GCE
MCID: GLY010
MIFTS: 57

Glycine Encephalopathy (GCE)

Categories: Genetic diseases, Metabolic diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Glycine Encephalopathy

MalaCards integrated aliases for Glycine Encephalopathy:

Name: Glycine Encephalopathy 57 12 20 43 58 72 13 15
Non-Ketotic Hyperglycinemia 12 20 43 58 72 29 6
Nonketotic Hyperglycinemia 12 73 25 20 43 36 70
Nkh 57 25 43 72
Hyperglycinemia, Nonketotic 57 44
Hyperglycinemia Nonketotic 20 54
Gce 57 72
Infantile Non-Ketotic Hyperglycinemia 58
Neonatal Non-Ketotic Hyperglycinemia 58
Hyperglycinemia, Nonketotic; Nkh 57
Infantile Glycine Encephalopathy 58
Neonatal Glycine Encephalopathy 58
Classic Glycine Encephalopathy 58
Glycine Synthase Deficiency 20
Encephalopathy, Glycine 39
Infantile Nkh 58
Neonatal Nkh 58
Nka 58

Characteristics:

Orphanet epidemiological data:

58
glycine encephalopathy
Inheritance: Autosomal recessive; Prevalence: 1-9/1000000 (Europe); Age of onset: Infancy,Neonatal; Age of death: any age;
neonatal glycine encephalopathy
Inheritance: Autosomal recessive; Age of onset: Infancy,Neonatal;
infantile glycine encephalopathy
Inheritance: Autosomal recessive; Age of onset: Infancy,Neonatal;

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal recessive

Miscellaneous:
death in infancy common for patients with the classic neonatal form
patients with atypical form have milder disease, with onset in the first months of life and increased survival


HPO:

31
glycine encephalopathy:
Onset and clinical course death in infancy
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare neurological diseases
Inborn errors of metabolism


Summaries for Glycine Encephalopathy

MedlinePlus Genetics : 43 Nonketotic hyperglycinemia is a disorder characterized by abnormally high levels of a molecule called glycine in the body (hyperglycinemia). The excess glycine builds up in tissues and organs, particularly the brain. Affected individuals have serious neurological problems.Nonketotic hyperglycinemia has two forms, the severe form and the attenuated form. Both forms usually begin shortly after birth, although in some cases, signs and symptoms can begin in the first few months of life. Only the attenuated form begins later in infancy. The forms are distinguished by the seriousness of the signs and symptoms. Severe nonketotic hyperglycinemia is more common. Affected babies experience extreme sleepiness (lethargy) that worsens over time and can lead to coma. They can also have weak muscle tone (hypotonia) and life-threatening breathing problems in the first days or weeks of life. Most children who survive these early signs and symptoms develop feeding difficulties, abnormal muscle stiffness (spasticity), profound intellectual disability and seizures that are difficult to control. Most affected children do not achieve normal developmental milestones, such as drinking from a bottle, sitting up, or grabbing objects, and they may lose any acquired skills over time.The signs and symptoms of the attenuated form of nonketotic hyperglycinemia are similar to, but milder than, those of the severe form of the condition. Children with attenuated nonketotic hyperglycinemia typically reach developmental milestones, although the skills they achieve vary widely. Despite delayed development, many affected children eventually learn to walk and are able to interact with others, often using sign language. Some affected children develop seizures; if present, seizures are usually mild and can be treated. Other features can include spasticity, involuntary jerking movements (chorea), or hyperactivity.Individuals with nonketotic hyperglycinemia can also have certain changes in the brain, which can be seen using magnetic resonance imaging (MRI). For example, in children with the severe form of the condition, the tissue that connects the left and right halves of the brain (the corpus callosum) is smaller than average.

MalaCards based summary : Glycine Encephalopathy, also known as non-ketotic hyperglycinemia, is related to atypical glycine encephalopathy and lipoic acid biosynthesis defects, and has symptoms including seizures, myoclonus and lethargy. An important gene associated with Glycine Encephalopathy is AMT (Aminomethyltransferase), and among its related pathways/superpathways are Glycine, serine and threonine metabolism and Biosynthesis of cofactors. Affiliated tissues include brain, eye and spinal cord, and related phenotypes are recurrent singultus and hypoplasia of the corpus callosum

Disease Ontology : 12 An amino acid metabolic disorder that involves abnormally high levels of the amino acid glycine in bodily fluids and tissues.

GARD : 20 Glycine encephalopathy is an inherited metabolic disease characterized by abnormally high levels of an amino acid called glycine. Glycine is a chemical messenger that transmits signals in the brain. According to the symptoms the disease onset, glycine encephalopathy may be divided in: Classical neonatal form (most common): Symptoms start within a few days of life and may include poor feeding, lack of energy (lethargy), weak muscle tone ( hypotonia ), hiccups, breathing problems, seizures, hiccups, and coma. Infantile form: Symptoms start only after 6 months of age, as intellectual disability, abnormal movements, and behavioral problems Late onset: Symptoms include tightness or stiffness of the legs or arms (spastic diplegia), and vision loss due to a damage of the eye nerve (optic atrophy). Transient form: Symptoms are similar to the classic form, but glycine levels decrease and the symptoms may improve within time. Glycine encephalopathy is caused by changes ( mutations ) in the AMT, GLDC or GCSH genes which result in a deficiency of the enzyme that break-up the glycine. Diagnosis is based in the symptoms, the high glycine levels and the enzyme deficiency, as well as genetic testing. Inheritance is autosomal recessive. Treatment may include sodium benzoate to reduce the levels of glycine, N-methyl D-aspartate (NMDA) receptor site antagonists, anti-seizure drugs and ketogenic diet. About half of the babies with the classic form, die within a few weeks of life and the survivors may have motor delay, very small head, seizures and stiffness. In the transient form symptoms may improve with time.

KEGG : 36 Nonketotic hyperglycinemia is an inborn error of glycine metabolism caused by a deficiency of the glycine cleavage system, which is composed of four proteins in the mitochondria and results in severe neurologic dysfunctions.

UniProtKB/Swiss-Prot : 72 Non-ketotic hyperglycinemia: Autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.

Wikipedia : 73 Glycine encephalopathy is a rare autosomal recessive disorder of glycine metabolism. After... more...

More information from OMIM: 605899
GeneReviews: NBK1357

Related Diseases for Glycine Encephalopathy

Diseases related to Glycine Encephalopathy via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 147)
# Related Disease Score Top Affiliating Genes
1 atypical glycine encephalopathy 32.2 SLC6A9 NICN1 GLDC GCSH AMT
2 lipoic acid biosynthesis defects 32.1 NFU1 LIPT1 LIAS GLRX5 BOLA3
3 multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemia 31.7 NFU1 LIAS ISCA2 IBA57 BOLA3
4 autosomal recessive disease 30.7 PRODH GLDC GCSH AMT
5 early myoclonic encephalopathy 30.6 PNPO PCDH19 AMT ABAT
6 maple syrup urine disease 30.6 SUOX PRODH GLDC
7 epilepsy, idiopathic generalized 30.5 PCDH19 GLDC ABAT
8 leukodystrophy 30.4 NFU1 ISCA2 IBA57 GLRX5
9 lactic acidosis 30.4 NFU1 LIPT1 LIAS ISCA2 IBA57 BOLA3
10 hyperekplexia 30.3 SUOX SLC6A9 SLC6A5
11 glycine encephalopathy with normal serum glycine 11.7
12 d-glyceric aciduria 11.6
13 hyperglycinemia, lactic acidosis, and seizures 10.9
14 spasticity, childhood-onset, with hyperglycinemia 10.9
15 encephalopathy 10.6
16 carbonic anhydrase va deficiency, hyperammonemia due to 10.4
17 hyperekplexia 3 10.4 SLC6A9 SLC6A5
18 histidine metabolism disease 10.4 PRODH GLDC AMT
19 histidinemia 10.4 PRODH GLDC AMT
20 hyperlysinemia, type i 10.4 SUOX PRODH
21 hyperprolinemia, type i 10.4 SUOX PRODH
22 cystathioninuria 10.4 PRODH AMT
23 cutis laxa, autosomal dominant 3 10.4 MYBPH GLDC GCSH AMT
24 phosphoserine aminotransferase deficiency 10.4 SUOX AMT
25 cutis laxa, autosomal dominant 2 10.4 MYBPH GLDC GCSH AMT
26 hyperprolinemia, type ii 10.4 PRODH PNPO
27 cutis laxa, autosomal dominant 1 10.4 MYBPH GLDC GCSH AMT
28 gamma-amino butyric acid metabolism disorder 10.4 PRODH ABAT
29 mitochondrial metabolism disease 10.3 PRODH NFU1 BOLA3
30 anemia, sideroblastic, and spinocerebellar ataxia 10.3 NFU1 ISCA2 GLRX5
31 cerebral creatine deficiency syndrome 2 10.3 SUOX PNPO
32 frank-ter haar syndrome 10.3 PRODH AMT
33 anemia, sideroblastic, 1 10.3 ISCA2 IBA57 GLRX5
34 hypotonia 10.3
35 combined oxidative phosphorylation deficiency 19 10.3 ISCA2 IBA57 GLRX5 BOLA3
36 alacrima, achalasia, and mental retardation syndrome 10.3
37 propionic acidemia 10.3
38 3-methylglutaconic aciduria, type iii 10.3
39 seizure disorder 10.3
40 purine-pyrimidine metabolic disorder 10.3 SUOX PRODH
41 multiple mitochondrial dysfunctions syndrome 4 10.2 NFU1 LIAS ISCA2 IBA57 BOLA3
42 multiple mitochondrial dysfunctions syndrome 3 10.2 NFU1 LIAS ISCA2 IBA57 BOLA3
43 infancy electroclinical syndrome 10.2 PNPO PCDH19
44 hyperglycinuria 10.2
45 scoliosis 10.2
46 spastic diplegia 10.2
47 pathologic nystagmus 10.2
48 multiple mitochondrial dysfunctions syndrome 1 10.2 NFU1 MYBPH LIPT1 LIAS IBA57 BOLA3
49 multiple mitochondrial dysfunctions syndrome 10.2 NFU1 LIAS ISCA2 IBA57 GLRX5 BOLA3
50 pyruvate dehydrogenase e1-alpha deficiency 10.2 SUOX NFU1 LIPT1 LIAS IBA57 BOLA3

Graphical network of the top 20 diseases related to Glycine Encephalopathy:



Diseases related to Glycine Encephalopathy

Symptoms & Phenotypes for Glycine Encephalopathy

Human phenotypes related to Glycine Encephalopathy:

58 31 (show all 29)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 recurrent singultus 58 31 hallmark (90%) Very frequent (99-80%) HP:0100247
2 hypoplasia of the corpus callosum 58 31 hallmark (90%) Very frequent (99-80%) HP:0002079
3 hyperglycinemia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002154
4 eeg with burst suppression 58 31 hallmark (90%) Very frequent (99-80%) HP:0010851
5 abnormal metabolic brain imaging by mrs 58 31 hallmark (90%) Very frequent (99-80%) HP:0012705
6 hypotonia 31 hallmark (90%) HP:0001252
7 lethargy 58 31 frequent (33%) Frequent (79-30%) HP:0001254
8 poor suck 58 31 frequent (33%) Frequent (79-30%) HP:0002033
9 breathing dysregulation 58 31 frequent (33%) Frequent (79-30%) HP:0005957
10 respiratory acidosis 58 31 frequent (33%) Frequent (79-30%) HP:0005972
11 generalized myoclonic seizure 31 frequent (33%) HP:0002123
12 intellectual disability 31 HP:0001249
13 seizures 58 Very frequent (99-80%)
14 agenesis of corpus callosum 31 HP:0001274
15 hyperreflexia 31 HP:0001347
16 eeg abnormality 58 Very frequent (99-80%)
17 myoclonus 31 HP:0001336
18 irritability 31 HP:0000737
19 generalized myoclonic seizures 58 Frequent (79-30%)
20 hyporeflexia 31 HP:0001265
21 encephalopathy 31 HP:0001298
22 restlessness 31 HP:0000711
23 aggressive behavior 31 HP:0000718
24 hyperactivity 31 HP:0000752
25 generalized hypotonia 31 HP:0001290
26 central hypotonia 58 Very frequent (99-80%)
27 impulsivity 31 HP:0100710
28 hyperglycinuria 31 HP:0003108
29 seizure 31 HP:0001250

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Neurologic Central Nervous System:
seizures
lethargy
hypotonia
hiccups
mental retardation
more
Laboratory Abnormalities:
hyperglycinemia
hyperglycinuria
hepatic glycine cleavage defect
elevated csf glycine
elevated csf/plasma glycine ratio

Neurologic Behavioral Psychiatric Manifestations:
irritability
restlessness
hyperactivity
impulsivity
aggressiveness

Clinical features from OMIM®:

605899 (Updated 20-May-2021)

UMLS symptoms related to Glycine Encephalopathy:


seizures; myoclonus; lethargy; restlessness

GenomeRNAi Phenotypes related to Glycine Encephalopathy according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased shRNA abundance GR00297-A 9.02 AMT GLRX5 ISCA2 OCA2 SUOX

Drugs & Therapeutics for Glycine Encephalopathy

Search Clinical Trials , NIH Clinical Center for Glycine Encephalopathy

Cochrane evidence based reviews: hyperglycinemia, nonketotic

Genetic Tests for Glycine Encephalopathy

Genetic tests related to Glycine Encephalopathy:

# Genetic test Affiliating Genes
1 Non-Ketotic Hyperglycinemia 29 AMT GCSH GLDC

Anatomical Context for Glycine Encephalopathy

MalaCards organs/tissues related to Glycine Encephalopathy:

40
Brain, Eye, Spinal Cord, Liver, Cortex, Cerebellum, Kidney

Publications for Glycine Encephalopathy

Articles related to Glycine Encephalopathy:

(show top 50) (show all 272)
# Title Authors PMID Year
1
A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among patients with glycine encephalopathy in Jerusalem. 25 57 54 6 61
15864413 2005
2
Molecular genetic and potential biochemical characteristics of patients with T-protein deficiency as a cause of glycine encephalopathy (NKH). 6 25 57 61
12948742 2003
3
Nonketotic hyperglycinemia (glycine encephalopathy): laboratory diagnosis. 25 57 6 61
11592811 2001
4
d-Glyceric aciduria does not cause nonketotic hyperglycinemia: A historic co-occurrence. 57 25 6
28462797 2017
5
Using whole-exome sequencing to identify inherited causes of autism. 6 57 25
23352163 2013
6
Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. 6 57 54 61
15851735 2005
7
Persistent NKH with transient or absent symptoms and a homozygous GLDC mutation. 6 57 25
15236413 2004
8
Glycine decarboxylase mutations: a distinctive phenotype of nonketotic hyperglycinemia in adults. 6 57 54
15824356 2005
9
Ketogenic diet in early myoclonic encephalopathy due to non ketotic hyperglycinemia. 61 25 6
22261077 2012
10
D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK). 6 57
20949620 2010
11
Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. 25 54 6
16450403 2006
12
Treatment from birth of nonketotic hyperglycinemia due to a novel GLDC mutation. 25 61 57
16404748 2006
13
Recurrent mutations in P- and T-proteins of the glycine cleavage complex and a novel T-protein mutation (N145I): a strategy for the molecular investigation of patients with nonketotic hyperglycinemia (NKH). 6 25 54
11286506 2001
14
Human glycine decarboxylase gene (GLDC) and its highly conserved processed pseudogene (psiGLDC): their structure and expression, and the identification of a large deletion in a family with nonketotic hyperglycinemia. 25 6 54
10798358 2000
15
Acute hydrocephalus in nonketotic hyperglycinemia. 25 57 61
10680820 2000
16
Letter: Hyperglycericacidaemia with hyperglycinaemia: a new inborn error of metabolism. 57 6
4434100 1974
17
Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease. 25 6
28244183 2017
18
The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT. 6 25
27362913 2017
19
Neurodevelopmental Outcome and Treatment Efficacy of Benzoate and Dextromethorphan in Siblings with Attenuated Nonketotic Hyperglycinemia. 6 25
26749113 2016
20
Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia. 6 25
26179960 2015
21
Mutations in genes encoding the glycine cleavage system predispose to neural tube defects in mice and humans. 25 6
22171071 2012
22
Genetic heterogeneity of the GLDC gene in 28 unrelated patients with glycine encephalopathy. 61 54 6
16601880 2006
23
Mild variant of nonketotic hyperglycinemia with typical neonatal presentations: mutational and in vitro expression analyses in two patients. 25 6
15192636 2004
24
Biochemical and molecular investigations of patients with nonketotic hyperglycinemia. 25 6
10873393 2000
25
Non-concordance of CVS and liver glycine cleavage enzyme in three families with non-ketotic hyperglycinaemia (NKH) leading to false negative prenatal diagnoses. 25 57
10820402 2000
26
Identification of a common mutation in Finnish patients with nonketotic hyperglycinemia. 6 25
1634607 1992
27
Mutation analysis of glycine decarboxylase, aminomethyltransferase and glycine cleavage system protein-H genes in 13 unrelated families with glycine encephalopathy. 6 61
25231368 2014
28
Diagnosis of glycine encephalopathy in a pediatric patient by detection of a GLDC mutation during initial next generation DNA sequencing. 61 6
24407464 2014
29
Two novel missense mutations observed in nonketotic hyperglycinemia. 61 6
22633639 2012
30
A novel missense mutation in a neonate with nonketotic hyperglycinemia. 6 61
20933183 2010
31
Atypical glycine encephalopathy in an extremely low birth weight infant: description of a new mutation and clinical and electroencephalographic analysis. 61 6
19299230 2009
32
Non-ketotic hyperglycinemia is usually not detectable by tandem mass spectrometry newborn screening. 61 57
17207649 2007
33
Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. 6 61
16051266 2005
34
Glycine encephalopathy (nonketotic hyperglycinaemia) : review and update. 61 6
15272469 2004
35
Novel mutations in the P-protein (glycine decarboxylase) gene in patients with glycine encephalopathy (non-ketotic hyperglycinemia). 6 61
12126939 2002
36
Identification of the first reported splice site mutation (IVS7-1G-->A) in the aminomethyltransferase (T-protein) gene (AMT) of the glycine cleavage complex in 3 unrelated families with nonketotic hyperglycinemia. 6 54
11139253 2001
37
Benzoate therapy and carnitine deficiency in non-ketotic hyperglycinemia. 61 57
8585564 1995
38
The glycine cleavage system: structure of a cDNA encoding human H-protein, and partial characterization of its gene in patients with hyperglycinemias. 6 54
1671321 1991
39
Defective glycine cleavage system in nonketotic hyperglycinemia. Occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein. 61 6
6790577 1981
40
Clinical utility of a targeted next generation sequencing panel in severe and pediatric onset Mendelian diseases. 6
31319225 2019
41
Development of a Novel Next-Generation Sequencing Assay for Carrier Screening in Old Order Amish and Mennonite Populations of Pennsylvania. 6
31028937 2019
42
Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project. 6
30609409 2019
43
Correction: The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT. 6
29300369 2018
44
Mutations of the glycine cleavage system genes possibly affect the negative symptoms of schizophrenia through metabolomic profile changes. 6
29232014 2018
45
Comment on Late-Onset Nonketotic Hyperglycinemia With a Heterozygous Novel Point Mutation of the GLDC Gene. 6
29239742 2018
46
Diagnosing childhood-onset inborn errors of metabolism by next-generation sequencing. 6
28468868 2017
47
[Clinical and molecular genetic study of nonketotic hyperglycinemia in a Chinese family]. 6
28302194 2017
48
A comprehensive global genotype-phenotype database for rare diseases. 6
28116331 2017
49
Nonketotic Hyperglycinemia of Infants in Taiwan. 6
26947380 2016
50
Nonketotic hyperglycinemia: novel mutation in the aminomethyl transferase gene. Case report. 6
27164344 2016

Variations for Glycine Encephalopathy

ClinVar genetic disease variations for Glycine Encephalopathy:

6 (show top 50) (show all 866)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 GLDC NM_000170.2(GLDC):c.1691G>T (p.Ser564Ile) SNV Pathogenic 11982 rs121964974 GRCh37: 9:6588417-6588417
GRCh38: 9:6588417-6588417
2 GLDC GLDC, 30-KB DEL Deletion Pathogenic 11984 GRCh37:
GRCh38:
3 GLDC NM_000170.2(GLDC):c.2281G>C (p.Gly761Arg) SNV Pathogenic 11986 rs386833549 GRCh37: 9:6554703-6554703
GRCh38: 9:6554703-6554703
4 GLDC NM_000170.2(GLDC):c.2405C>T (p.Ala802Val) SNV Pathogenic 11987 rs121964977 GRCh37: 9:6553420-6553420
GRCh38: 9:6553420-6553420
5 GLDC NM_000170.2(GLDC):c.2T>C (p.Met1Thr) SNV Pathogenic 11988 rs121964978 GRCh37: 9:6645498-6645498
GRCh38: 9:6645498-6645498
6 GLDC NM_000170.2(GLDC):c.1166C>T (p.Ala389Val) SNV Pathogenic 11989 rs121964979 GRCh37: 9:6595109-6595109
GRCh38: 9:6595109-6595109
7 GLDC GLDC, 2607C-A SNV Pathogenic 11991 GRCh37:
GRCh38:
8 GCSH GCSH, COMPLEX REARRANGEMENT (1 patient) Variation Pathogenic 11973 GRCh37:
GRCh38:
9 AMT NM_000481.4(AMT):c.806G>A (p.Gly269Asp) SNV Pathogenic 11974 rs121964981 GRCh37: 3:49456475-49456475
GRCh38: 3:49419042-49419042
10 AMT NM_000481.4(AMT):c.139G>A (p.Gly47Arg) SNV Pathogenic 11975 rs121964982 GRCh37: 3:49459656-49459656
GRCh38: 3:49422223-49422223
11 AMT NM_000481.4(AMT):c.125A>G (p.His42Arg) SNV Pathogenic 11976 rs121964983 GRCh37: 3:49459670-49459670
GRCh38: 3:49422237-49422237
12 AMT AMT, 1-BP DEL, 183C Deletion Pathogenic 11977 GRCh37:
GRCh38:
13 GLDC NM_000170.2(GLDC):c.1009C>T (p.Arg337Ter) SNV Pathogenic 56036 rs386833517 GRCh37: 9:6604637-6604637
GRCh38: 9:6604637-6604637
14 GLDC NM_000170.2(GLDC):c.1654A>G (p.Met552Val) SNV Pathogenic 56048 rs386833529 GRCh37: 9:6588629-6588629
GRCh38: 9:6588629-6588629
15 GLDC NM_000170.2(GLDC):c.2186del (p.Ala729fs) Deletion Pathogenic 56062 rs386833543 GRCh37: 9:6556169-6556169
GRCh38: 9:6556169-6556169
16 GLDC NM_000170.2(GLDC):c.2203-2A>G SNV Pathogenic 56064 rs386833545 GRCh37: 9:6554783-6554783
GRCh38: 9:6554783-6554783
17 GLDC NM_000170.2(GLDC):c.2316-1G>A SNV Pathogenic 56073 rs386833554 GRCh37: 9:6553510-6553510
GRCh38: 9:6553510-6553510
18 GLDC NM_000170.2(GLDC):c.2607C>A (p.Pro869=) SNV Pathogenic 56084 rs386833565 GRCh37: 9:6540109-6540109
GRCh38: 9:6540109-6540109
19 GLDC NM_000170.2(GLDC):c.2919+1G>A SNV Pathogenic 56093 rs386833575 GRCh37: 9:6534707-6534707
GRCh38: 9:6534707-6534707
20 AMT NM_000481.4(AMT):c.452_466del (p.Lys151_Leu155del) Deletion Pathogenic 56232 rs386833683 GRCh37: 3:49457649-49457663
GRCh38: 3:49420216-49420230
21 AMT NM_000481.4(AMT):c.887G>A (p.Arg296His) SNV Pathogenic 56239 rs386833690 GRCh37: 3:49455397-49455397
GRCh38: 3:49417964-49417964
22 AMT , NICN1 NM_032316.3(NICN1):c.*2328C>T SNV Pathogenic 56225 rs386833677 GRCh37: 3:49459938-49459938
GRCh38: 3:49422505-49422505
23 AMT NM_000481.4(AMT):c.870G>A (p.Trp290Ter) SNV Pathogenic 208562 rs797045082 GRCh37: 3:49456411-49456411
GRCh38: 3:49418978-49418978
24 GLDC NM_000170.2(GLDC):c.2544C>G (p.Tyr848Ter) SNV Pathogenic 437461 rs1554643354 GRCh37: 9:6550828-6550828
GRCh38: 9:6550828-6550828
25 GLDC NC_000009.11:g.(?_6565334)_(6565449_?)dup Duplication Pathogenic 462849 GRCh37: 9:6565334-6565449
GRCh38: 9:6565334-6565449
26 GLDC and overlap with 1 gene(s) NC_000009.12:g.(?_6532997)_(6645519_?)del Deletion Pathogenic 462848 GRCh37: 9:6532997-6645519
GRCh38: 9:6532997-6645519
27 GLDC NM_000170.2(GLDC):c.1580+2T>G SNV Pathogenic 462856 rs1554646710 GRCh37: 9:6589193-6589193
GRCh38: 9:6589193-6589193
28 GLDC NM_000170.2(GLDC):c.1145G>A (p.Cys382Tyr) SNV Pathogenic 531778 rs759133707 GRCh37: 9:6602119-6602119
GRCh38: 9:6602119-6602119
29 GLDC NC_000009.12:g.(?_6558539)_(6565449_?)del Deletion Pathogenic 531791 GRCh37: 9:6558539-6565449
GRCh38: 9:6558539-6565449
30 GLDC and overlap with 1 gene(s) NC_000009.12:g.(?_6550783)_(6620339_?)del Deletion Pathogenic 531792 GRCh37: 9:6550783-6620339
GRCh38: 9:6550783-6620339
31 GLDC NC_000009.12:g.(?_6594994)_(6620339_?)del Deletion Pathogenic 531793 GRCh37: 9:6594994-6620339
GRCh38: 9:6594994-6620339
32 AMT NM_000481.3(AMT):c.1033+2T>C SNV Pathogenic 551739 rs1553638247 GRCh37: 3:49455249-49455249
GRCh38: 3:49417816-49417816
33 GLDC NM_000170.2(GLDC):c.24G>A (p.Trp8Ter) SNV Pathogenic 553731 rs1163356968 GRCh37: 9:6645476-6645476
GRCh38: 9:6645476-6645476
34 GLDC NM_000170.2(GLDC):c.1888C>T (p.Arg630Ter) SNV Pathogenic 554522 rs751025203 GRCh37: 9:6565392-6565392
GRCh38: 9:6565392-6565392
35 GLDC NM_000170.2(GLDC):c.334+1G>T SNV Pathogenic 557987 rs978795483 GRCh37: 9:6644613-6644613
GRCh38: 9:6644613-6644613
36 GLDC NM_000170.2(GLDC):c.2278dup (p.His760fs) Duplication Pathogenic 565866 rs1563834980 GRCh37: 9:6554705-6554706
GRCh38: 9:6554705-6554706
37 AMT NM_000481.4(AMT):c.164G>A (p.Trp55Ter) SNV Pathogenic 565538 rs1559530507 GRCh37: 3:49459631-49459631
GRCh38: 3:49422198-49422198
38 GLDC NM_000170.2(GLDC):c.411_412insAATA (p.Tyr138fs) Insertion Pathogenic 583199 rs1563864784 GRCh37: 9:6620242-6620243
GRCh38: 9:6620242-6620243
39 GLDC NM_000170.2(GLDC):c.1580G>C (p.Ser527Thr) SNV Pathogenic 580889 rs1247180998 GRCh37: 9:6589195-6589195
GRCh38: 9:6589195-6589195
40 AMT , NICN1 NM_000481.4(AMT):c.18_19TG[1] (p.Val7fs) Microsatellite Pathogenic 623331 rs1575309867 GRCh37: 3:49459863-49459864
GRCh38: 3:49422430-49422431
41 GLDC NM_000170.2(GLDC):c.1058+2T>A SNV Pathogenic 643420 rs1587959976 GRCh37: 9:6604586-6604586
GRCh38: 9:6604586-6604586
42 GLDC NC_000009.12:g.(?_6644594)_(6645519_?)del Deletion Pathogenic 643709 GRCh37: 9:6644594-6645519
GRCh38: 9:6644594-6645519
43 GLDC NM_000170.2(GLDC):c.1337del (p.Val446fs) Deletion Pathogenic 635297 rs1587951033 GRCh37: 9:6592915-6592915
GRCh38: 9:6592915-6592915
44 GLDC and overlap with 1 gene(s) NC_000009.12:g.(?_6550793)_(6610366_?)del Deletion Pathogenic 640451 GRCh37: 9:6550793-6610366
GRCh38: 9:6550793-6610366
45 GLDC NM_000170.2(GLDC):c.2919+1G>C SNV Pathogenic 641943 rs386833575 GRCh37: 9:6534707-6534707
GRCh38: 9:6534707-6534707
46 GLDC NM_000170.2(GLDC):c.538C>T (p.Gln180Ter) SNV Pathogenic 650449 rs762989914 GRCh37: 9:6610289-6610289
GRCh38: 9:6610289-6610289
47 AMT NM_000481.4(AMT):c.886C>T (p.Arg296Cys) SNV Pathogenic 656955 rs1056820947 GRCh37: 3:49455398-49455398
GRCh38: 3:49417965-49417965
48 GLDC NM_000170.3(GLDC):c.1629del (p.Asn543fs) Deletion Pathogenic 657819 rs1345599468 GRCh37: 9:6588654-6588654
GRCh38: 9:6588654-6588654
49 GLDC NC_000009.12:g.(?_6644604)_(6645509_?)del Deletion Pathogenic 659612 GRCh37: 9:6644604-6645509
GRCh38: 9:6644604-6645509
50 AMT NM_000481.4(AMT):c.256C>T (p.Gln86Ter) SNV Pathogenic 660464 rs1575308888 GRCh37: 3:49459539-49459539
GRCh38: 3:49422106-49422106

UniProtKB/Swiss-Prot genetic disease variations for Glycine Encephalopathy:

72 (show all 33)
# Symbol AA change Variation ID SNP ID
1 AMT p.His42Arg VAR_007951 rs121964983
2 AMT p.Gly47Arg VAR_007952 rs121964982
3 AMT p.Gly269Asp VAR_007953 rs121964981
4 AMT p.Asp276His VAR_007954 rs121964984
5 AMT p.Arg320His VAR_007955 rs121964985
6 AMT p.Asn145Ile VAR_016847 rs386833682
7 AMT p.Glu211Lys VAR_016848 rs116192290
8 AMT p.Arg265Cys VAR_074107 rs779483959
9 AMT p.Arg94Trp VAR_078794 rs1126422
10 AMT p.Arg222Cys VAR_078795 rs781466698
11 AMT p.Arg296Cys VAR_078796 rs105682094
12 GLDC p.Ser564Ile VAR_004979 rs121964974
13 GLDC p.Ala283Pro VAR_016849 rs386833589
14 GLDC p.Arg515Ser VAR_016851 rs121964976
15 GLDC p.Thr146Lys VAR_078776 rs376578742
16 GLDC p.Leu173Pro VAR_078777
17 GLDC p.Pro267Ala VAR_078778 rs155464811
18 GLDC p.Arg362Cys VAR_078779 rs10975674
19 GLDC p.Arg373Trp VAR_078780 rs150171524
20 GLDC p.Lys376Glu VAR_078781 rs774093619
21 GLDC p.Arg461Trp VAR_078782 rs761957837
22 GLDC p.Leu548Pro VAR_078783
23 GLDC p.His580Tyr VAR_078784
24 GLDC p.Pro581Arg VAR_078785 rs772871471
25 GLDC p.Ala624Asp VAR_078786
26 GLDC p.Gly763Asp VAR_078787 rs137411069
27 GLDC p.Gly768Glu VAR_078788
28 GLDC p.Arg790Trp VAR_078789 rs386833556
29 GLDC p.Asp866His VAR_078790
30 GLDC p.Val905Gly VAR_078791 rs188269735
31 GLDC p.Ile933Thr VAR_078792 rs758029533
32 GLDC p.Gly994Arg VAR_078793 rs140671310
33 GLDC p.Tyr839Cys VAR_079313

Copy number variations for Glycine Encephalopathy from CNVD:

7
# CNVD ID Chromosome Start End Type Gene Symbol CNVD Disease
1 249413 9 14100000 19900000 Copy number GLDC Glycine encephalopathy

Expression for Glycine Encephalopathy

Search GEO for disease gene expression data for Glycine Encephalopathy.

Pathways for Glycine Encephalopathy

Pathways related to Glycine Encephalopathy according to KEGG:

36
# Name Kegg Source Accession
1 Glycine, serine and threonine metabolism hsa00260

GO Terms for Glycine Encephalopathy

Cellular components related to Glycine Encephalopathy according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 mitochondrion GO:0005739 9.77 SUOX PRODH NFU1 LIPT1 LIAS ISCA2
2 mitochondrial matrix GO:0005759 9.36 SUOX PRODH LIPT1 LIAS ISCA2 IBA57
3 dense core granule GO:0031045 9.26 SLC6A9 SLC6A5
4 glycine cleavage complex GO:0005960 9.16 GLDC GCSH

Biological processes related to Glycine Encephalopathy according to GeneCards Suite gene sharing:

(show all 11)
# Name GO ID Score Top Affiliating Genes
1 oxidation-reduction process GO:0055114 9.89 SUOX PRODH PNPO GLRX5 GLDC
2 protein maturation by iron-sulfur cluster transfer GO:0097428 9.48 NFU1 ISCA2
3 glycine transport GO:0015816 9.46 SLC6A9 SLC6A5
4 small molecule metabolic process GO:0044281 9.43 ISCA2 GLRX5
5 iron-sulfur cluster assembly GO:0016226 9.43 NFU1 ISCA2 IBA57
6 cellular nitrogen compound metabolic process GO:0034641 9.4 LIPT1 LIAS
7 protein maturation by [4Fe-4S] cluster transfer GO:0106035 9.37 ISCA2 GLRX5
8 protein lipoylation GO:0009249 9.33 LIPT1 LIAS GCSH
9 glycine import across plasma membrane GO:1903804 9.32 SLC6A9 SLC6A5
10 glycine decarboxylation via glycine cleavage system GO:0019464 9.13 GLDC GCSH AMT
11 glycine catabolic process GO:0006546 8.8 GLDC GCSH AMT

Molecular functions related to Glycine Encephalopathy according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 pyridoxal phosphate binding GO:0030170 9.5 PNPO GLDC ABAT
2 2 iron, 2 sulfur cluster binding GO:0051537 9.43 ISCA2 GLRX5
3 4 iron, 4 sulfur cluster binding GO:0051539 9.43 NFU1 LIAS ISCA2
4 transaminase activity GO:0008483 9.4 AMT ABAT
5 glycine transmembrane transporter activity GO:0015187 9.37 SLC6A9 SLC6A5
6 aminomethyltransferase activity GO:0004047 9.16 GCSH AMT
7 iron-sulfur cluster binding GO:0051536 9.02 NFU1 LIAS ISCA2 GLRX5 ABAT
8 glycine:sodium symporter activity GO:0015375 8.96 SLC6A9 SLC6A5

Sources for Glycine Encephalopathy

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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