MCID: GLY015
MIFTS: 37

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 54 12 50 24 56 71 29 13 69
Gnmt Deficiency 12 50 71 52
Hypermethioninemia Due to Glycine N-Methyltransferase Deficiency 12 50 56
Hypermethioninemia Due to Gnmt Deficiency 12 50 56
Hypermethioninemia 71 69
Glycine N-Methyltransferase Deficiency,gnmt Deficiency 24
Hepatic Methionine Adenosyltransferase Deficiency 69
Glycine N-Methyltransferase 13

Characteristics:

OMIM:

54
Inheritance:
autosomal recessive


HPO:

32
glycine n-methyltransferase deficiency:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 56  
Inborn errors of metabolism


External Ids:

OMIM 54 606664
Disease Ontology 12 DOID:0111037
ICD10 33 E72.1
Orphanet 56 ORPHA289891
UMLS via Orphanet 70 C1847720
ICD10 via Orphanet 34 E72.1
MedGen 40 C1847720

Summaries for Glycine N-Methyltransferase Deficiency

NIH Rare Diseases : 50 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 hepatitis, and has symptoms including hepatomegaly, hypermethioninemia and elevated hepatic transaminases. An important gene associated with Glycine N-Methyltransferase Deficiency is GNMT (Glycine N-Methyltransferase), and among its related pathways/superpathways are Metabolism and Carbon metabolism. 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 15)
id Related Disease Score Top Affiliating Genes
1 hypermethioninemia 11.3
2 hepatitis 9.9
3 dysostosis 9.8 ADPRH NPC2
4 homocystinuria due to mthfr deficiency 9.8 CBS MTHFR
5 megacolon 9.8 CBS MTHFR
6 homologous wasting disease 9.8 CBS MTHFR
7 homocystinuria 9.8 CBS MTHFR
8 ectopic pregnancy 9.7 CBS MTHFR
9 pregnancy loss, recurrent 2 9.6 CBS MTHFR
10 ovarian clear cell malignant adenofibroma 9.6 CBS MTHFR
11 malignant type ab thymoma 9.6 CBS MTHFR
12 primary cerebellar degeneration 9.5 CBS MTHFR
13 jmp syndrome 9.3 CBS GNMT MAT1A MAT2A
14 priapism 9.3 CBS MTHFR
15 candidiasis, familial, 6, autosomal dominant 7.4 ADPRH CBS GNMT MAT1A MAT2A 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:

54

Abdomen- Liver:
hepatomegaly

Laboratory- Abnormalities:
elevated transaminases
hypermethioninemia


Clinical features from OMIM:

606664

Human phenotypes related to Glycine N-Methyltransferase Deficiency:

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

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:

id Genetic test Affiliating Genes
1 Glycine N-Methyltransferase Deficiency 29 24 GNMT

Anatomical Context for Glycine N-Methyltransferase Deficiency

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

39
Liver

Publications for Glycine N-Methyltransferase Deficiency

Articles related to Glycine N-Methyltransferase Deficiency:

id 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
id 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
id 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:

id Super pathways Score Top Affiliating Genes
1
Show member pathways
13.51 CBS GNMT MAT1A MAT2A MTHFR NPC2
2
Show member pathways
11.78 CBS MAT1A MAT2A MTHFR
3
Show member pathways
11.58 CBS MAT1A MAT2A
4
Show member pathways
11.41 CBS MAT1A MAT2A MTHFR
5
Show member pathways
11.08 CBS GNMT
6
Show member pathways
10.21 CBS MTHFR
7
Show member pathways
10.21 CBS MAT1A MAT2A

GO Terms for Glycine N-Methyltransferase Deficiency

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

id 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 S-adenosylmethionine metabolic process GO:0046500 9.32 GNMT MTHFR
5 methionine metabolic process GO:0006555 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:

id Name GO ID Score Top Affiliating Genes
1 modified amino acid binding GO:0072341 8.96 CBS MTHFR
2 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
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 MedGen
42 MeSH
43 MESH via Orphanet
44 MGI
46 NCI
47 NCIt
48 NDF-RT
51 NINDS
52 Novoseek
54 OMIM
55 OMIM via Orphanet
59 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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