Mutagenetix > Incidental Mutation

Incidental Mutation 'R4659:Gnmt'

352717

Institutional Source

Beutler Lab

Gene Symbol

Gnmt

Ensembl Gene

ENSMUSG00000002769

Gene Name

glycine N-methyltransferase

Synonyms

glycine N methyl transferase

MMRRC Submission

041919-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.320) question?

Stock #

R4659 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

47036590-47040091 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 47036892 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 239 (F239S)

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: F239S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: F239S

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144964

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147112

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148872

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181301

Meta Mutation Damage Score

0.8940

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

96% (74/77)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc9	C	A	6: 142,618,321 (GRCm39)		probably null	Het
Ankrd22	C	T	19: 34,102,968 (GRCm39)	V118I	probably damaging	Het
Aoc1	A	T	6: 48,883,010 (GRCm39)	E295D	probably benign	Het
Arap2	T	C	5: 62,811,469 (GRCm39)	N1114S	possibly damaging	Het
AU021092	C	G	16: 5,030,011 (GRCm39)	A335P	probably damaging	Het
Carhsp1	T	C	16: 8,482,129 (GRCm39)	T51A	probably benign	Het
Cdc42bpb	T	C	12: 111,306,325 (GRCm39)	D152G	probably damaging	Het
Cep70	T	A	9: 99,178,394 (GRCm39)	D497E	possibly damaging	Het
Chrm5	T	C	2: 112,310,102 (GRCm39)	N338S	probably benign	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Clhc1	T	A	11: 29,528,229 (GRCm39)	*586K	probably null	Het
Cplane1	G	T	15: 8,245,760 (GRCm39)		probably benign	Het
Dop1a	T	A	9: 86,384,085 (GRCm39)		probably benign	Het
Dync1h1	T	C	12: 110,595,201 (GRCm39)	F1371S	possibly damaging	Het
Eif6	A	G	2: 155,668,101 (GRCm39)	I46T	probably damaging	Het
Esco2	G	A	14: 66,064,035 (GRCm39)	T383M	possibly damaging	Het
Exoc8	T	C	8: 125,624,271 (GRCm39)	D32G	probably damaging	Het
Fam149b	G	T	14: 20,417,941 (GRCm39)	S216I	probably benign	Het
Fam219a	T	C	4: 41,521,645 (GRCm39)	D87G	probably null	Het
Fbxw26	A	T	9: 109,573,939 (GRCm39)	V71D	probably damaging	Het
Gabra4	T	A	5: 71,798,487 (GRCm39)	K164M	probably damaging	Het
Gm57858	T	C	3: 36,080,103 (GRCm39)	D218G	possibly damaging	Het
Gm8603	G	A	17: 13,737,290 (GRCm39)		noncoding transcript	Het
Gpsm1	G	A	2: 26,209,843 (GRCm39)		probably benign	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Kcnj1	A	T	9: 32,305,444 (GRCm39)	D2V	probably benign	Het
Limch1	C	T	5: 67,184,900 (GRCm39)	R797C	probably damaging	Het
Lrrc9	T	A	12: 72,517,038 (GRCm39)	F597I	probably damaging	Het
Lrriq3	T	A	3: 154,835,090 (GRCm39)	I275N	possibly damaging	Het
Mcoln1	T	A	8: 3,560,840 (GRCm39)	S387R	probably damaging	Het
Mgst3	T	A	1: 167,204,848 (GRCm39)	Q58L	probably damaging	Het
Mical1	G	A	10: 41,362,932 (GRCm39)		probably benign	Het
Mmp3	C	A	9: 7,453,673 (GRCm39)	D431E	probably benign	Het
Mx1	T	C	16: 97,256,439 (GRCm39)		probably null	Het
Myo7a	A	G	7: 97,734,673 (GRCm39)	L607P	probably damaging	Het
Myt1l	A	G	12: 29,899,456 (GRCm39)	N153D	probably damaging	Het
Nfu1	A	T	6: 86,996,408 (GRCm39)	T120S	probably damaging	Het
Nhlrc2	T	C	19: 56,564,699 (GRCm39)	V341A	possibly damaging	Het
Notch1	T	C	2: 26,360,901 (GRCm39)	E1148G	probably damaging	Het
Nqo1	C	T	8: 108,117,676 (GRCm39)		probably null	Het
Nwd1	T	A	8: 73,421,949 (GRCm39)	D998E	probably benign	Het
Or8k18	G	A	2: 86,085,357 (GRCm39)	Q227*	probably null	Het
Oxct2a	T	C	4: 123,216,473 (GRCm39)	I303V	probably benign	Het
Parp10	A	T	15: 76,127,185 (GRCm39)	D58E	probably damaging	Het
Pcdha6	T	A	18: 37,102,292 (GRCm39)	V495E	probably damaging	Het
Pitrm1	T	A	13: 6,603,218 (GRCm39)	S88R	probably benign	Het
Pxdn	T	C	12: 30,044,552 (GRCm39)	V510A	probably benign	Het
Ranbp17	T	A	11: 33,216,288 (GRCm39)	D820V	probably damaging	Het
Sec24c	G	T	14: 20,733,212 (GRCm39)	G180C	probably damaging	Het
Serpina3n	T	C	12: 104,379,752 (GRCm39)	S382P	probably benign	Het
Sestd1	A	T	2: 77,042,843 (GRCm39)	M237K	probably null	Het
Sf3a2	T	C	10: 80,639,418 (GRCm39)	I136T	probably damaging	Het
Sh3tc2	A	G	18: 62,107,580 (GRCm39)	Y197C	probably benign	Het
Speer4b	T	C	5: 27,702,893 (GRCm39)	K204E	probably benign	Het
Speer4f1	A	C	5: 17,681,221 (GRCm39)	E33A	possibly damaging	Het
Sspo	T	A	6: 48,461,147 (GRCm39)	D3529E	probably damaging	Het
Stard13	T	C	5: 150,986,253 (GRCm39)	D419G	probably benign	Het
Tg	A	G	15: 66,545,769 (GRCm39)	S164G	possibly damaging	Het
Thap12	A	G	7: 98,359,298 (GRCm39)		probably benign	Het
Thsd1	C	A	8: 22,749,314 (GRCm39)	Y667*	probably null	Het
Tnks	A	C	8: 35,316,465 (GRCm39)	Y885D	possibly damaging	Het
Ttll3	A	G	6: 113,391,102 (GRCm39)	I896V	probably benign	Het
Txnip	T	G	3: 96,466,743 (GRCm39)	F190C	probably damaging	Het
Urb1	T	C	16: 90,573,017 (GRCm39)	D1005G	probably damaging	Het
Usp3	T	C	9: 66,434,352 (GRCm39)		probably null	Het
Usp54	G	T	14: 20,615,060 (GRCm39)	Q794K	probably damaging	Het
Xrn2	A	G	2: 146,903,394 (GRCm39)	Q798R	probably benign	Het
Zfp189	A	G	4: 49,530,342 (GRCm39)	I482V	probably benign	Het
Zfp28	A	G	7: 6,396,506 (GRCm39)	N314D	probably benign	Het
Zmym4	A	G	4: 126,842,221 (GRCm39)		probably null	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
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
R7423:Gnmt	UTSW	17	47,037,066 (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'- ATATCTGCATTAGGGGATGGTC -3'
(R):5'- AAGCCCACATGGTAACCCTG -3'

Sequencing Primer
(F):5'- TTCTGGGAGCCGGAGAAACTC -3'
(R):5'- TGGTAACCCTGGACTACACAGTG -3'

Posted On

2015-10-08