Mutagenetix > Incidental Mutation

Incidental Mutation 'R0940:Gnmt'

81466

Institutional Source

Beutler Lab

Gene Symbol

Gnmt

Ensembl Gene

ENSMUSG00000002769

Gene Name

glycine N-methyltransferase

Synonyms

glycine N methyl transferase

MMRRC Submission

039079-MU

Accession Numbers

Essential gene?

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

Stock #

R0940 (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 47037271 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 171 (L171P)

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: L171P

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

SMART Domains

Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: L171P

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

0.9479

Coding Region Coverage

1x: 99.5%
3x: 99.1%
10x: 98.0%
20x: 96.7%

Validation Efficiency

100% (68/68)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810064F22Rik	C	T	9: 22,119,367 (GRCm39)		noncoding transcript	Het
2610021A01Rik	T	G	7: 41,275,858 (GRCm39)	I520M	probably damaging	Het
Ackr4	A	G	9: 103,976,831 (GRCm39)	F39L	probably damaging	Het
Adgre5	C	T	8: 84,460,126 (GRCm39)	S92N	probably damaging	Het
Adrb2	T	C	18: 62,312,762 (GRCm39)	D21G	probably benign	Het
Akr1c6	G	A	13: 4,486,372 (GRCm39)	E60K	probably benign	Het
Bcl7c	T	A	7: 127,306,503 (GRCm39)	N96I	possibly damaging	Het
Brca1	A	T	11: 101,422,969 (GRCm39)	S106R	possibly damaging	Het
C6	A	T	15: 4,764,717 (GRCm39)	T138S	probably benign	Het
Cul3	T	C	1: 80,300,564 (GRCm39)		probably benign	Het
Dnah8	T	A	17: 31,022,217 (GRCm39)	M3939K	probably damaging	Het
Dock4	T	A	12: 40,681,626 (GRCm39)		probably benign	Het
Dsc2	T	G	18: 20,183,116 (GRCm39)	T101P	probably damaging	Het
Dynlt1b	T	C	17: 6,697,649 (GRCm39)		probably benign	Het
E330013P04Rik	A	G	19: 60,150,354 (GRCm39)		noncoding transcript	Het
Fggy	A	G	4: 95,585,238 (GRCm39)	E39G	probably benign	Het
Fhip1a	A	G	3: 85,572,797 (GRCm39)	V952A	possibly damaging	Het
Fmo6	A	T	1: 162,753,795 (GRCm39)	C116S	probably benign	Het
Gadd45a	A	G	6: 67,013,813 (GRCm39)	I44T	possibly damaging	Het
Gmps	A	G	3: 63,883,743 (GRCm39)		probably benign	Het
Hnrnpm	G	A	17: 33,868,976 (GRCm39)	R523C	probably damaging	Het
Inpp5a	T	C	7: 139,105,654 (GRCm39)	Y202H	probably damaging	Het
Kank3	C	T	17: 34,036,450 (GRCm39)	S106F	probably damaging	Het
Lmcd1	A	G	6: 112,305,658 (GRCm39)	D253G	probably benign	Het
Lrrk2	A	T	15: 91,613,284 (GRCm39)	I803F	possibly damaging	Het
Mybpc2	T	C	7: 44,156,311 (GRCm39)	K834R	probably benign	Het
Mycbp2	A	T	14: 103,500,129 (GRCm39)		probably benign	Het
Myh4	A	T	11: 67,133,689 (GRCm39)	N243Y	probably damaging	Het
Myorg	A	G	4: 41,497,996 (GRCm39)	Y545H	probably damaging	Het
Nfatc1	C	T	18: 80,679,110 (GRCm39)	M759I	probably benign	Het
Nipal4	A	G	11: 46,041,139 (GRCm39)	I352T	possibly damaging	Het
Nomo1	A	G	7: 45,683,329 (GRCm39)	E25G	possibly damaging	Het
Or10j27	A	G	1: 172,958,020 (GRCm39)	S255P	probably benign	Het
Or13a19	T	C	7: 139,903,065 (GRCm39)	I151T	probably benign	Het
Or14j7	A	G	17: 38,234,591 (GRCm39)	I45V	probably damaging	Het
Or1e32	T	C	11: 73,705,050 (GRCm39)	N286S	probably damaging	Het
Or4c116	T	A	2: 88,942,419 (GRCm39)	I146L	probably benign	Het
Or5p66	T	C	7: 107,886,264 (GRCm39)	D23G	probably benign	Het
Pabpn1l	A	G	8: 123,349,183 (GRCm39)	V78A	probably benign	Het
Pde6b	T	A	5: 108,568,203 (GRCm39)	I327N	possibly damaging	Het
Phrf1	T	C	7: 140,834,768 (GRCm39)		probably benign	Het
Pkm	C	T	9: 59,575,818 (GRCm39)		probably benign	Het
Plxna2	G	A	1: 194,482,863 (GRCm39)	V1519I	probably benign	Het
Ppp2cb	T	C	8: 34,105,689 (GRCm39)		probably null	Het
Prickle2	A	G	6: 92,387,984 (GRCm39)	Y473H	probably benign	Het
Prpf3	A	G	3: 95,751,535 (GRCm39)	W389R	probably damaging	Het
Psme4	G	A	11: 30,765,264 (GRCm39)	E544K	possibly damaging	Het
Relb	A	T	7: 19,345,767 (GRCm39)	D395E	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf213	A	G	11: 119,307,389 (GRCm39)	N683S	probably benign	Het
Rtel1	T	C	2: 180,964,596 (GRCm39)	C102R	probably benign	Het
Sel1l3	C	T	5: 53,301,379 (GRCm39)		probably benign	Het
Slc8a2	A	G	7: 15,878,887 (GRCm39)	T458A	probably benign	Het
Smc3	T	A	19: 53,629,340 (GRCm39)	M931K	probably benign	Het
Sorbs2	T	C	8: 46,249,539 (GRCm39)	V795A	probably benign	Het
Tgm3	A	G	2: 129,854,326 (GRCm39)	S2G	probably benign	Het
Tpbpa	T	C	13: 61,087,867 (GRCm39)	T75A	probably damaging	Het
Trub1	A	G	19: 57,473,495 (GRCm39)		probably benign	Het
Uggt2	A	G	14: 119,328,604 (GRCm39)		probably null	Het
Ugt2a3	A	G	5: 87,475,065 (GRCm39)	V393A	possibly damaging	Het
Vav3	T	A	3: 109,470,151 (GRCm39)	M532K	possibly damaging	Het
Zfp616	A	T	11: 73,975,850 (GRCm39)	K706N	probably damaging	Het
Zkscan1	T	C	5: 138,091,432 (GRCm39)	F55S	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
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
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'- ATACCTGAAGCCAGGAGAGCCATC -3'
(R):5'- TGCTCACTTGCCAGACTGCAAAG -3'

Sequencing Primer
(F):5'- AGAGCCATCTCTGCCAGTG -3'
(R):5'- CTGATAAGGCAGACCTGCATTTTG -3'

Posted On

2013-11-07