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

Sources

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 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

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

Sources

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 hypermethioninemia and methionine adenosyltransferase i/iii deficiency. An important gene associated with Glycine N-Methyltransferase Deficiency is GNMT (Glycine N-Methyltransferase), and among its related pathways/superpathways are Metabolism and Folate Metabolism. Affiliated tissues include liver, and related phenotypes are hepatomegaly and elevated hepatic transaminases

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

Sources

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 12)

#	Related Disease	Score	Top Affiliating Genes
1	hypermethioninemia	31.9	CBS GNMT MAT1A
2	methionine adenosyltransferase i/iii deficiency	10.1	CBS MAT1A
3	hepatitis	10.0
4	sphingolipidosis	9.8	ADPRH NPC2
5	lens subluxation	9.6	CBS MTHFR
6	amino acid metabolic disorder	9.6	CBS MTHFR
7	myelomeningocele	9.5	CBS MTHFR
8	thrombophilia due to thrombin defect	9.4	CBS MTHFR
9	homocysteinemia	9.3	CBS MTHFR
10	inherited metabolic disorder	9.2	CBS MTHFR
11	homocystinuria	9.1	CBS MAT1A MTHFR
12	cerebrovascular disease	9.0	CBS MTHFR

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

Sources

Symptoms & Phenotypes for Glycine N-Methyltransferase Deficiency

Symptoms via clinical synopsis from OMIM:

⁵⁷

Abdomen Liver:
hepatomegaly

Laboratory Abnormalities:
hypermethioninemia
elevated transaminases

Clinical features from OMIM:

606664

Human phenotypes related to Glycine N-Methyltransferase Deficiency:

³²

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

Sources

Drugs & Therapeutics for Glycine N-Methyltransferase Deficiency

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

Sources

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

Sources

Anatomical Context for Glycine N-Methyltransferase Deficiency

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

⁴¹

Liver

Sources

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	Glycine N-methyltransferase deficiency affects Niemann-Pick type C2 protein stability and regulates hepatic cholesterol homeostasis. ( 22183894 )	Liao Y.J....Chen Y.M.	2012
4	Glycine N-methyltransferase deficiency: a new patient with a novel mutation. ( 14739680 )	Augoustides-Savvopoulou P....Mudd S.H.	2003
5	Glycine N-methyltransferase deficiency: a novel inborn error causing persistent isolated hypermethioninaemia. ( 11596649 )	Mudd S.H....Wagner C.	2001

Sources

Genes for Glycine N-Methyltransferase Deficiency

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

- Elite gene

- Cancer Census gene in COSMIC

#	Symbol	Description	Category	Score	Evidence	PubmedIds
1	GNMT	Glycine N-Methyltransferase	Protein Coding	1700.76	Molecular basis known ⁵⁷ Pathogenic ⁶ Causative germline mutation (loss of function) ⁵⁹ Causative variation ⁷⁵ Genetic Tests ²⁹ Novoseek inferred ⁵⁵ GeneCards inferred via : Disorders Publications Variants (show sections)	14739680 11596649 17937387 (more) 12566990 19585268
2	MAT1A	Methionine Adenosyltransferase 1A	Protein Coding	17.43	GeneCards inferred via : Publications (show sections)
3	MAT2A	Methionine Adenosyltransferase 2A	Protein Coding	17.09	GeneCards inferred via : Publications (show sections)
4	CBS	Cystathionine-Beta-Synthase	Protein Coding	17.09	GeneCards inferred via : Publications (show sections)
5	NPC2	NPC Intracellular Cholesterol Transporter 2	Protein Coding	17.09	GeneCards inferred via : Publications (show sections)
6	MTHFR	Methylenetetrahydrofolate Reductase	Protein Coding	17.09	GeneCards inferred via : Publications (show sections)
7	CNPY3-GNMT	CNPY3-GNMT Readthrough	Protein Coding	8.63	GeneCards inferred via : Variants (show sections)
8	ADPRH	ADP-Ribosylarginine Hydrolase	Protein Coding	7.09	GeneCards inferred via : Publications (show sections)

Sources

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

Sources

Expression for Glycine N-Methyltransferase Deficiency

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

Sources

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	13.57	CBS GNMT MAT1A MAT2A MTHFR NPC2
2	Folate Metabolism ¹ Show member pathways Selenium Micronutrient Network ¹ thioredoxin pathway ¹ Vitamin B12 Metabolism ¹	11.91	CBS MAT1A MTHFR
3	Carbon metabolism ³⁷ Show member pathways 2-Oxocarboxylic acid metabolism ³⁷ Biosynthesis of amino acids ³⁷ formaldehyde oxidation ¹	11.78	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	11.58	CBS MAT1A MAT2A
5	Glycine, serine and threonine metabolism ³⁷ Show member pathways glycine betaine degradation ¹ superpathway of choline degradation to L-serine ¹	11.15	CBS GNMT
6	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	11.07	CBS MAT1A MAT2A MTHFR
7	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
8	S-adenosyl-L-methionine biosynthesis ¹ Show member pathways methionine degradation ¹ Methylation Pathways ¹	10.57	MAT1A MAT2A
9	Folate-Alcohol and Cancer Pathway ¹ Show member pathways One carbon donor ¹	10.21	CBS MTHFR

Sources

GO Terms for Glycine N-Methyltransferase Deficiency

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

#	Name	GO ID	Score	Top Affiliating Genes
1	methylation	GO:0032259	9.54	GNMT MAT1A MAT2A
2	cellular protein modification process	GO:0006464	9.43	ADPRH GNMT
3	protein homotetramerization	GO:0051289	9.4	GNMT MAT1A
4	homocysteine metabolic process	GO:0050667	9.32	CBS MTHFR
5	methionine metabolic process	GO:0006555	9.26	GNMT MTHFR
6	S-adenosylmethionine metabolic process	GO:0046500	9.16	GNMT MTHFR
7	S-adenosylmethionine biosynthetic process	GO:0006556	8.96	MAT1A MAT2A
8	one-carbon metabolic process	GO:0006730	8.92	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	identical protein binding	GO:0042802	9.46	CBS GNMT MAT1A MAT2A
2	modified amino acid binding	GO:0072341	8.96	CBS MTHFR
3	methionine adenosyltransferase activity	GO:0004478	8.62	MAT1A MAT2A

Sources

Sources for Glycine N-Methyltransferase Deficiency

¹ BioSystems

² BitterDB

³ CDC

⁴ Cell Signaling Technology

⁵ ClinicalTrials

⁶ ClinVar

⁷ CNVD

⁸ Cochrane Library

⁹ Cosmic

¹⁰ dbSNP

¹¹ DGIdb

¹² Disease Ontology

¹³ diseasecard

¹⁴ DiseaseEnhancer

¹⁵ DISEASES

¹⁶ DrugBank

¹⁷ ExPASy

¹⁸ FDA Approved Drugs

¹⁹ FMA

²⁰ GeneAnalytics

²¹ GeneCards

²² GeneGo (Thomson Reuters)

²³ GeneHancer via GeneCards

²⁴ GeneReviews

²⁵ Genetics Home Reference

²⁶ GenomeRNAi

²⁷ GEO DataSets

²⁸ GO

²⁹ GTR

³⁰ HGMD

³¹ HMDB

³² HPO

³³ ICD10

³⁴ ICD10 via Orphanet

³⁵ ICD9CM

³⁶ IUPHAR

³⁷ KEGG

³⁸ LifeMap

³⁹ LncRNADisease

⁴⁰ LOVD

⁴¹ MalaCards

⁴² MedGen

⁴³ MedlinePlus

⁴⁴ MeSH

⁴⁵ MESH via Orphanet

⁴⁶ MGI

⁴⁷ miR2Disease

⁴⁸ NCBI Bookshelf

⁴⁹ NCI

⁵⁰ NCIt

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

⁶⁰ PathCards

⁶¹ PharmGKB

⁶² PubMed

⁶³ PubMed Health

⁶⁴ QIAGEN

⁶⁵ R&D Systems

⁶⁶ Reactome

⁶⁷ Sino Biological

⁶⁸ SNOMED-CT

⁶⁹ SNOMED-CT via HPO

⁷⁰ SNOMED-CT via Orphanet

⁷¹ TGDB

⁷² Tocris

⁷³ UMLS

⁷⁴ UMLS via Orphanet

⁷⁵ UniProtKB/Swiss-Prot

⁷⁶ Wikipedia