Glycine N-Methyltransferase Deficiency disease: Malacards - Research Articles, Drugs, Genes, Clinical Trials

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Aliases & Classifications for Glycine N-Methyltransferase Deficiency

MalaCards integrated aliases for Glycine N-Methyltransferase Deficiency:

Name: Glycine N-Methyltransferase Deficiency ⁵⁷ ¹² ⁵³ ⁵⁹ ⁷⁵ ²⁹ ¹³ ⁶ ¹⁵ ⁴⁰ ⁷³

Gnmt Deficiency ⁵⁷ ¹² ⁵³ ⁷⁵ ⁵⁵

Hypermethioninemia Due to Glycine N-Methyltransferase Deficiency ¹² ⁵³ ⁵⁹

Hypermethioninemia Due to Gnmt Deficiency ¹² ⁵³ ⁵⁹

Hypermethioninemia ⁷⁵ ⁷³

Hepatic Methionine Adenosyltransferase Deficiency ⁷³

Glycine N-Methyltransferase ¹³

Characteristics:

OMIM:

⁵⁷

Inheritance:
autosomal recessive

HPO:

³²

glycine n-methyltransferase deficiency:
Inheritance autosomal recessive inheritance

Classifications:

MalaCards categories:
Global: Genetic diseases Rare diseases Metabolic diseases
Anatomical: Liver diseases Blood diseases

See all MalaCards categories (disease lists)

ICD10: ³³ ³⁴

Endocrine, nutritional and metabolic diseases

Metabolic disorders

Other disorders of amino-acid metabolism

Disorders of sulfur-bearing amino-acid metabolism

Orphanet: ⁵⁹

Inborn errors of metabolism

External Ids:

OMIM ⁵⁷ 606664

Disease Ontology ¹² DOID:0111037

ICD10 ³³ E72.1

Orphanet ⁵⁹ ORPHA289891

UMLS via Orphanet ⁷⁴ C1847720

ICD10 via Orphanet ³⁴ E72.1

MedGen ⁴² C1847720

SNOMED-CT via HPO ⁶⁹ 258211005 80515008 166603001 more

UMLS ⁷³ C1847720 C0268621 C4048705

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Summaries for Glycine N-Methyltransferase Deficiency

NIH Rare Diseases : ⁵³ Glycine N-methyltransferase deficiency (GNMT deficiency) is a very rare condition characterized by persistent and isolated excess levels of methionine in the blood (hypermethioninemia). The only clinical abnormalities are mild increase of the liver size (hepatomegaly) and chronic elevation of the transaminase levels in the blood without liver disease. Methionine may also be increased in urine. However, because elevated levels of methionine in the blood itself is a risk factor for development of neurological signs and symptoms, people with GNMT deficiency can have neurological problems when methionine levels are greater than 800 μmol/L. GNMT deficiency is caused by mutations in the GNMT gene. Inheritance is autosomal recessive. Treatment is not needed in most cases.

MalaCards based summary : Glycine N-Methyltransferase Deficiency, also known as gnmt deficiency, is related to methionine adenosyltransferase i/iii deficiency and hypermethioninemia. An important gene associated with Glycine N-Methyltransferase Deficiency is GNMT (Glycine N-Methyltransferase), and among its related pathways/superpathways are Metabolism and Selenium Micronutrient Network. Affiliated tissues include liver, prostate and nk cells, and related phenotypes are hepatomegaly and hypermethioninemia

Disease Ontology : ¹² A hypermethioninemia characterized by autosomal recessive inheritance of persistent isolated hypermethioninemia without cystathionine beta-synthase deficiency, tyrosinemia type I, or liver disease that has material basis in homozygous or compound heterozygous mutation in the GNMT gene on chromosome 6p21.

UniProtKB/Swiss-Prot : ⁷⁵ Glycine N-methyltransferase deficiency: The only clinical abnormalities in patients with this deficiency are mild hepatomegaly and chronic elevation of serum transaminases.

Wikipedia : ⁷⁶ Hypermethioninemia is an excess of the amino acid methionine, in the blood. This condition can occur... more...

Description from OMIM: 606664

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Related Diseases for Glycine N-Methyltransferase Deficiency

Diseases related to Glycine N-Methyltransferase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 38)

#	Related Disease	Score	Top Affiliating Genes
1	methionine adenosyltransferase i/iii deficiency	33.1	CBS MAT1A
2	hypermethioninemia	32.5	AHCY CBS GNMT MAT1A MAT2A
3	homocystinuria	30.2	CBS MAT1A MTHFR
4	hypermethioninemia due to adenosine kinase deficiency	12.6
5	hypermethioninemia with s-adenosylhomocysteine hydrolase deficiency	12.5
6	methionine adenosyltransferase deficiency	11.4
7	alcoholic hepatitis	10.5
8	pancreatic ductal adenocarcinoma	10.5
9	hepatocellular carcinoma	10.4
10	prostate cancer	10.3
11	tyrosinemia	10.3
12	hypertrichosis universalis congenita, ambras type	10.2	MAT1A MAT2A
13	lens subluxation	10.2	CBS MTHFR
14	alpha-methylacetoacetic aciduria	10.1
15	grange syndrome	10.1	CBS MTHFR
16	niemann-pick disease type c, severe perinatal form	10.1	NPC1 NPC2
17	niemann-pick disease type c, late infantile neurologic onset	10.1	NPC1 NPC2
18	niemann-pick disease type c, severe early infantile neurologic onset	10.1	NPC1 NPC2
19	niemann-pick disease type c, adult neurologic onset	10.1	NPC1 NPC2
20	niemann-pick disease type c, juvenile neurologic onset	10.1	NPC1 NPC2
21	homocysteinemia	10.1	AHCY CBS MTHFR
22	cystathioninuria	10.0	CBS MTHFR
23	hyperinsulinemic hypoglycemia	10.0
24	cholestasis	10.0
25	encephalopathy	10.0
26	cleft palate, isolated	10.0
27	cholangiocarcinoma	10.0
28	glycogen storage disease	10.0
29	hepatitis	10.0
30	ulcerative colitis	10.0
31	colitis	10.0
32	kidney disease	10.0
33	cleft lip	10.0
34	allergic encephalomyelitis	10.0
35	niemann-pick disease, type a	10.0	NPC1 NPC2
36	niemann-pick disease, type c2	10.0	NPC1 NPC2
37	sphingolipidosis	9.9	ADPRH NPC1 NPC2
38	niemann-pick disease, type b	9.9	NPC1 NPC2

Graphical network of the top 20 diseases related to Glycine N-Methyltransferase Deficiency:

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Symptoms & Phenotypes for Glycine N-Methyltransferase Deficiency

Symptoms via clinical synopsis from OMIM:

⁵⁷

Abdomen Liver:
hepatomegaly

Laboratory Abnormalities:
elevated transaminases
hypermethioninemia

Clinical features from OMIM:

606664

Human phenotypes related to Glycine N-Methyltransferase Deficiency:

³²

#	Description	HPO Source Accession
1	hepatomegaly ³²	HP:0002240
2	hypermethioninemia ³²	HP:0003235
3	elevated hepatic transaminase ³²	HP:0002910

MGI Mouse Phenotypes related to Glycine N-Methyltransferase Deficiency:

⁴⁶

#	Description	MGI Source Accession	Score	Top Affiliating Genes
1	immune system	MP:0005387	9.65	ABCB4 ABCG1 ADPRH C5 GNMT MAT1A
2	liver/biliary system	MP:0005370	9.23	ABCB4 ABCG1 C5 GNMT MAT1A MTHFR

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Drugs & Therapeutics for Glycine N-Methyltransferase Deficiency

Search Clinical Trials , NIH Clinical Center for Glycine N-Methyltransferase Deficiency

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Genetic Tests for Glycine N-Methyltransferase Deficiency

Genetic tests related to Glycine N-Methyltransferase Deficiency:

#	Genetic test	Affiliating Genes
1	Glycine N-Methyltransferase Deficiency ²⁹	GNMT

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Anatomical Context for Glycine N-Methyltransferase Deficiency

MalaCards organs/tissues related to Glycine N-Methyltransferase Deficiency:

⁴¹

Liver, Prostate, Nk Cells

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Publications for Glycine N-Methyltransferase Deficiency

Articles related to Glycine N-Methyltransferase Deficiency:

#	Title	Authors	Year
1	Glycine N-methyltransferase deficiency in female mice impairs insulin signaling and promotes gluconeogenesis by modulating the PI3K/Akt pathway in the liver. ( 27716281 )	Liao Y.J....Chen Y.A.	2016
2	Glycine N-Methyltransferase Deficiency: A Member of Dysmethylating Liver Disorders? ( 27207470 )	BariA8 I....FumiA8 K.	2016
3	TRAIL-producing NK cells contribute to liver injury and related fibrogenesis in the context of GNMT deficiency. ( 25531568 )	Fern?ndez-?lvarez S...Beraza N	2015
4	Glycine N-methyltransferase deficiency affects Niemann-Pick type C2 protein stability and regulates hepatic cholesterol homeostasis. ( 22183894 )	Liao Y.J....Chen Y.M.	2012
5	Glycine N-methyltransferase deficiency: a new patient with a novel mutation. ( 14739680 )		2003
6	Glycine N-methyltransferase deficiency: a novel inborn error causing persistent isolated hypermethioninaemia. ( 11596649 )	Mudd S.H....Wagner C.	2001

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Genes for Glycine N-Methyltransferase Deficiency

Genes related to Glycine N-Methyltransferase Deficiency (1 elite genes):

(show all 17)

- Elite gene

- Cancer Census gene in COSMIC

#	Symbol	Description	Category	Score	Evidence	PubmedIds
1	GNMT	Glycine N-Methyltransferase	Protein Coding	1708.79	Molecular basis known ⁵⁷ Pathogenic ⁶ Causative germline mutation (loss of function) ⁵⁹ Causative variation ⁷⁵ Genetic Tests ²⁹ DISEASES inferred ¹⁵ Novoseek inferred ⁵⁵ GeneCards inferred via : Disorders Publications Variants (show sections)	14739680 11596649 17937387 (more) 12566990 19585268
2	MAT1A	Methionine Adenosyltransferase 1A	Protein Coding	23.66	DISEASES inferred ¹⁵ GeneCards inferred via : Publications (show sections)
3	MAT2A	Methionine Adenosyltransferase 2A	Protein Coding	22.37	DISEASES inferred ¹⁵ GeneCards inferred via : Publications (show sections)
4	NPC2	NPC Intracellular Cholesterol Transporter 2	Protein Coding	22.3	DISEASES inferred ¹⁵ GeneCards inferred via : Publications (show sections)
5	CBS	Cystathionine-Beta-Synthase	Protein Coding	20.98	DISEASES inferred ¹⁵ GeneCards inferred via : Publications (show sections)
6	MTHFR	Methylenetetrahydrofolate Reductase	Protein Coding	20.21	DISEASES inferred ¹⁵ GeneCards inferred via : Publications (show sections)
7	AHCY	Adenosylhomocysteinase	Protein Coding	15.17	DISEASES inferred ¹⁵
8	C5	Complement C5	Protein Coding	15.04	DISEASES inferred ¹⁵
9	ABCB4	ATP Binding Cassette Subfamily B Member 4	Protein Coding	14.38	DISEASES inferred ¹⁵
10	TNFRSF10B	TNF Receptor Superfamily Member 10b	Protein Coding	13.7	DISEASES inferred ¹⁵
11	MOG	Myelin Oligodendrocyte Glycoprotein	Protein Coding	13.7	DISEASES inferred ¹⁵
12	ABCG1	ATP Binding Cassette Subfamily G Member 1	Protein Coding	13.06	DISEASES inferred ¹⁵
13	NPC1	NPC Intracellular Cholesterol Transporter 1	Protein Coding	12.99	DISEASES inferred ¹⁵
14	CNPY3-GNMT	CNPY3-GNMT Readthrough	Protein Coding	8.56	GeneCards inferred via : Variants (show sections)
15	ADPRH	ADP-Ribosylarginine Hydrolase	Protein Coding	7	GeneCards inferred via : Publications (show sections)
16	DEPTOR	DEP Domain Containing MTOR Interacting Protein	Protein Coding	5.47	DISEASES inferred ¹⁵
17	MIR7-3HG	MIR7-3 Host Gene	RNA Gene	3.36	DISEASES inferred ¹⁵

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Variations for Glycine N-Methyltransferase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Glycine N-Methyltransferase Deficiency:

⁷⁵

#	Symbol	AA change	Variation ID	SNP ID
1	GNMT	p.Leu50Pro	VAR_012766	rs121907888
2	GNMT	p.His177Asn	VAR_012767	rs121907889
3	GNMT	p.Asn141Ser	VAR_019840	rs864321678

ClinVar genetic disease variations for Glycine N-Methyltransferase Deficiency:

⁶

#	Gene	Variation	Type	Significance	SNP ID	Assembly	Location
1	GNMT	NM_018960.5(GNMT): c.149T> C (p.Leu50Pro)	single nucleotide variant	Pathogenic	rs121907888	GRCh37	Chromosome 6, 42928654: 42928654
2	GNMT	NM_018960.5(GNMT): c.149T> C (p.Leu50Pro)	single nucleotide variant	Pathogenic	rs121907888	GRCh38	Chromosome 6, 42960916: 42960916
3	GNMT	NM_018960.5(GNMT): c.529C> A (p.His177Asn)	single nucleotide variant	Pathogenic	rs121907889	GRCh37	Chromosome 6, 42930887: 42930887
4	GNMT	NM_018960.5(GNMT): c.529C> A (p.His177Asn)	single nucleotide variant	Pathogenic	rs121907889	GRCh38	Chromosome 6, 42963149: 42963149
5	GNMT	NM_018960.5(GNMT): c.422A> G (p.Asn141Ser)	single nucleotide variant	Pathogenic	rs864321678	GRCh37	Chromosome 6, 42930587: 42930587
6	GNMT	NM_018960.5(GNMT): c.422A> G (p.Asn141Ser)	single nucleotide variant	Pathogenic	rs864321678	GRCh38	Chromosome 6, 42962849: 42962849

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Expression for Glycine N-Methyltransferase Deficiency

Search GEO for disease gene expression data for Glycine N-Methyltransferase Deficiency.

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Pathways for Glycine N-Methyltransferase Deficiency

Pathways related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

#	Super pathways	Score	Top Affiliating Genes
1	Metabolism ⁶⁶ Show member pathways Metabolic pathways ³⁷ Metabolism of lipids and lipoproteins ⁶⁶	13.79	ABCB4 ABCG1 AHCY CBS GNMT MAT1A
2	Selenium Micronutrient Network ¹ Show member pathways Folate Metabolism ¹ Metabolism of ingested MeSeO2H into MeSeH ⁶⁶ thioredoxin pathway ¹ Vitamin B12 Metabolism ¹	11.96	AHCY CBS MAT1A MTHFR
3	Carbon metabolism ³⁷ Show member pathways 2-Oxocarboxylic acid metabolism ³⁷ Biosynthesis of amino acids ³⁷ formaldehyde oxidation ¹	11.88	CBS MAT1A MAT2A MTHFR
4	Sulfur amino acid metabolism ⁶⁶ Show member pathways Cysteine and methionine metabolism ³⁷ Degradation of cysteine and homocysteine ⁶⁶ L-serine degradation ¹ methionine salvage cycle III ¹ Methionine salvage pathway ⁶⁶ S-methyl-5-thioadenosine degradation ¹ spermidine biosynthesis ¹ Sulfide oxidation to sulfate ⁶⁶ sulfite oxidation ¹ taurine biosynthesis ¹ Trans-sulfuration pathway ¹ Valine, leucine and isoleucine biosynthesis ³⁷	11.55	AHCY CBS MAT1A MAT2A
5	One carbon pool by folate ³⁷ Show member pathways Antimetabolite Pathway - Folate Cycle, Pharmacodynamics ⁶¹ dTMP de novo biosynthesis (mitochondrial) ¹ folate transformations I ¹ Methionine metabolism ²² methionine salvage ¹ Methotrexate Pathway (Cancer Cell), Pharmacodynamics ⁶¹ One Carbon Metabolism ¹ tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate ¹ Trans-sulfuration and one carbon metabolism ¹	11.17	AHCY CBS MAT1A MAT2A MTHFR
6	Nuclear Receptors in Lipid Metabolism and Toxicity ¹	11.02	ABCB4 ABCG1
7	methionine degradation ¹ Show member pathways Methylation Pathways ¹ S-adenosyl-L-methionine biosynthesis ¹	10.64	MAT1A MAT2A
8	superpathway of methionine degradation ¹ Show member pathways 2-oxobutanoate degradation ¹ 2-oxoisovalerate decarboxylation to isobutanoyl-CoA ¹ cysteine biosynthesis ¹ L-cysteine degradation I ¹ L-cysteine degradation II ¹	10.61	CBS MAT1A MAT2A
9	Cholesterol and Sphingolipids transport / Distribution to the intracellular membrane compartments (normal and CF) ²² Show member pathways Cholesterol and Sphingolipids transport / Generic schema (normal and CF) ²²	10.55	NPC1 NPC2
10	Folate-Alcohol and Cancer Pathway ¹	10.27	CBS MTHFR

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GO Terms for Glycine N-Methyltransferase Deficiency

Biological processes related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

(show all 14)

#	Name	GO ID	Score	Top Affiliating Genes
1	methylation	GO:0032259	9.71	AHCY GNMT MAT1A
2	cholesterol homeostasis	GO:0042632	9.69	ABCG1 NPC1 NPC2
3	cholesterol metabolic process	GO:0008203	9.67	ABCG1 NPC1 NPC2
4	lipid transport	GO:0006869	9.62	ABCB4 ABCG1 NPC1 NPC2
5	low-density lipoprotein particle clearance	GO:0034383	9.52	NPC1 NPC2
6	homocysteine metabolic process	GO:0050667	9.48	CBS MTHFR
7	methionine metabolic process	GO:0006555	9.46	GNMT MTHFR
8	S-adenosylmethionine metabolic process	GO:0046500	9.43	GNMT MTHFR
9	cholesterol transport	GO:0030301	9.43	ABCG1 NPC1 NPC2
10	sulfur amino acid metabolic process	GO:0000096	9.4	AHCY MAT1A
11	S-adenosylmethionine biosynthetic process	GO:0006556	9.37	MAT1A MAT2A
12	cholesterol efflux	GO:0033344	9.33	ABCG1 NPC1 NPC2
13	intracellular cholesterol transport	GO:0032367	9.13	ABCG1 NPC1 NPC2
14	one-carbon metabolic process	GO:0006730	9.02	AHCY GNMT MAT1A MAT2A MTHFR

Molecular functions related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

#	Name	GO ID	Score	Top Affiliating Genes
1	phospholipid transporter activity	GO:0005548	9.37	ABCB4 ABCG1
2	cholesterol transporter activity	GO:0017127	9.32	ABCG1 NPC2
3	S-adenosyl-L-methionine binding	GO:1904047	9.26	CBS GNMT
4	modified amino acid binding	GO:0072341	9.16	CBS MTHFR
5	cholesterol binding	GO:0015485	9.13	ABCG1 NPC1 NPC2
6	methionine adenosyltransferase activity	GO:0004478	8.62	MAT1A MAT2A

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Sources for Glycine N-Methyltransferase Deficiency

¹ BioSystems

² BitterDB

³ CDC

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⁵ ClinicalTrials

⁶ ClinVar

⁷ CNVD

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⁹ Cosmic

¹⁰ dbSNP

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¹⁶ DrugBank

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²⁰ GeneAnalytics

²¹ GeneCards

²² GeneGo (Thomson Reuters)

²³ GeneHancer via GeneCards

²⁴ GeneReviews

²⁵ Genetics Home Reference

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²⁷ GEO DataSets

²⁸ GO

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³³ ICD10

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³⁹ LncRNADisease

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⁴¹ MalaCards

⁴² MedGen

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⁴⁴ MeSH

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⁴⁸ NCBI Bookshelf

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⁵¹ NDF-RT

⁵² NIH Clinical Center

⁵³ NIH Rare Diseases

⁵⁴ NINDS

⁵⁵ Novoseek

⁵⁶ Novus Biologicals

⁵⁷ OMIM

⁵⁸ OMIM via Orphanet

⁵⁹ Orphanet

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⁶¹ PharmGKB

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⁶⁸ SNOMED-CT

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⁷⁰ SNOMED-CT via Orphanet

⁷¹ TGDB

⁷² Tocris

⁷³ UMLS

⁷⁴ UMLS via Orphanet

⁷⁵ UniProtKB/Swiss-Prot

⁷⁶ Wikipedia

Glycine N-Methyltransferase Deficiency (GNMT DEFICIENCY)

Aliases & Classifications for Glycine N-Methyltransferase Deficiency

MalaCards integrated aliases for Glycine N-Methyltransferase Deficiency:

Characteristics:

OMIM:

HPO:

Classifications:

External Ids:

Summaries for Glycine N-Methyltransferase Deficiency

Related Diseases for Glycine N-Methyltransferase Deficiency

Diseases related to Glycine N-Methyltransferase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

Graphical network of the top 20 diseases related to Glycine N-Methyltransferase Deficiency:

Symptoms & Phenotypes for Glycine N-Methyltransferase Deficiency

Symptoms via clinical synopsis from OMIM:

Clinical features from OMIM:

Human phenotypes related to Glycine N-Methyltransferase Deficiency:

MGI Mouse Phenotypes related to Glycine N-Methyltransferase Deficiency:

Drugs & Therapeutics for Glycine N-Methyltransferase Deficiency

Genetic Tests for Glycine N-Methyltransferase Deficiency

Genetic tests related to Glycine N-Methyltransferase Deficiency:

Anatomical Context for Glycine N-Methyltransferase Deficiency

MalaCards organs/tissues related to Glycine N-Methyltransferase Deficiency:

Publications for Glycine N-Methyltransferase Deficiency

Articles related to Glycine N-Methyltransferase Deficiency:

Genes for Glycine N-Methyltransferase Deficiency

Genes related to Glycine N-Methyltransferase Deficiency (1 elite genes):

Variations for Glycine N-Methyltransferase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Glycine N-Methyltransferase Deficiency:

ClinVar genetic disease variations for Glycine N-Methyltransferase Deficiency:

Expression for Glycine N-Methyltransferase Deficiency

Pathways for Glycine N-Methyltransferase Deficiency

Pathways related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

GO Terms for Glycine N-Methyltransferase Deficiency

Biological processes related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

Molecular functions related to Glycine N-Methyltransferase Deficiency according to GeneCards Suite gene sharing:

Sources for Glycine N-Methyltransferase Deficiency