GNMT DEFICIENCY
MCID: GLY015
MIFTS: 43

Glycine N-Methyltransferase Deficiency (GNMT DEFICIENCY)

Categories: Blood diseases, Genetic diseases, Liver diseases, Metabolic diseases, Rare diseases

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:

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

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

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:



Diseases related to Glycine N-Methyltransferase Deficiency

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 Frequency 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

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 29 GNMT

Anatomical Context for Glycine N-Methyltransferase Deficiency

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

41
Liver, Prostate, Nk Cells

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 )
2016
2
Glycine N-Methyltransferase Deficiency: A Member of Dysmethylating Liver Disorders? ( 27207470 )
2016
3
TRAIL-producing NK cells contribute to liver injury and related fibrogenesis in the context of GNMT deficiency. ( 25531568 )
2015
4
Glycine N-methyltransferase deficiency affects Niemann-Pick type C2 protein stability and regulates hepatic cholesterol homeostasis. ( 22183894 )
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 )
2001

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

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
13.79 ABCB4 ABCG1 AHCY CBS GNMT MAT1A
2
Show member pathways
11.96 AHCY CBS MAT1A MTHFR
3
Show member pathways
11.88 CBS MAT1A MAT2A MTHFR
4
Show member pathways
11.55 AHCY CBS MAT1A MAT2A
5
Show member pathways
11.17 AHCY CBS MAT1A MAT2A MTHFR
6 11.02 ABCB4 ABCG1
7
Show member pathways
10.64 MAT1A MAT2A
8
Show member pathways
10.61 CBS MAT1A MAT2A
9
Show member pathways
10.55 NPC1 NPC2
10 10.27 CBS MTHFR

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

Sources for Glycine N-Methyltransferase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 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 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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