GNMT (glycine N-methyltransferase)

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Gene: GNMT (glycine N-methyltransferase) Homo sapiens

Analyze

Symbol:

GNMT

Name:

glycine N-methyltransferase

RGD ID:

732912

HGNC Page

HGNC

Description:

Exhibits glycine N-methyltransferase activity; glycine binding activity; and identical protein binding activity. Involved in S-adenosylmethionine metabolic process and protein homotetramerization. Localizes to cytosol. Implicated in glycine N-methyltransferase deficiency.

Type:

protein-coding

RefSeq Status:

REVIEWED

Also known as:

epididymis secretory sperm binding protein Li 182mP; HEL-S-182mP

RGD Orthologs

Mouse

Rat

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Gnmt (glycine N-methyltransferase)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Gnmt (glycine N-methyltransferase)	HGNC	EggNOG, Ensembl, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Gnmt (glycine N-methyltransferase)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	GNMT (glycine N-methyltransferase)	NCBI	Ortholog
Canis lupus familiaris (dog):	GNMT (glycine N-methyltransferase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Gnmt (glycine N-methyltransferase)	NCBI	Ortholog
Sus scrofa (pig):	GNMT (glycine N-methyltransferase)	HGNC	Ensembl, Inparanoid, NCBI, OrthoDB, Panther
Chlorocebus sabaeus (African green monkey):	GNMT (glycine N-methyltransferase)	NCBI	Ortholog
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Gnmt (glycine N-methyltransferase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Rattus norvegicus (Norway rat):	Gnmt (glycine N-methyltransferase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Gnmt (glycine N-methyltransferase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|Roundup\|TreeFam)
Danio rerio (zebrafish):	gnmt (glycine N-methyltransferase)	Alliance	DIOPT (PhylomeDB\|TreeFam\|ZFIN)
Drosophila melanogaster (fruit fly):	Gnmt	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|Roundup\|TreeFam)

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	42,960,754 - 42,963,880 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	42,960,754 - 42,963,880 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	42,928,492 - 42,931,618 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	43,036,478 - 43,039,596 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	43,036,477 - 43,039,595	NCBI
Celera	6	44,480,758 - 44,483,869 (+)	NCBI
Cytogenetic Map	6	p21.1	NCBI
HuRef	6	42,645,801 - 42,648,911 (+)	NCBI		HuRef
CHM1_1	6	42,930,961 - 42,934,095 (+)	NCBI		CHM1_1

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Chronic Hepatitis (EXP)

glycine N-methyltransferase deficiency (IAGP)

hepatitis (EXP)

hepatocellular carcinoma (EXP)

hyperhomocysteinemia (EXP)

hypermethioninemia (EXP)

Liver Neoplasms (EXP)

non-alcoholic fatty liver disease (EXP)

Prostatic Neoplasms (EXP)

Zellweger syndrome (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1-naphthyl isothiocyanate (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (EXP)

17beta-hydroxy-5alpha-androstan-3-one (EXP)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,6-di-tert-butyl-4-methylphenol (ISO)

2-nitrofluorene (ISO)

3-chloropropane-1,2-diol (ISO)

3-methylcholanthrene (EXP,ISO)

3H-1,2-dithiole-3-thione (ISO)

4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one (ISO)

4-hydroxyphenyl retinamide (ISO)

5-methyltetrahydrofolic acid (ISO)

acetamide (ISO)

aflatoxin B1 (EXP,ISO)

aflatoxin M1 (EXP)

aflatoxin Q1 (EXP)

ammonium chloride (ISO)

aristolochic acid (ISO)

Aroclor 1254 (ISO)

benzo[a]pyrene (EXP,ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bromobenzene (ISO)

cadmium dichloride (ISO)

calcitriol (EXP)

captan (ISO)

carbon nanotube (ISO)

chloroprene (ISO)

cisplatin (EXP)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (EXP)

cyclosporin A (EXP)

cylindrospermopsin (EXP)

dexamethasone (ISO)

dicrotophos (EXP)

elemental selenium (ISO)

endosulfan (EXP)

fenofibrate (EXP)

finasteride (ISO)

flavonoids (ISO)

flutamide (ISO)

folic acid (ISO)

fructose (ISO)

fumonisin B1 (ISO)

furan (ISO)

gefitinib (ISO)

genistein (ISO)

glafenine (ISO)

gliotoxin (ISO)

GW 4064 (ISO)

Lasiocarpine (EXP)

leflunomide (EXP)

MeIQx (EXP)

metformin (ISO)

methapyrilene (ISO)

methyl methanesulfonate (EXP)

N-nitrosodiethylamine (ISO)

N-nitrosodimethylamine (ISO)

N-Nitrosopyrrolidine (EXP)

naphthalene (ISO)

nefazodone (ISO)

nimesulide (ISO)

O-methyleugenol (EXP)

ochratoxin A (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (ISO)

perfluorononanoic acid (EXP)

perfluorooctane-1-sulfonic acid (ISO)

phenformin (ISO)

phenobarbital (ISO)

PhIP (EXP)

piperonyl butoxide (ISO)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

quercetin (EXP)

rotenone (ISO)

selenium atom (ISO)

senecionine (EXP)

sodium arsenite (EXP,ISO)

sodium dichromate (ISO)

streptozocin (ISO)

sulindac (ISO)

tebuconazole (EXP)

testosterone (EXP,ISO)

tetrachloromethane (ISO)

thioacetamide (ISO)

titanium dioxide (ISO)

triazines (ISO)

trichloroethene (ISO)

triphenyl phosphate (ISO)

troglitazone (EXP)

urethane (EXP)

valdecoxib (ISO)

vancomycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

carboxylic acid metabolic process (TAS)

cellular protein modification process (NAS)

glycine metabolic process (ISO)

glycogen metabolic process (IEA,ISO)

methionine metabolic process (IEA,ISO)

methylation (IEA)

one-carbon metabolic process (IBA,ISO)

protein homotetramerization (IBA,IPI)

regulation of gluconeogenesis (IBA,ISO)

S-adenosylhomocysteine metabolic process (IBA,ISO)

S-adenosylmethionine metabolic process (IBA,IDA,ISO)

sarcosine metabolic process (IBA,ISO)

Cellular Component

cytosol (IBA,IDA,ISO,TAS)

methyltransferase complex (ISO)

nucleus (ISO)

Molecular Function

folic acid binding (IEA,ISO)

glycine binding (IBA,IDA)

glycine N-methyltransferase activity (IBA,IDA,ISO)

identical protein binding (IBA,IPI,ISO)

protein binding (IPI)

S-adenosyl-L-methionine binding (IBA)

S-adenosylmethionine-dependent methyltransferase activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

dihydropyrimidine dehydrogenase deficiency pathway (EXP)

dimethylglycine dehydrogenase deficiency pathway (EXP)

folate mediated one-carbon metabolic pathway (ISO)

folate metabolic pathway (ISO)

glycine, serine and threonine metabolic pathway (IEA)

homocysteine metabolic pathway (ISO)

methionine cycle/metabolic pathway (TAS)

nonketotic hyperglycinemia pathway (EXP)

sarcosinemia pathway (EXP)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Autosomal recessive inheritance (IAGP)

Elevated hepatic transaminase (IAGP)

Hepatomegaly (IAGP)

Hypermethioninemia (IAGP)

References

References - curated


1.	Cavuoto P and Fenech MF, Cancer Treat Rev. 2012 Oct;38(6):726-36. doi: 10.1016/j.ctrv.2012.01.004. Epub 2012 Feb 17.
2.	GOA_HUMAN data from the GO Consortium
3.	KEGG
4.	Lu SC and Mato JM, Physiol Rev. 2012 Oct;92(4):1515-42. doi: 10.1152/physrev.00047.2011.
5.	OMIM Disease Annotation Pipeline
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	Pipeline to import SMPDB annotations from SMPDB into RGD
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	RGD automated import pipeline for human HPO-to-gene-to-disease annotations

Additional References at PubMed

PMID:2722853	PMID:6157075	PMID:8281755	PMID:9261130	PMID:9495250	PMID:10843803	PMID:11596649	PMID:11810299	PMID:12477932	PMID:12566309	PMID:12697024	PMID:14651980
PMID:14739680	PMID:15340920	PMID:15489334	PMID:16189514	PMID:16317120	PMID:17332283	PMID:17660255	PMID:18029348	PMID:18624901	PMID:19035462	PMID:19048631	PMID:19146867
PMID:19161160	PMID:19439180	PMID:20634891	PMID:21044950	PMID:21411609	PMID:21516116	PMID:21572396	PMID:21691217	PMID:21873635	PMID:21988832	PMID:22160218	PMID:22183894
PMID:22264868	PMID:22415010	PMID:22807109	PMID:22850906	PMID:23475283	PMID:23883094	PMID:23997240	PMID:24651765	PMID:24800880	PMID:25416956	PMID:25502805	PMID:26871637
PMID:27107014	PMID:28205209	PMID:30021884	PMID:30115977	PMID:30318092	PMID:30796242	PMID:31057302	PMID:31199045	PMID:31515488	PMID:32296183

Genomics

Comparative Map Data

GNMT
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	42,960,754 - 42,963,880 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	42,960,754 - 42,963,880 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	42,928,492 - 42,931,618 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	43,036,478 - 43,039,596 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	43,036,477 - 43,039,595	NCBI
Celera	6	44,480,758 - 44,483,869 (+)	NCBI
Cytogenetic Map	6	p21.1	NCBI
HuRef	6	42,645,801 - 42,648,911 (+)	NCBI		HuRef
CHM1_1	6	42,930,961 - 42,934,095 (+)	NCBI		CHM1_1

Gnmt
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	47,036,590 - 47,040,137 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	17	47,036,590 - 47,040,094 (-)	Ensembl
GRCm38	17	46,725,664 - 46,729,211 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	46,725,664 - 46,729,168 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	46,862,613 - 46,866,114 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	46,188,855 - 46,192,356 (-)	NCBI			mm8
Celera	17	50,161,350 - 50,164,841 (-)	NCBI		Celera
Cytogenetic Map	17	C	NCBI
cM Map	17	22.9	NCBI

Gnmt
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	14,254,675 - 14,258,028 (+)	NCBI
Rnor_6.0 Ensembl	9	16,565,225 - 16,568,627 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	9	16,565,274 - 16,568,626 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	9	15,471,889 - 15,475,241 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	10,127,092 - 10,130,444 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	9	10,124,413 - 10,127,766 (+)	NCBI
Celera	9	12,003,123 - 12,006,473 (+)	NCBI		Celera
Cytogenetic Map	9	q12	NCBI

Gnmt
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955437	8,944,047 - 8,946,642 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955437	8,944,288 - 8,946,642 (+)	NCBI	ChiLan1.0	ChiLan1.0

GNMT
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	6	43,846,560 - 43,849,679 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	43,846,560 - 43,849,679 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	42,550,631 - 42,554,385 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

GNMT
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	11,500,363 - 11,503,075 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	11,500,392 - 11,503,481 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	11,527,380 - 11,530,090 (+)	NCBI
ROS_Cfam_1.0	12	11,981,562 - 11,984,272 (+)	NCBI
UMICH_Zoey_3.1	12	11,509,980 - 11,512,694 (+)	NCBI
UNSW_CanFamBas_1.0	12	11,594,281 - 11,596,795 (+)	NCBI
UU_Cfam_GSD_1.0	12	11,688,299 - 11,691,025 (+)	NCBI

Gnmt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_ltri_2	NW_024404946	46,995,031 - 46,998,424 (+)	NCBI
SpeTri2.0	NW_004936476	16,961,734 - 16,965,487 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

GNMT
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	38,038,358 - 38,041,218 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	38,038,359 - 38,041,218 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	43,486,726 - 43,489,585 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

GNMT
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	17	29,196,142 - 29,199,728 (-)	NCBI
ChlSab1.1 Ensembl	17	29,196,321 - 29,198,947 (-)	Ensembl

Position Markers

D6S1532E

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	42,931,819 - 42,931,922	UniSTS	GRCh37
Build 36	6	43,039,797 - 43,039,900	RGD	NCBI36
Celera	6	44,484,066 - 44,484,169	RGD
Cytogenetic Map	6	p12	UniSTS
Cytogenetic Map	6	p21.1	UniSTS
HuRef	6	42,649,108 - 42,649,211	UniSTS

GNMT

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	42,930,811 - 42,931,128	UniSTS	GRCh37
Build 36	6	43,038,789 - 43,039,106	RGD	NCBI36
Celera	6	44,483,062 - 44,483,379	RGD
HuRef	6	42,648,105 - 42,648,421	UniSTS

STS-U56602

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	42,931,840 - 42,932,037	UniSTS	GRCh37
Build 36	6	43,039,818 - 43,040,015	RGD	NCBI36
Celera	6	44,484,087 - 44,484,284	RGD
Cytogenetic Map	6	p12	UniSTS
Cytogenetic Map	6	p21.1	UniSTS
HuRef	6	42,649,129 - 42,649,326	UniSTS
GeneMap99-GB4 RH Map	6	164.99	UniSTS
NCBI RH Map	6	653.1	UniSTS

STS-D20352

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	42,931,751 - 42,931,940	UniSTS	GRCh37
Build 36	6	43,039,729 - 43,039,918	RGD	NCBI36
Celera	6	44,483,998 - 44,484,187	RGD
Cytogenetic Map	6	p12	UniSTS
Cytogenetic Map	6	p21.1	UniSTS
HuRef	6	42,649,040 - 42,649,229	UniSTS
GeneMap99-GB4 RH Map	6	164.26	UniSTS
NCBI RH Map	6	643.1	UniSTS

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	344
Count of miRNA genes:	325
Interacting mature miRNAs:	342
Transcripts:	ENST00000372808
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system

circulatory system

endocrine system

exocrine system

hemolymphoid system

hepatobiliary system

integumental system

musculoskeletal system

nervous system

renal system

reproductive system

respiratory system

sensory system

adipose tissue

appendage

entire extraembryonic component

pharyngeal arch

High

Medium

251

534

445

388

151

221

Low

2027

2737

1168

174

1739

4062

1857

3408

345

1196

1511

113

1161

2555

Below cutoff

151

181

274

284

155

218

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NG_008396	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001318865	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_018960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NR_134899	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF101475	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF101477	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL158815	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC032627	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471081	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ224320	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HY010451	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KU178603	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KU178604	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KU178605	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X62250	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENST00000372808 ⟹ ENSP00000361894

RefSeq Status:

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p13 Ensembl	6	42,960,754 - 42,963,880 (+)	Ensembl

RefSeq Acc Id:

NM_001318865 ⟹ NP_001305794

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	42,960,754 - 42,963,880 (+)	NCBI
CHM1_1	6	42,930,961 - 42,934,095 (+)	NCBI

Sequence:

show sequence

AGGCGCGGCGCAGGATGGTGGACAGCGTGTACCGGACCCGCTCCCTGGGGGTGGCGGCCGAAGG
GCTCCCGGACCAGTACGCGGACGGGGAGGCGGCGCGCGTGTGGCAGCTGTATATCGGAGACACC
CGCAGCCGCACCGCCGAGTACAAGGCATGGCTGCTTGGGCTGCTGCGCCAGCACGGCTGCCAGC
GGGTGCTCGACGTAGCCTGTGGCACTGGGGTGGACTCCATTATGCTGGTGGAAGAGGGCTTCAG
TGTGACGAGTGTGGATGCCAGTGACAAGATGCTGAAGTATGCACTTAAGGAGCGCTGGAACCGG
CGGCACGAGCCCGCCTTCGACAAGTGGGTCATCGAAGAAGCCAACTGGATGACTCTGGACAAAG
ATGTGCCCCAGTCAGCAGAGGGTGGCTTTGATGCTGTCATCTGCCTTGGAAACAGTTTCGCTCA
CTTGCCAGACTGCAAAGGGGGCCTACTGGTCATTGATCATCGCAACTACGACCACATCCTCAGT
ACAGGCTGTGCACCCCCAGGGAAGAACATCTACTATAAGAGTGACTTGACCAAGGACGTCACAA
CATCAGTGCTGATAGTGAACAACAAGGCCCACATGGTGACCCTGGACTATACGGTGCAGGTGCC
GGGGGCTGGCCAGGATGGCTCTCCTGGCTTGAGTAAGTTCCGGCTCTCCTACTACCCACACTGT
CTGGCATCCTTCACGGAGCTGCTCCAAGCAGCCTTCGGAGGTAAGTGCCAGCACAGCGTCCTGG
GCGACTTCAAGCCTTACAAGCCAGGCCAAACCTACATTCCCTGCTACTTCATCCACGTGCTCAA
GAGGACAGACTGAGTGTGGCCTCAGCTCCCACAAGCCTCTGCCCAGGCACTGCTAGGCTCTGTC
TGGAAGATGGGGACCAGCAGCCCCACACCAGGGCCAGCCTCTAGAGCAGACTACAGCTGGGGTG
CAGGGATGTGGGTTCCACAGACGGAAGGGTAAACAATATAGTCTTTTTCAGTTCCTGCAAAAAA
AAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

NM_018960 ⟹ NP_061833

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	42,960,754 - 42,963,880 (+)	NCBI
GRCh37	6	42,928,500 - 42,931,618 (+)	ENTREZGENE
Build 36	6	43,036,478 - 43,039,596 (+)	NCBI Archive
HuRef	6	42,645,801 - 42,648,911 (+)	ENTREZGENE
CHM1_1	6	42,930,961 - 42,934,095 (+)	NCBI

Sequence:

show sequence

AGGCGCGGCGCAGGATGGTGGACAGCGTGTACCGGACCCGCTCCCTGGGGGTGGCGGCCGAAGG
GCTCCCGGACCAGTACGCGGACGGGGAGGCGGCGCGCGTGTGGCAGCTGTATATCGGAGACACC
CGCAGCCGCACCGCCGAGTACAAGGCATGGCTGCTTGGGCTGCTGCGCCAGCACGGCTGCCAGC
GGGTGCTCGACGTAGCCTGTGGCACTGGGGTGGACTCCATTATGCTGGTGGAAGAGGGCTTCAG
TGTGACGAGTGTGGATGCCAGTGACAAGATGCTGAAGTATGCACTTAAGGAGCGCTGGAACCGG
CGGCACGAGCCCGCCTTCGACAAGTGGGTCATCGAAGAAGCCAACTGGATGACTCTGGACAAAG
ATGTGCCCCAGTCAGCAGAGGGTGGCTTTGATGCTGTCATCTGCCTTGGAAACAGTTTCGCTCA
CTTGCCAGACTGCAAAGGGGACCAGAGTGAGCACCGGCTGGCGCTGAAAAACATTGCGAGCATG
GTGCGGGCAGGGGGCCTACTGGTCATTGATCATCGCAACTACGACCACATCCTCAGTACAGGCT
GTGCACCCCCAGGGAAGAACATCTACTATAAGAGTGACTTGACCAAGGACGTCACAACATCAGT
GCTGATAGTGAACAACAAGGCCCACATGGTGACCCTGGACTATACGGTGCAGGTGCCGGGGGCT
GGCCAGGATGGCTCTCCTGGCTTGAGTAAGTTCCGGCTCTCCTACTACCCACACTGTCTGGCAT
CCTTCACGGAGCTGCTCCAAGCAGCCTTCGGAGGTAAGTGCCAGCACAGCGTCCTGGGCGACTT
CAAGCCTTACAAGCCAGGCCAAACCTACATTCCCTGCTACTTCATCCACGTGCTCAAGAGGACA
GACTGAGTGTGGCCTCAGCTCCCACAAGCCTCTGCCCAGGCACTGCTAGGCTCTGTCTGGAAGA
TGGGGACCAGCAGCCCCACACCAGGGCCAGCCTCTAGAGCAGACTACAGCTGGGGTGCAGGGAT
GTGGGTTCCACAGACGGAAGGGTAAACAATATAGTCTTTTTCAGTTCCTGCAAAAAAAAAAAAA
AAAAAAAAAAA

hide sequence

RefSeq Acc Id:

NR_134899

RefSeq Status:

REVIEWED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	42,960,754 - 42,963,880 (+)	NCBI
CHM1_1	6	42,930,961 - 42,934,095 (+)	NCBI

Sequence:

show sequence

AGGCGCGGCGCAGGATGGTGGACAGCGTGTACCGGACCCGCTCCCTGGGGGTGGCGGCCGAAGG
GCTCCCGGACCAGTACGCGGACGGGGAGGCGGCGCGCGTGTGGCAGCTGTATATCGGAGACACC
CGCAGCCGCACCGCCGAGTACAAGGCATGGCTGCTTGGGCTGCTGCGCCAGCACGGCTGCCAGC
GGGTGCTCGACGTAGCCTGTGGCACTGGGGTGGACTCCATTATGCTGGTGGAAGAGGGCTTCAG
TGTGACGAGTGTGGATGCCAGTGACAAGATGCTGAAGTATGCACTTAAGGAGCGCTGGAACCGG
CGGCACGAGCCCGCCTTCGACAAGTGGGTCATCGAAGAAGCCAACTGGATGACTCTGGACAAAG
ATGTGCCCCAGTCAGCAGAGGGTGGCTTTGATGCTGTCATCTGCCTTGGAAACAGTTTCGCTCA
CTTGCCAGACTGCAAAGAGTGACTTGACCAAGGACGTCACAACATCAGTGCTGATAGTGAACAA
CAAGGCCCACATGGTGACCCTGGACTATACGGTGCAGGTGCCGGGGGCTGGCCAGGATGGCTCT
CCTGGCTTGAGTAAGTTCCGGCTCTCCTACTACCCACACTGTCTGGCATCCTTCACGGAGCTGC
TCCAAGCAGCCTTCGGAGGTAAGTGCCAGCACAGCGTCCTGGGCGACTTCAAGCCTTACAAGCC
AGGCCAAACCTACATTCCCTGCTACTTCATCCACGTGCTCAAGAGGACAGACTGAGTGTGGCCT
CAGCTCCCACAAGCCTCTGCCCAGGCACTGCTAGGCTCTGTCTGGAAGATGGGGACCAGCAGCC
CCACACCAGGGCCAGCCTCTAGAGCAGACTACAGCTGGGGTGCAGGGATGTGGGTTCCACAGAC
GGAAGGGTAAACAATATAGTCTTTTTCAGTTCCTGCAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001305794	(Get FASTA)	NCBI Sequence Viewer
	NP_061833	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF78289	(Get FASTA)	NCBI Sequence Viewer
	AAF78290	(Get FASTA)	NCBI Sequence Viewer
	AAH32627	(Get FASTA)	NCBI Sequence Viewer
	ACI46012	(Get FASTA)	NCBI Sequence Viewer
	ALQ34061	(Get FASTA)	NCBI Sequence Viewer
	ALQ34062	(Get FASTA)	NCBI Sequence Viewer
	ALQ34063	(Get FASTA)	NCBI Sequence Viewer
	CAA44164	(Get FASTA)	NCBI Sequence Viewer
	EAX04123	(Get FASTA)	NCBI Sequence Viewer
	EAX04124	(Get FASTA)	NCBI Sequence Viewer
	Q14749	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_061833 ⟸ NM_018960
- Peptide Label:	isoform 1
- UniProtKB:	Q14749 (UniProtKB/Swiss-Prot), V9HW60 (UniProtKB/TrEMBL)
- Sequence:	show sequence MVDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDV ACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVPQS AEGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNYDHILSTGCAPPG KNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTVQVPGAGQDGSPGLSKFRLSYYPHCLASFTEL LQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRTD hide sequence

RefSeq Acc Id:	NP_001305794 ⟸ NM_001318865
- Peptide Label:	isoform 2
- UniProtKB:	Q14749 (UniProtKB/Swiss-Prot), A0A0S2Z5F2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MVDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDV ACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVPQS AEGGFDAVICLGNSFAHLPDCKGGLLVIDHRNYDHILSTGCAPPGKNIYYKSDLTKDVTTSVLI VNNKAHMVTLDYTVQVPGAGQDGSPGLSKFRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKP YKPGQTYIPCYFIHVLKRTD hide sequence

RefSeq Acc Id:

ENSP00000361894 ⟸ ENST00000372808

Protein Domains

Methyltransf_25

Promoters

RGD ID:

6804272

Promoter ID:

HG_KWN:53602

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, HeLa_S3, Lymphoblastoid

Transcripts:

OTTHUMT00000040568

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	6	43,036,191 - 43,036,792 (+)	MPROMDB

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_018960.6(GNMT):c.149T>C (p.Leu50Pro)	single nucleotide variant	Glycine N-methyltransferase deficiency [RCV000004386]	Chr6:42960916 [GRCh38] Chr6:42928654 [GRCh37] Chr6:6p21.1	pathogenic
NM_018960.6(GNMT):c.529C>A (p.His177Asn)	single nucleotide variant	Glycine N-methyltransferase deficiency [RCV000004387]\|Peroxisome biogenesis disorders, Zellweger syndrome spectrum [RCV001208834]	Chr6:42963149 [GRCh38] Chr6:42930887 [GRCh37] Chr6:6p21.1	pathogenic\|likely benign\|uncertain significance
GRCh38/hg38 6p21.1(chr6:42368558-44590544)x1	copy number loss	See cases [RCV000051011]	Chr6:42368558..44590544 [GRCh38] Chr6:42336296..44558281 [GRCh37] Chr6:42444274..44666259 [NCBI36] Chr6:6p21.1	pathogenic
GRCh38/hg38 6p21.1(chr6:42133625-44106194)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051899]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051899]\|See cases [RCV000051899]	Chr6:42133625..44106194 [GRCh38] Chr6:42101363..44073931 [GRCh37] Chr6:42209341..44181909 [NCBI36] Chr6:6p21.1	pathogenic
GRCh38/hg38 6p21.2-21.1(chr6:37777369-45653843)x1	copy number loss	See cases [RCV000052181]	Chr6:37777369..45653843 [GRCh38] Chr6:37745145..45621580 [GRCh37] Chr6:37853123..45729558 [NCBI36] Chr6:6p21.2-21.1	pathogenic
GRCh38/hg38 6p21.1-12.3(chr6:41638061-46512949)x1	copy number loss	See cases [RCV000052182]	Chr6:41638061..46512949 [GRCh38] Chr6:41605799..46480686 [GRCh37] Chr6:41713777..46588645 [NCBI36] Chr6:6p21.1-12.3	pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3	copy number gain	See cases [RCV000143497]	Chr6:156974..46789291 [GRCh38] Chr6:156974..46757028 [GRCh37] Chr6:101974..46864987 [NCBI36] Chr6:6p25.3-12.3	pathogenic
NM_018960.6(GNMT):c.422A>G (p.Asn141Ser)	single nucleotide variant	Glycine N-methyltransferase deficiency [RCV000203283]	Chr6:42962849 [GRCh38] Chr6:42930587 [GRCh37] Chr6:6p21.1	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3	copy number gain	See cases [RCV000512067]	Chr6:156975..170919482 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)	copy number gain	See cases [RCV000510595]	Chr6:156975..170919482 [GRCh37] Chr6:6p25.3-q27	pathogenic
NM_018960.6(GNMT):c.25C>G (p.Arg9Gly)	single nucleotide variant	not provided [RCV001052288]	Chr6:42960792 [GRCh38] Chr6:42928530 [GRCh37] Chr6:6p21.1	uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3	copy number gain	not provided [RCV000745403]	Chr6:108666..170980171 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3	copy number gain	not provided [RCV000745400]	Chr6:60107..171054786 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3	copy number gain	not provided [RCV000745404]	Chr6:165632..170919470 [GRCh37] Chr6:6p25.3-q27	pathogenic
NM_018960.6(GNMT):c.189C>T (p.Asp63=)	single nucleotide variant	not provided [RCV000926847]	Chr6:42960956 [GRCh38] Chr6:42928694 [GRCh37] Chr6:6p21.1	likely benign
NM_018960.6(GNMT):c.312C>T (p.His104=)	single nucleotide variant	not provided [RCV000898855]	Chr6:42962317 [GRCh38] Chr6:42930055 [GRCh37] Chr6:6p21.1	likely benign
NM_018960.6(GNMT):c.430G>A (p.Ala144Thr)	single nucleotide variant	not provided [RCV001070051]	Chr6:42962857 [GRCh38] Chr6:42930595 [GRCh37] Chr6:6p21.1	uncertain significance
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367)	copy number gain	not provided [RCV000767714]	Chr6:29455465..81447367 [GRCh37] Chr6:6p22.1-q14.1	pathogenic
NM_018960.6(GNMT):c.411C>T (p.Ile137=)	single nucleotide variant	not provided [RCV000960884]	Chr6:42962838 [GRCh38] Chr6:42930576 [GRCh37] Chr6:6p21.1	benign
GRCh37/hg19 6p21.1(chr6:42903316-42954083)x3	copy number gain	not provided [RCV000849694]	Chr6:42903316..42954083 [GRCh37] Chr6:6p21.1	uncertain significance
GRCh37/hg19 6p21.1(chr6:42903316-42955264)x3	copy number gain	not provided [RCV000849537]	Chr6:42903316..42955264 [GRCh37] Chr6:6p21.1	uncertain significance
NM_018960.6(GNMT):c.519G>A (p.Leu173=)	single nucleotide variant	not provided [RCV000884985]	Chr6:42963139 [GRCh38] Chr6:42930877 [GRCh37] Chr6:6p21.1	benign
NM_018960.6(GNMT):c.10A>G (p.Ser4Gly)	single nucleotide variant	not provided [RCV001242540]	Chr6:42960777 [GRCh38] Chr6:42928515 [GRCh37] Chr6:6p21.1	uncertain significance
NM_018960.6(GNMT):c.508G>C (p.Gly170Arg)	single nucleotide variant	not provided [RCV001067237]	Chr6:42963128 [GRCh38] Chr6:42930866 [GRCh37] Chr6:6p21.1	uncertain significance
NC_000006.12:g.(?_42923027)_(42984704_?)dup	duplication	Peroxisome biogenesis disorders, Zellweger syndrome spectrum [RCV001033858]	Chr6:42890765..42952442 [GRCh37] Chr6:6p21.1	uncertain significance

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:4415	AgrOrtholog
COSMIC	GNMT	COSMIC
Ensembl Genes	ENSG00000124713	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSP00000361894	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000372808	ENTREZGENE, UniProtKB/Swiss-Prot
GTEx	ENSG00000124713	GTEx
HGNC ID	HGNC:4415	ENTREZGENE
Human Proteome Map	GNMT	Human Proteome Map
InterPro	Gly/Sar_N_MeTrfase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Methyltransf_25	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SAM-dependent_MTases	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	hsa:27232	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	27232	ENTREZGENE
OMIM	606628	OMIM
	606664	OMIM
PANTHER	PTHR16458	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Methyltransf_25	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	PA28794	PharmGKB
PIRSF	Gly_N-mtase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	SAM_GNMT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF53335	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0S2Z594_HUMAN	UniProtKB/TrEMBL
	A0A0S2Z5F2	ENTREZGENE, UniProtKB/TrEMBL
	GNMT_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
	V9HW60	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	Q5T8W2	UniProtKB/Swiss-Prot
	Q9NNZ1	UniProtKB/Swiss-Prot
	Q9NS24	UniProtKB/Swiss-Prot

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)