Mutagenetix > Incidental Mutation

Incidental Mutation 'R7423:Gnmt'

575876

Institutional Source

Beutler Lab

Gene Symbol

Gnmt

Ensembl Gene

ENSMUSG00000002769

Gene Name

glycine N-methyltransferase

Synonyms

glycine N methyl transferase

MMRRC Submission

045501-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.306) question?

Stock #

R7423 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

47036590-47040091 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 47037066 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Tyrosine at position 211 (N211Y)

Ref Sequence

ENSEMBL: ENSMUSP00000002846 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002840] [ENSMUST00000002846]

AlphaFold

Q9QXF8

PDB Structure

Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form) [X-RAY DIFFRACTION]
Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form) [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000002840

SMART Domains

Protein: ENSMUSP00000002840
Gene: ENSMUSG00000002763

Domain	Start	End	E-Value	Type
low complexity region	17	31	N/A	INTRINSIC
low complexity region	72	86	N/A	INTRINSIC
low complexity region	87	104	N/A	INTRINSIC
low complexity region	112	128	N/A	INTRINSIC
low complexity region	173	200	N/A	INTRINSIC
AAA	463	598	6.1e-7	SMART
AAA	737	875	6e-24	SMART
Blast:AAA	928	973	1e-14	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000002846
AA Change: N211Y

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: N211Y

Domain	Start	End	E-Value	Type
Pfam:Methyltransf_23	27	217	9e-11	PFAM
Pfam:Methyltransf_31	56	224	1.3e-15	PFAM
Pfam:Methyltransf_18	57	176	1.5e-15	PFAM
Pfam:Methyltransf_25	61	169	1.4e-10	PFAM
Pfam:Methyltransf_12	62	171	4e-12	PFAM
Pfam:Methyltransf_11	62	173	2.4e-11	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.8%

Validation Efficiency

96% (91/95)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an enzyme that catalyzes the conversion of S-adenosyl-L-methionine (along with glycine) to S-adenosyl-L-homocysteine and sarcosine. This protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between the upstream CNPY3 (canopy FGF signaling regulator 3) gene and this gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for a null mutation display elevated levels of methionine and S-adenosylmethionine in the liver. Mice homozygous for another null allele exhibit hepatitis, increased hepatic glycogen storage, and hepatocellular carcinoma. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsbg2	A	T	17: 57,175,257 (GRCm39)	M85K	probably benign	Het
Actn4	C	T	7: 28,593,680 (GRCm39)	A905T	probably damaging	Het
Aff1	T	A	5: 103,994,967 (GRCm39)	V1055D	probably damaging	Het
Aox3	A	G	1: 58,160,228 (GRCm39)	E137G	possibly damaging	Het
Apaf1	A	T	10: 90,895,468 (GRCm39)	D443E	probably damaging	Het
Arl5b	C	A	2: 15,072,983 (GRCm39)	A28E	probably damaging	Het
Atg16l1	T	C	1: 87,714,023 (GRCm39)	V478A	probably damaging	Het
Atp6v1f	G	C	6: 29,468,105 (GRCm39)	E13Q	probably null	Het
Atpaf1	A	T	4: 115,647,827 (GRCm39)	K162M	probably damaging	Het
C3	A	T	17: 57,521,767 (GRCm39)	L1100Q	probably damaging	Het
Ccr1	A	G	9: 123,764,422 (GRCm39)	L36P	probably damaging	Het
Cct3	T	C	3: 88,216,503 (GRCm39)	L153S	probably benign	Het
Chd4	A	G	6: 125,105,822 (GRCm39)	D1813G	possibly damaging	Het
Chrm3	T	C	13: 9,928,845 (GRCm39)	I64V	probably benign	Het
Cnot2	A	T	10: 116,328,303 (GRCm39)	V477E	probably damaging	Het
Csf2rb2	T	A	15: 78,176,760 (GRCm39)	I211F	possibly damaging	Het
Dnah8	T	C	17: 30,923,743 (GRCm39)	L1237P	possibly damaging	Het
Dnttip2	T	C	3: 122,069,175 (GRCm39)	V130A	probably benign	Het
Dock10	G	A	1: 80,501,497 (GRCm39)	A1852V	possibly damaging	Het
Dock3	A	G	9: 106,844,370 (GRCm39)	V910A	probably damaging	Het
Drgx	A	G	14: 32,350,778 (GRCm39)	S205G	probably damaging	Het
Fbrs	G	A	7: 127,088,633 (GRCm39)	W738*	probably null	Het
Fmnl3	T	A	15: 99,227,281 (GRCm39)	D162V	probably damaging	Het
Fosl2	A	G	5: 32,307,807 (GRCm39)	R133G	probably damaging	Het
Frmpd1	A	G	4: 45,256,948 (GRCm39)	Q172R	probably damaging	Het
Fsd1l	A	T	4: 53,686,406 (GRCm39)	D273V	probably damaging	Het
Fstl4	T	A	11: 52,959,382 (GRCm39)	M141K	possibly damaging	Het
Gcfc2	A	G	6: 81,923,541 (GRCm39)	D535G	probably damaging	Het
Gm19410	A	C	8: 36,271,761 (GRCm39)	D1277A	probably benign	Het
Hic2	A	G	16: 17,075,993 (GRCm39)	D274G	probably damaging	Het
Hnrnpu	A	G	1: 178,156,849 (GRCm39)		probably benign	Het
Icam5	T	C	9: 20,948,201 (GRCm39)	S670P	probably benign	Het
Ighv5-4	A	T	12: 113,561,120 (GRCm39)	L100Q	probably damaging	Het
Il17rb	A	T	14: 29,719,072 (GRCm39)	S337T	probably damaging	Het
Inf2	G	T	12: 112,576,172 (GRCm39)	R883L	unknown	Het
Inhbc	C	T	10: 127,193,275 (GRCm39)	C247Y	probably damaging	Het
Ints4	A	G	7: 97,156,926 (GRCm39)	K333E	probably damaging	Het
Iyd	A	T	10: 3,497,088 (GRCm39)	I148F	probably damaging	Het
Klk1b26	A	T	7: 43,664,193 (GRCm39)	D16V	probably damaging	Het
Krt15	A	T	11: 100,026,386 (GRCm39)	V100E	possibly damaging	Het
Lama2	A	T	10: 27,088,222 (GRCm39)	S852T	probably benign	Het
Mbtd1	A	G	11: 93,834,622 (GRCm39)	E600G	probably benign	Het
Mfap3	T	G	11: 57,420,329 (GRCm39)	N103K	probably damaging	Het
Mtor	G	A	4: 148,640,801 (GRCm39)	E2536K	possibly damaging	Het
Mug2	G	A	6: 122,056,685 (GRCm39)	S1210N	probably benign	Het
Nat8	G	A	6: 85,807,477 (GRCm39)	L219F	probably benign	Het
Nisch	A	G	14: 30,893,658 (GRCm39)	V1305A	probably benign	Het
Nup153	A	T	13: 46,850,120 (GRCm39)		probably null	Het
Or3a1b	G	A	11: 74,012,811 (GRCm39)	R232H	probably benign	Het
Otud6b	A	T	4: 14,825,858 (GRCm39)		probably null	Het
Pbld2	A	G	10: 62,883,783 (GRCm39)	T83A	probably damaging	Het
Pcx	A	T	19: 4,671,206 (GRCm39)	M1144L	probably benign	Het
Pdpk1	C	A	17: 24,329,874 (GRCm39)	R81L	probably benign	Het
Pik3cd	A	T	4: 149,736,220 (GRCm39)		probably null	Het
Plch2	A	C	4: 155,068,194 (GRCm39)	D1477E	probably damaging	Het
Plek2	A	G	12: 78,946,884 (GRCm39)	I51T	probably damaging	Het
Plekhn1	A	G	4: 156,315,142 (GRCm39)	V505A	probably benign	Het
Pofut2	T	C	10: 77,098,273 (GRCm39)	S129P	possibly damaging	Het
Prdx5	C	A	19: 6,887,370 (GRCm39)		probably benign	Het
Proca1	G	T	11: 78,085,643 (GRCm39)		probably benign	Het
Ptprs	A	C	17: 56,721,793 (GRCm39)	Y1752D	probably damaging	Het
Pum1	G	A	4: 130,501,856 (GRCm39)	V1127M	probably damaging	Het
Ralbp1	T	C	17: 66,165,976 (GRCm39)	R403G	probably damaging	Het
Reps1	A	T	10: 17,969,635 (GRCm39)	H246L	possibly damaging	Het
Rps6kc1	A	C	1: 190,531,293 (GRCm39)	M903R	probably damaging	Het
Rubcnl	A	G	14: 75,287,083 (GRCm39)	T584A	probably benign	Het
Samd9l	A	T	6: 3,374,408 (GRCm39)	V951E	probably damaging	Het
Sbf2	A	G	7: 110,038,055 (GRCm39)	F463L	possibly damaging	Het
Sdr16c6	G	A	4: 4,076,921 (GRCm39)		probably benign	Het
Shoc1	A	T	4: 59,076,264 (GRCm39)	S560T	probably benign	Het
Slc26a8	A	G	17: 28,867,177 (GRCm39)	I548T	probably benign	Het
Slc2a13	T	A	15: 91,456,883 (GRCm39)	I140F	probably damaging	Het
Smtn	A	T	11: 3,481,200 (GRCm39)		probably null	Het
Sobp	G	T	10: 42,898,564 (GRCm39)	C340*	probably null	Het
Sox6	A	T	7: 115,149,258 (GRCm39)	V413E	probably benign	Het
Spin1	T	C	13: 51,277,326 (GRCm39)		probably null	Het
Sra1	T	C	18: 36,800,536 (GRCm39)	T224A	probably benign	Het
Sv2c	A	T	13: 96,185,056 (GRCm39)	F207Y	probably benign	Het
Tcp10c	T	A	17: 13,581,503 (GRCm39)		probably null	Het
Tkt	G	A	14: 30,292,992 (GRCm39)	G490S	possibly damaging	Het
Tpgs1	G	T	10: 79,511,655 (GRCm39)	A266S	probably damaging	Het
Tprg1	T	G	16: 25,241,003 (GRCm39)	S260A	probably damaging	Het
Trdv2-1	T	A	14: 54,183,935 (GRCm39)	W56R	probably damaging	Het
Trgv6	G	T	13: 19,374,814 (GRCm39)	G40W	possibly damaging	Het
Trpc4	T	A	3: 54,225,450 (GRCm39)	V933E	probably benign	Het
Ulk4	A	T	9: 120,932,687 (GRCm39)	M1051K	possibly damaging	Het
Unc119b	A	G	5: 115,272,743 (GRCm39)	L76P	probably damaging	Het
Vmn2r15	G	A	5: 109,445,394 (GRCm39)	S10F	probably benign	Het
Vwce	A	G	19: 10,641,704 (GRCm39)	E810G	probably benign	Het
Wdr7	T	A	18: 63,910,451 (GRCm39)		probably null	Het
Wnk2	T	A	13: 49,191,608 (GRCm39)	E1283V	probably benign	Het
Zfp28	T	C	7: 6,396,956 (GRCm39)	C464R	probably damaging	Het
Zpld1	C	T	16: 55,054,027 (GRCm39)	C255Y	probably damaging	Het

Other mutations in Gnmt

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01351:Gnmt	APN	17	47,037,606 (GRCm39)	missense	probably benign	0.28
health_nut	UTSW	17	47,037,271 (GRCm39)	missense	probably damaging	1.00
impulsive	UTSW	17	47,036,892 (GRCm39)	missense	probably damaging	1.00
Incautious	UTSW	17	47,038,313 (GRCm39)	missense	probably damaging	1.00
rash	UTSW	17	47,036,662 (GRCm39)	utr 3 prime	probably benign
R0480:Gnmt	UTSW	17	47,036,854 (GRCm39)	missense	probably benign	0.06
R0938:Gnmt	UTSW	17	47,037,271 (GRCm39)	missense	probably damaging	1.00
R0939:Gnmt	UTSW	17	47,037,271 (GRCm39)	missense	probably damaging	1.00
R0940:Gnmt	UTSW	17	47,037,271 (GRCm39)	missense	probably damaging	1.00
R0941:Gnmt	UTSW	17	47,037,271 (GRCm39)	missense	probably damaging	1.00
R3619:Gnmt	UTSW	17	47,039,963 (GRCm39)	missense	possibly damaging	0.63
R4173:Gnmt	UTSW	17	47,037,047 (GRCm39)	missense	probably damaging	1.00
R4456:Gnmt	UTSW	17	47,039,910 (GRCm39)	missense	probably benign	0.07
R4498:Gnmt	UTSW	17	47,036,662 (GRCm39)	utr 3 prime	probably benign
R4659:Gnmt	UTSW	17	47,036,892 (GRCm39)	missense	probably damaging	1.00
R4669:Gnmt	UTSW	17	47,037,225 (GRCm39)	nonsense	probably null
R4827:Gnmt	UTSW	17	47,038,245 (GRCm39)	missense	possibly damaging	0.77
R5112:Gnmt	UTSW	17	47,037,256 (GRCm39)	missense	probably damaging	1.00
R5133:Gnmt	UTSW	17	47,036,860 (GRCm39)	missense	probably benign
R5797:Gnmt	UTSW	17	47,037,305 (GRCm39)	missense	probably damaging	1.00
R7825:Gnmt	UTSW	17	47,040,019 (GRCm39)	missense	probably damaging	0.99
R8785:Gnmt	UTSW	17	47,038,313 (GRCm39)	missense	probably damaging	1.00
R8861:Gnmt	UTSW	17	47,037,618 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGAACTTACTGCAACAGGGC -3'
(R):5'- GAACATTGCAAGCATGGTGC -3'

Sequencing Primer
(F):5'- GCCCCCAGCCAGATATGAG -3'
(R):5'- TACGACTATATCCTCAGCACAGG -3'

Posted On

2019-10-07