N/A	INTRINSIC
Pfam:tRNA_m1G_MT	111	165	2.6e-15	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161791

Predicted Effect

probably benign
Transcript: ENSMUST00000162864
AA Change: I42K

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000125749
Gene: ENSMUSG00000004127
AA Change: I42K

Domain	Start	End	E-Value	Type
low complexity region	44	82	N/A	INTRINSIC
Pfam:tRNA_m1G_MT	111	277	2.7e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197680

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.3%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased circulating magnesium level. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6820408C15Rik	G	T	2: 152,282,788 (GRCm39)	L214F	probably damaging	Het
Abcb1b	T	C	5: 8,877,410 (GRCm39)	S657P	probably benign	Het
Abcb5	T	A	12: 118,875,234 (GRCm39)	Y646F	probably benign	Het
Agl	A	T	3: 116,575,277 (GRCm39)	L620Q	probably damaging	Het
Anapc15	C	T	7: 101,547,810 (GRCm39)	P68L	probably damaging	Het
Arhgap23	A	G	11: 97,391,743 (GRCm39)	N1420S	probably damaging	Het
Barx2	A	G	9: 31,765,407 (GRCm39)		probably null	Het
Birc6	C	A	17: 74,911,573 (GRCm39)	S28R	possibly damaging	Het
Bmal2	T	G	6: 146,724,159 (GRCm39)	D350E	probably damaging	Het
Btbd19	G	A	4: 116,980,957 (GRCm39)	A104V	probably damaging	Het
Casp4	A	T	9: 5,324,928 (GRCm39)	K247*	probably null	Het
Ccdc196	A	C	12: 78,244,227 (GRCm39)	N60T	probably damaging	Het
Clk4	T	C	11: 51,166,084 (GRCm39)	Y17H	probably damaging	Het
Cntnap1	A	G	11: 101,074,142 (GRCm39)	Q722R	probably benign	Het
Col6a6	A	G	9: 105,586,306 (GRCm39)	V1905A	possibly damaging	Het
Csmd1	C	A	8: 16,760,613 (GRCm39)	G174V	probably damaging	Het
Cul1	T	A	6: 47,462,018 (GRCm39)		probably null	Het
Cux1	T	C	5: 136,281,458 (GRCm39)	E568G	possibly damaging	Het
Dnaaf2	A	G	12: 69,243,516 (GRCm39)	I515T	probably damaging	Het
Fbn1	T	C	2: 125,174,253 (GRCm39)	I1868V	possibly damaging	Het
Fcgbp	G	T	7: 27,804,480 (GRCm39)	V1863L	probably benign	Het
G2e3	T	C	12: 51,403,977 (GRCm39)		probably null	Het
Gabrr2	T	C	4: 33,071,458 (GRCm39)		probably null	Het
Gad1-ps	G	A	10: 99,281,009 (GRCm39)		noncoding transcript	Het
Gbgt1	C	T	2: 28,393,230 (GRCm39)	P106L	probably damaging	Het
Golga3	A	G	5: 110,352,890 (GRCm39)	E927G	probably damaging	Het
Hfm1	T	A	5: 107,065,428 (GRCm39)	I84F	possibly damaging	Het
Htt	G	T	5: 35,034,495 (GRCm39)	D1989Y	probably damaging	Het
Ihh	C	T	1: 74,985,436 (GRCm39)	A350T	probably benign	Het
Irx4	G	C	13: 73,413,658 (GRCm39)	A43P	probably benign	Het
Itk	A	G	11: 46,228,938 (GRCm39)	V414A	probably benign	Het
Itsn2	A	T	12: 4,703,535 (GRCm39)	I744L	probably benign	Het
Kdm5b	G	A	1: 134,549,836 (GRCm39)		probably null	Het
Kif14	A	G	1: 136,431,062 (GRCm39)	D1153G	probably benign	Het
Morc3	A	G	16: 93,659,427 (GRCm39)		probably null	Het
Mplkipl1	C	T	19: 61,164,364 (GRCm39)	G24R	unknown	Het
Msc	A	T	1: 14,825,780 (GRCm39)	C65S	probably benign	Het
Mybpc1	A	G	10: 88,358,876 (GRCm39)	V343A	probably damaging	Het
Myo5c	T	C	9: 75,195,356 (GRCm39)	I1218T	possibly damaging	Het
Mypn	C	T	10: 62,955,965 (GRCm39)	V1163I	probably benign	Het
Obox3	A	T	7: 15,360,213 (GRCm39)	M152K	probably benign	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or2t47	A	G	11: 58,442,969 (GRCm39)	V32A	probably benign	Het
Or4c106	T	A	2: 88,682,999 (GRCm39)	L235H	probably damaging	Het
Or4c3	T	A	2: 89,852,267 (GRCm39)	T48S	probably benign	Het
Pcdhb21	G	T	18: 37,648,772 (GRCm39)	V634L	probably benign	Het
Ppp1r9b	G	A	11: 94,882,974 (GRCm39)	A201T	probably benign	Het
Pramel25	T	C	4: 143,521,602 (GRCm39)	F406S	probably benign	Het
Prss23	A	T	7: 89,159,174 (GRCm39)	D298E	probably benign	Het
Rab4b	A	T	7: 26,875,587 (GRCm39)	N31K	probably benign	Het
Ros1	A	G	10: 51,967,040 (GRCm39)		probably null	Het
Rragb	G	A	X: 151,923,550 (GRCm39)	G24E	probably damaging	Het
Rtl1	A	T	12: 109,556,736 (GRCm39)	L1701Q	probably damaging	Het
Sbno1	T	A	5: 124,530,804 (GRCm39)	N831Y	probably benign	Het
Selp	A	G	1: 163,954,155 (GRCm39)	K152E	possibly damaging	Het
Sema4b	A	G	7: 79,874,634 (GRCm39)	T675A	probably benign	Het
Slc36a3	T	C	11: 55,037,006 (GRCm39)	I100V	possibly damaging	Het
Slco1a4	T	A	6: 141,776,433 (GRCm39)	I196F	probably damaging	Het
Spata13	G	A	14: 60,984,990 (GRCm39)	S828N	probably benign	Het
Stard13	A	T	5: 150,971,266 (GRCm39)	Y643*	probably null	Het
Tll1	T	C	8: 64,538,522 (GRCm39)	H374R	probably damaging	Het
Trmu	A	T	15: 85,780,609 (GRCm39)		probably null	Het
Trp53	T	A	11: 69,479,372 (GRCm39)	D183E	probably benign	Het
Ttc22	T	G	4: 106,493,954 (GRCm39)	F305V	probably damaging	Het
Unc13c	A	G	9: 73,656,970 (GRCm39)	F1077S	possibly damaging	Het
Utrn	T	A	10: 12,516,727 (GRCm39)	Q2289L	probably damaging	Het
Vmn1r65	C	A	7: 6,011,809 (GRCm39)	E142*	probably null	Het
Vmn2r63	A	T	7: 42,577,701 (GRCm39)	V279D	probably benign	Het
Zfp810	G	A	9: 22,190,125 (GRCm39)	T261I	possibly damaging	Het
Zkscan17	A	G	11: 59,393,744 (GRCm39)		probably null	Het

Other mutations in Trmt10a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00562:Trmt10a	APN	3	137,853,177 (GRCm39)	missense	probably damaging	0.97
IGL00563:Trmt10a	APN	3	137,853,177 (GRCm39)	missense	probably damaging	0.97
IGL00771:Trmt10a	APN	3	137,856,216 (GRCm39)	missense	probably benign	0.08
IGL01140:Trmt10a	APN	3	137,862,459 (GRCm39)	splice site	probably benign
IGL02869:Trmt10a	APN	3	137,857,945 (GRCm39)	splice site	probably null
R0898:Trmt10a	UTSW	3	137,855,279 (GRCm39)	missense	probably damaging	1.00
R0975:Trmt10a	UTSW	3	137,862,570 (GRCm39)	missense	probably benign	0.41
R1511:Trmt10a	UTSW	3	137,857,945 (GRCm39)	splice site	probably null
R1872:Trmt10a	UTSW	3	137,862,481 (GRCm39)	missense	probably damaging	1.00
R4856:Trmt10a	UTSW	3	137,854,146 (GRCm39)	nonsense	probably null
R4880:Trmt10a	UTSW	3	137,857,972 (GRCm39)	missense	possibly damaging	0.64
R4886:Trmt10a	UTSW	3	137,854,146 (GRCm39)	nonsense	probably null
R5516:Trmt10a	UTSW	3	137,857,957 (GRCm39)	missense	possibly damaging	0.91
R5994:Trmt10a	UTSW	3	137,862,475 (GRCm39)	missense	probably damaging	1.00
R7272:Trmt10a	UTSW	3	137,860,527 (GRCm39)	missense	probably damaging	1.00
X0028:Trmt10a	UTSW	3	137,860,556 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCATGTAGTGATCTCTATTGGCC -3'
(R):5'- GGGCGGAGTCTAAGTTCATTAG -3'

Sequencing Primer
(F):5'- CCATTTGGCCATTTGGGTAATTTTAC -3'
(R):5'- CGGAGTCTAAGTTCATTAGTATTGC -3'

Posted On

2016-09-06