MCID: AGT001
MIFTS: 42

Agat Deficiency malady

Genetic diseases, Rare diseases, Neuronal diseases categories
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Summaries for Agat Deficiency

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Sources:
8Disease Ontology, 21Genetics Home Reference, 47OMIM, 33MalaCards
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Genetics Home Reference:21 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:8 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:47 612718

Aliases & Classifications for Agat Deficiency

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Sources:
8Disease Ontology, 9diseasecard, 43NIH Rare Diseases, 21Genetics Home Reference, 10DISEASES, 22GTR, 49Orphanet, 47OMIM, 20GeneTests, 26ICD10 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):

49
arginine:glycine amidinotransferase deficiency:
Inheritance: Autosomal recessive; Prevalence: <1/1000000; Age of onset: Childhood


Aliases & Descriptions:

agat deficiency 8 9 43 21 10
arginine:glycine amidinotransferase deficiency 8 43 22 21 49
l-arginine:glycine amidinotransferase deficiency 43 20 21
cerebral creatine deficiency syndrome 3 8 47
creatine deficiency syndrome due to agat deficiency 21
gatm deficiency 21


External Ids:

Disease Ontology8 DOID:0050712
OMIM47 612718
ICD10 via Orphanet26 E72.8

Related Diseases for Agat Deficiency

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17GeneCards, 18GeneDecks
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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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47OMIM
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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:
42NIH Clinical Center, 6ClinicalTrials
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Drug clinical trials:

Search ClinicalTrials for Agat Deficiency

Search NIH Clinical Center for Agat Deficiency

Genetic Tests for Agat Deficiency

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20GeneTests, 22GTR
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Genetic tests related to Agat Deficiency:

id Genetic test Affiliating Genes
1 L-Arginine:glycine Amidinotransferase Deficiency20 GATM
2 Arginine:glycine Amidinotransferase Deficiency22

Anatomical Context for Agat Deficiency

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33MalaCards
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MalaCards organs/tissues related to Agat Deficiency:

33
Brain

Animal Models for Agat Deficiency or affiliated genes

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Sources:
37MGI
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MGI Mouse Phenotypes related to Agat Deficiency:

37
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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52PubMed
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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:
64UniProtKB/Swiss-Prot, 1 National Center for Biotechnology Information (Clinvar)
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UniProtKB/Swiss-Prot genetic disease variations for Agat Deficiency:

64
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, 15Gene 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:
50PathCards, 30KEGG, 55Reactome, 38NCBI 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 cycle38
arginine degradation I (arginase pathway)38
proline degradation38
glutamine degradation I38
proline biosynthesis I38
superpathway of citrulline metabolism38
proline biosynthesis II (from arginine)38
citrulline biosynthesis38
arginine degradation VI (arginase 2 pathway)38
Urea cycle and metabolism of amino groups38
asparagine biosynthesis I38
4-hydroxyproline degradation I38
citrulline degradation38
9.0GATM, GAMT
2
Show member pathways
choline degradation I38
glycine biosynthesis III38
serine and glycine biosynthesis38
glycine betaine degradation38
glycine biosynthesis38
9.0GAMT, GATM
3
Show member pathways
8.5SLC6A8, GAMT, GATM
4
Show member pathways
creatine-phosphate biosynthesis38
glycine degradation (creatine biosynthesis)38
putrescine biosynthesis III38
spermidine biosynthesis I38
tryptophan degradation via kynurenine38
spermine biosynthesis38
urea cycle38
S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation I38
tyrosine degradation I38
L-carnitine biosynthesis38
methylthiopropionate biosynthesis38
2-oxoglutarate decarboxylation to succinyl-CoA38
S-methyl-5-thioadenosine degradation II38
8.5SLC6A8, GAMT, GATM

Compounds for genes affiliated with Agat Deficiency

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Sources:
24HMDB, 45Novoseek, 11DrugBank
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Compounds related to Agat Deficiency according to GeneCards/GeneDecks:

idCompoundScoreTop Affiliating Genes
1Guanidoacetic acid249.0GAMT, GATM
2ornithine45 2410.0GATM, GAMT
3guanidinoacetate458.6SLC6A8, GATM, GAMT
4Creatine24 119.6GATM, GAMT, SLC6A8
5creatinine458.4GATM, GAMT, SLC6A8
6arginine458.2GATM, GAMT, SLC6A8

GO Terms for genes affiliated with Agat Deficiency

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16Gene 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
13ExPASy
14FMA
22GTR
23HGMD
24HMDB
25ICD10
26ICD10 via Orphanet
27ICD9CM
29IUPHAR
30KEGG
35MeSH
36MESH via Orphanet
37MGI
40NCIt
41NDF-RT
44NINDS
45Novoseek
47OMIM
48OMIM via Orphanet
52PubMed
53QIAGEN
59SNOMED-CT via Orphanet
62UMLS
63UMLS via Orphanet