Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00562:Trmt10a'

277756

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Trmt10a

Ensembl Gene

ENSMUSG00000004127

Gene Name

tRNA methyltransferase 10A

Synonyms

3110023L08Rik, Rg9mtd2

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL00562

Quality Score

Status

Chromosome

Chromosomal Location

137849214-137865582 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 137853177 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 13 (E13K)

Ref Sequence

ENSEMBL: ENSMUSP00000125681 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000040321
AA Change: E13K

PolyPhen 2 Score 0.857 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000042082
Gene: ENSMUSG00000004127
AA Change: E13K

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

possibly damaging
Transcript: ENSMUST00000159481
AA Change: E13K

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000124465
Gene: ENSMUSG00000004127
AA Change: E13K

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

Predicted Effect

unknown
Transcript: ENSMUST00000159622
AA Change: E13K

SMART Domains

Protein: ENSMUSP00000130478
Gene: ENSMUSG00000004127
AA Change: E13K

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000161141
AA Change: E13K

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000125681
Gene: ENSMUSG00000004127
AA Change: E13K

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

possibly damaging
Transcript: ENSMUST00000162864
AA Change: E13K

PolyPhen 2 Score 0.857 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125749
Gene: ENSMUSG00000004127
AA Change: E13K

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

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: 27 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1500035N22Rik	T	C	5: 25,202,619 (GRCm39)		probably benign	Het
AU016765	C	A	17: 64,826,877 (GRCm39)		noncoding transcript	Het
Chaf1b	T	C	16: 93,697,079 (GRCm39)		probably benign	Het
Clstn2	A	G	9: 97,464,505 (GRCm39)		probably benign	Het
Crip1	T	A	12: 113,117,232 (GRCm39)		probably null	Het
Cubn	A	G	2: 13,299,041 (GRCm39)	S3211P	probably benign	Het
Dlx6	C	T	6: 6,865,143 (GRCm39)	R172W	probably damaging	Het
Fktn	A	T	4: 53,747,007 (GRCm39)		probably null	Het
Focad	T	A	4: 88,267,046 (GRCm39)	M1019K	unknown	Het
Fuca2	A	T	10: 13,381,651 (GRCm39)	D188V	probably damaging	Het
Kcna3	A	G	3: 106,944,046 (GRCm39)	D103G	probably damaging	Het
Mrpl19	A	G	6: 81,942,853 (GRCm39)	V19A	probably benign	Het
Ndufb3	T	A	1: 58,634,958 (GRCm39)	H103Q	possibly damaging	Het
Pkd1l3	T	C	8: 110,382,779 (GRCm39)	V1675A	possibly damaging	Het
Ptger4	A	T	15: 5,272,614 (GRCm39)	S2T	probably benign	Het
Saxo1	C	T	4: 86,363,809 (GRCm39)	E225K	probably damaging	Het
Sftpb	G	T	6: 72,286,845 (GRCm39)	A228S	probably benign	Het
Slc22a29	T	A	19: 8,138,993 (GRCm39)	T490S	probably benign	Het
Slc29a1	T	C	17: 45,900,918 (GRCm39)	N50S	probably damaging	Het
Smc6	T	A	12: 11,351,532 (GRCm39)	S854T	probably benign	Het
Smim23	T	C	11: 32,771,893 (GRCm39)	T58A	probably benign	Het
Tas2r134	T	C	2: 51,518,100 (GRCm39)	I193T	possibly damaging	Het
Thsd7a	G	T	6: 12,379,658 (GRCm39)		probably null	Het
Trav13n-4	T	G	14: 53,601,423 (GRCm39)	V64G	possibly damaging	Het
Txndc11	T	C	16: 10,922,496 (GRCm39)	S239G	probably damaging	Het
Vmn2r96	T	A	17: 18,804,077 (GRCm39)	N442K	probably benign	Het
Vps13a	C	T	19: 16,712,078 (GRCm39)		probably null	Het

Other mutations in Trmt10a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R5399:Trmt10a	UTSW	3	137,853,265 (GRCm39)	missense	probably damaging	0.97
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

Posted On

2015-04-16