MCID: AGT001
MIFTS: 42

Agat Deficiency malady

Genetic diseases, Rare diseases, Neuronal diseases categories

Summaries for Agat Deficiency

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Sources:
9Disease Ontology, 22Genetics Home Reference, 48OMIM, 34MalaCards
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Genetics Home Reference:22 Arginine:glycine amidinotransferase deficiency is an inherited disorder that primarily affects the brain. People with this disorder have mild to moderate intellectual disability and delayed speech development. Some affected individuals develop autistic behaviors that affect communication and social interaction. They may experience seizures, especially when they have a fever.

MalaCards: Agat Deficiency, also known as arginine:glycine amidinotransferase deficiency, is related to creatine deficiency syndromes and encephalomyopathy. An important gene associated with Agat Deficiency is GATM (glycine amidinotransferase (L-arginine:glycine amidinotransferase)), and among its related pathways are Arginine and proline metabolism and Glycine, serine and threonine metabolism. The compounds Guanidoacetic acid and ornithine have been mentioned in the context of this disorder. Affiliated tissues include brain, and related mouse phenotypes are adipose tissue and homeostasis/metabolism.

Disease Ontology:9 An amino acid metabolic disorder that has material basis in a mutation in the gatm gene resulting in deficiency of arginine:glycine amidinotransferase which then limits creatine synthesis.

Description from OMIM:48 612718

Aliases & Classifications for Agat Deficiency

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Sources:
9Disease Ontology, 10diseasecard, 44NIH Rare Diseases, 22Genetics Home Reference, 11DISEASES, 23GTR, 50Orphanet, 48OMIM, 21GeneTests, 27ICD10 via Orphanet
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Classifications:

Malacards categories (disease lists): (See all malacards categories)
Global: Genetic diseases, Rare diseases
Anatomical: Neuronal diseases


Characteristics (Orphanet epidemiological data):

50
arginine:glycine amidinotransferase deficiency:
Inheritance: Autosomal recessive; Prevalence: <1/1000000; Age of onset: Childhood


Aliases & Descriptions:

agat deficiency 9 10 44 22 11
arginine:glycine amidinotransferase deficiency 9 44 23 22 50
l-arginine:glycine amidinotransferase deficiency 44 21 22
cerebral creatine deficiency syndrome 3 9 48
creatine deficiency syndrome due to agat deficiency 22
gatm deficiency 22


External Ids:

Disease Ontology9 DOID:0050712
OMIM48 612718
ICD10 via Orphanet27 E72.8

Related Diseases for Agat Deficiency

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18GeneCards, 19GeneDecks
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Diseases related to Agat Deficiency via text searches within MalaCards or GeneCards/GeneDecks gene sharing:

idRelated DiseaseScoreTop Affiliating Genes
1creatine deficiency syndromes30.1GATM, GAMT, SLC6A8
2encephalomyopathy10.4
3myopathy10.1
4epilepsy syndrome10.0SLC6A8, GAMT
5intellectual disability9.9GAMT, SLC6A8
6mental retardation9.9SLC6A8, GATM, GAMT

Graphical network of diseases related to Agat Deficiency:



Diseases related to agat deficiency

Symptoms for Agat Deficiency

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Sources:
48OMIM
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Symptoms by clinical synopsis from OMIM:

612718

Clinical features from OMIM:

612718

Drugs & Therapeutics for Agat Deficiency

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Sources:
6CenterWatch, 43NIH Clinical Center, 7ClinicalTrials
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Approved drugs:

Search CenterWatch for Agat Deficiency

Drug clinical trials:

Search ClinicalTrials for Agat Deficiency

Search NIH Clinical Center for Agat Deficiency

Search CenterWatch for Agat Deficiency

Genetic Tests for Agat Deficiency

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21GeneTests, 23GTR
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Genetic tests related to Agat Deficiency:

id Genetic test Affiliating Genes
1 L-Arginine:glycine Amidinotransferase Deficiency21 GATM
2 Arginine:glycine Amidinotransferase Deficiency23

Anatomical Context for Agat Deficiency

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Sources:
34MalaCards
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MalaCards organs/tissues related to Agat Deficiency:

34
Brain

Animal Models for Agat Deficiency or affiliated genes

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Sources:
38MGI
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MGI Mouse Phenotypes related to Agat Deficiency:

38
idDescriptionMGI Source AccessionScoreTop Affiliating Genes
1MP:00053758.5GATM, GAMT, SLC6A8
2MP:00053768.5GATM, GAMT, SLC6A8
3MP:00053868.4GATM, GAMT, SLC6A8
4MP:00053788.2GATM, GAMT, SLC6A8

Publications for Agat Deficiency

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Sources:
53PubMed
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Articles related to Agat Deficiency:

idTitleAuthorsYear
1
Creatine deficiency syndrome. A treatable myopathy due to arginine-glycine amidinotransferase (AGAT) deficiency. (23770102)
2013
2
l-arginine:glycine amidinotransferase (AGAT) deficiency: clinical presentation and response to treatment in two patients with a novel mutation. (20682460)
2010
3
Arginine:glycine amidinotransferase (AGAT) deficiency in a newborn: early treatment can prevent phenotypic expression of the disease. (16769397)
2006
4
Creatine depletion in a new case with AGAT deficiency: clinical and genetic study in a large pedigree. (12468279)
2002

Variations for Agat Deficiency

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Sources:
65UniProtKB/Swiss-Prot, 1 National Center for Biotechnology Information (Clinvar)
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UniProtKB/Swiss-Prot genetic disease variations for Agat Deficiency:

65
id Symbol AA change Variation ID SNP ID
1GATMp.Tyr203SerVAR_069816

Clinvar genetic disease variations for Agat Deficiency:

1
id Gene Name Type Significance SNP ID Assembly Location
1GATMNM_001482.2(GATM): c.484+1G> Tsingle nucleotide variantPathogenicrs80338738GRCh37Chr 15, 45661523: 45661523
2GATMNM_001482.2(GATM): c.1111dupA (p.Met371Asnfs)duplicationPathogenicrs397515542GRCh37Chr 15, 45656145: 45656146
3GATMNM_001482.2(GATM): c.505C> T (p.Arg169Ter)single nucleotide variantPathogenicrs397514708GRCh37Chr 15, 45660438: 45660438
4GATMGATM, IVS3DS, G-T, +1single nucleotide variantPathogenic
5GATMNM_001482.2(GATM): c.608A> C (p.Tyr203Ser)single nucleotide variantPathogenicrs397514709GRCh37Chr 15, 45660335: 45660335
6GATMNM_001482.2(GATM): c.446G> A (p.Trp149Ter)single nucleotide variantPathogenicrs80338737GRCh37Chr 15, 45661562: 45661562

Expression for genes affiliated with Agat Deficiency

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Sources:
2BioGPS, 16Gene Expression Omnibus DataSets
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Expression patterns in normal tissues for genes affiliated with Agat Deficiency

Search GEO for disease gene expression data for Agat Deficiency.

Pathways for genes affiliated with Agat Deficiency

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Sources:
51PathCards, 31KEGG, 56Reactome, 39NCBI BioSystems Database
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Pathways related to Agat Deficiency according to GeneCards/GeneDecks:

idSuper pathways (with members indented)ScoreTop Affiliating Genes
1
Show member pathways
citrulline-nitric oxide cycle39
arginine degradation I (arginase pathway)39
proline degradation39
glutamine degradation I39
proline biosynthesis I39
superpathway of citrulline metabolism39
proline biosynthesis II (from arginine)39
citrulline biosynthesis39
arginine degradation VI (arginase 2 pathway)39
Urea cycle and metabolism of amino groups39
asparagine biosynthesis I39
4-hydroxyproline degradation I39
citrulline degradation39
9.0GATM, GAMT
2
Show member pathways
choline degradation I39
glycine biosynthesis III39
serine and glycine biosynthesis39
glycine betaine degradation39
glycine biosynthesis39
9.0GAMT, GATM
3
Show member pathways
8.5SLC6A8, GAMT, GATM
4
Show member pathways
creatine-phosphate biosynthesis39
glycine degradation (creatine biosynthesis)39
putrescine biosynthesis III39
spermidine biosynthesis I39
tryptophan degradation via kynurenine39
spermine biosynthesis39
urea cycle39
S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation I39
tyrosine degradation I39
L-carnitine biosynthesis39
methylthiopropionate biosynthesis39
2-oxoglutarate decarboxylation to succinyl-CoA39
S-methyl-5-thioadenosine degradation II39
8.5SLC6A8, GAMT, GATM

Compounds for genes affiliated with Agat Deficiency

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Sources:
25HMDB, 46Novoseek, 12DrugBank
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Compounds related to Agat Deficiency according to GeneCards/GeneDecks:

idCompoundScoreTop Affiliating Genes
1Guanidoacetic acid259.0GAMT, GATM
2ornithine46 2510.0GATM, GAMT
3guanidinoacetate468.6SLC6A8, GATM, GAMT
4Creatine25 129.6GATM, GAMT, SLC6A8
5creatinine468.4GATM, GAMT, SLC6A8
6arginine468.2GATM, GAMT, SLC6A8

GO Terms for genes affiliated with Agat Deficiency

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Sources:
17Gene Ontology
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Biological processes related to Agat Deficiency according to GeneCards/GeneDecks:

idNameGO IDScoreTop Affiliating Genes
1creatine biosynthetic processGO:0066019.0GAMT, GATM
2muscle contractionGO:0069368.8SLC6A8, GAMT
3creatine metabolic processGO:0066008.6SLC6A8, GAMT, GATM
4small molecule metabolic processGO:0442818.5SLC6A8, GAMT, GATM
5cellular nitrogen compound metabolic processGO:0346418.4GATM, GAMT, SLC6A8

Products for genes affiliated with Agat Deficiency

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  • Antibodies
  • Proteins
  • Lysates
  • Antibodies

Sources for Agat Deficiency

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4CDC
14ExPASy
15FMA
23GTR
24HGMD
25HMDB
26ICD10
27ICD10 via Orphanet
28ICD9CM
30IUPHAR
31KEGG
36MeSH
37MESH via Orphanet
38MGI
41NCIt
42NDF-RT
45NINDS
46Novoseek
48OMIM
49OMIM via Orphanet
53PubMed
54QIAGEN
60SNOMED-CT via Orphanet
63UMLS
64UMLS via Orphanet