MCID: GLY015
MIFTS: 36

Glycine N-Methyltransferase Deficiency

Categories: Genetic diseases, Rare diseases, Metabolic diseases

Aliases & Classifications for Glycine N-Methyltransferase Deficiency

MalaCards integrated aliases for Glycine N-Methyltransferase Deficiency:

Name: Glycine N-Methyltransferase Deficiency 53 12 49 55 71 28 13 69
Gnmt Deficiency 53 12 49 71 51
Hypermethioninemia Due to Glycine N-Methyltransferase Deficiency 12 49 55
Hypermethioninemia Due to Gnmt Deficiency 12 49 55
Hypermethioninemia 71 69
Hepatic Methionine Adenosyltransferase Deficiency 69
Glycine N-Methyltransferase 13

Characteristics:

OMIM:

53
Inheritance:
autosomal recessive


HPO:

31
glycine n-methyltransferase deficiency:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 55  
Inborn errors of metabolism


External Ids:

OMIM 53 606664
Disease Ontology 12 DOID:0111037
ICD10 32 E72.1
Orphanet 55 ORPHA289891
UMLS via Orphanet 70 C1847720
ICD10 via Orphanet 33 E72.1
MedGen 39 C1847720

Summaries for Glycine N-Methyltransferase Deficiency

NIH Rare Diseases : 49 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. Last updated: 12/5/2016

MalaCards based summary : Glycine N-Methyltransferase Deficiency, also known as gnmt deficiency, is related to hypermethioninemia and methionine adenosyltransferase i/iii deficiency, and has symptoms including hepatomegaly, elevated hepatic transaminases 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.

UniProtKB/Swiss-Prot : 71 Glycine N-methyltransferase deficiency: The only clinical abnormalities in patients with this deficiency are mild hepatomegaly and chronic elevation of serum 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.

Description from OMIM: 606664

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 31.5 CBS GNMT MAT1A MAT2A
2 methionine adenosyltransferase i/iii deficiency 10.1 CBS MAT1A
3 hepatitis 10.0
4 sphingolipidosis 9.8 ADPRH NPC2
5 lens subluxation 9.8 CBS MTHFR
6 amino acid metabolic disorder 9.8 CBS MTHFR
7 myelomeningocele 9.8 CBS MTHFR
8 homocysteinemia 9.7 CBS MTHFR
9 inherited metabolic disorder 9.7 CBS MTHFR
10 homocystinuria 9.6 CBS MTHFR
11 cerebrovascular disease 9.6 CBS MTHFR
12 thrombophilia 9.4 CBS MTHFR

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



Diseases related to Glycine N-Methyltransferase Deficiency

Symptoms & Phenotypes for Glycine N-Methyltransferase Deficiency

Symptoms via clinical synopsis from OMIM:

53
Abdomen Liver:
hepatomegaly

Laboratory Abnormalities:
hypermethioninemia
elevated transaminases


Clinical features from OMIM:

606664

Human phenotypes related to Glycine N-Methyltransferase Deficiency:

31
# Description HPO Frequency HPO Source Accession
1 hepatomegaly 31 HP:0002240
2 elevated hepatic transaminases 31 HP:0002910
3 hypermethioninemia 31 HP:0003235

Drugs & Therapeutics for Glycine N-Methyltransferase Deficiency

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

Genetic Tests for Glycine N-Methyltransferase Deficiency

Genetic tests related to Glycine N-Methyltransferase Deficiency:

# Genetic test Affiliating Genes
1 Glycine N-Methyltransferase Deficiency 28 GNMT

Anatomical Context for Glycine N-Methyltransferase Deficiency

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

38
Liver

Publications for Glycine N-Methyltransferase Deficiency

Articles related to Glycine N-Methyltransferase Deficiency:

# Title Authors Year
1
Glycine N-Methyltransferase Deficiency: A Member of Dysmethylating Liver Disorders? ( 27207470 )
2016
2
Glycine N-methyltransferase deficiency in female mice impairs insulin signaling and promotes gluconeogenesis by modulating the PI3K/Akt pathway in the liver. ( 27716281 )
2016
3
Glycine N-methyltransferase deficiency affects Niemann-Pick type C2 protein stability and regulates hepatic cholesterol homeostasis. ( 22183894 )
2012
4
Glycine N-methyltransferase deficiency: a new patient with a novel mutation. ( 14739680 )
2003
5
Glycine N-methyltransferase deficiency: a novel inborn error causing persistent isolated hypermethioninaemia. ( 11596649 )
2001

Variations for Glycine N-Methyltransferase Deficiency

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

71
# 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.529C> A (p.His177Asn) single nucleotide variant Pathogenic rs121907889 GRCh37 Chromosome 6, 42930887: 42930887
3 GNMT NM_018960.5(GNMT): c.422A> G (p.Asn141Ser) single nucleotide variant Pathogenic rs864321678 GRCh37 Chromosome 6, 42930587: 42930587

Expression for Glycine N-Methyltransferase Deficiency

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

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
Show member pathways
13.56 CBS GNMT MAT1A MAT2A MTHFR NPC2
2
Show member pathways
11.91 CBS MAT1A MTHFR
3
Show member pathways
11.78 CBS MAT1A MAT2A MTHFR
4
Show member pathways
11.58 CBS MAT1A MAT2A
5
Show member pathways
11.15 CBS GNMT
6
Show member pathways
11.07 CBS MAT1A MAT2A MTHFR
7
Show member pathways
10.59 CBS MAT1A MAT2A
8
Show member pathways
10.57 MAT1A MAT2A
9
Show member pathways
10.21 CBS MTHFR

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 methionine metabolic process GO:0006555 9.32 GNMT MTHFR
5 S-adenosylmethionine metabolic process GO:0046500 9.26 GNMT MTHFR
6 homocysteine metabolic process GO:0050667 9.16 CBS MTHFR
7 S-adenosylmethionine biosynthetic process GO:0006556 8.96 MAT1A MAT2A
8 one-carbon metabolic process GO:0006730 8.8 GNMT MAT1A MAT2A

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 for Glycine N-Methyltransferase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
27 GO
28 GTR
29 HGMD
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 MedGen
41 MeSH
42 MESH via Orphanet
43 MGI
45 NCI
46 NCIt
47 NDF-RT
50 NINDS
51 Novoseek
53 OMIM
54 OMIM via Orphanet
58 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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