MCID: AGT001
MIFTS: 44

Agat Deficiency malady

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

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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 based summary: Agat Deficiency, also known as arginine:glycine amidinotransferase deficiency, is related to creatine deficiency syndromes and encephalomyopathy, and has symptoms including 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:46 612718

Aliases & Classifications for Agat Deficiency

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Agat Deficiency, Aliases & Descriptions:

Name: Agat Deficiency 8 9 42 21 10 62
Arginine:glycine Amidinotransferase Deficiency 8 42 22 21 48
L-Arginine:glycine Amidinotransferase Deficiency 42 20 21
 
Creatine Deficiency Syndrome Due to Agat Deficiency 21 62
Cerebral Creatine Deficiency Syndrome 3 8 46
Gatm Deficiency 21 62


Classifications:



Characteristics (Orphanet epidemiological data):

48
arginine:glycine amidinotransferase deficiency:
Inheritance: Autosomal recessive; Prevalence: <1/1000000; Age of onset: Childhood


External Ids:

Disease Ontology8 DOID:0050712
OMIM46 612718
ICD10 via Orphanet26 E72.8

Related Diseases for Agat Deficiency

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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 syndromes29.6GATM, GAMT, SLC6A8
2encephalomyopathy10.4
3myopathy10.1
4epilepsy syndrome9.9SLC6A8, GAMT
5intellectual disability multi-gene panels9.8GAMT, SLC6A8
6mental retardation9.6SLC6A8, GATM, GAMT

Graphical network of diseases related to Agat Deficiency:



Diseases related to agat deficiency

Symptoms for Agat Deficiency

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Symptoms by clinical synopsis from OMIM:

612718

Clinical features from OMIM:

612718

HPO human phenotypes related to Agat Deficiency:

(show all 10)
id Description Frequency HPO Source Accession
1 gowers sign rare (5%) HP:0003391
2 autosomal recessive inheritance HP:0000007
3 autism HP:0000717
4 delayed speech and language development HP:0000750
5 intellectual disability HP:0001249
6 global developmental delay HP:0001263
7 failure to thrive HP:0001508
8 organic aciduria HP:0001992
9 infantile onset HP:0003593
10 abnormality of creatine metabolism HP:0012113

Drugs & Therapeutics for Agat Deficiency

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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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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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MalaCards organs/tissues related to Agat Deficiency:

32
Brain

Animal Models for Agat Deficiency or affiliated genes

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MGI Mouse Phenotypes related to Agat Deficiency:

36
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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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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UniProtKB/Swiss-Prot genetic disease variations for Agat Deficiency:

64
id Symbol AA change Variation ID SNP ID
1GATMp.Tyr203SerVAR_069816
2GATMp.Arg413GlnVAR_071789
3GATMp.Arg413TrpVAR_071790

Clinvar genetic disease variations for Agat Deficiency:

6
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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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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Pathways related to Agat Deficiency according to GeneCards/GeneDecks:

idSuper pathways (with members indented)ScoreTop Affiliating Genes
1
Show member pathways
citrulline-nitric oxide cycle37
arginine degradation I (arginase pathway)37
proline degradation37
glutamine degradation I37
proline biosynthesis I37
superpathway of citrulline metabolism37
proline biosynthesis II (from arginine)37
citrulline biosynthesis37
arginine degradation VI (arginase 2 pathway)37
Urea cycle and metabolism of amino groups37
asparagine biosynthesis I37
4-hydroxyproline degradation I37
citrulline degradation37
9.0GATM, GAMT
2
Show member pathways
choline degradation I37
glycine biosynthesis III37
serine and glycine biosynthesis37
glycine betaine degradation37
glycine biosynthesis37
9.0GAMT, GATM
3
Show member pathways
8.5SLC6A8, GAMT, GATM
4
Show member pathways
creatine-phosphate biosynthesis37
glycine degradation (creatine biosynthesis)37
putrescine biosynthesis III37
spermidine biosynthesis I37
tryptophan degradation via kynurenine37
spermine biosynthesis37
urea cycle37
S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation I37
tyrosine degradation I37
L-carnitine biosynthesis37
methylthiopropionate biosynthesis37
2-oxoglutarate decarboxylation to succinyl-CoA37
S-methyl-5-thioadenosine degradation II37
8.5SLC6A8, GAMT, GATM

Compounds for genes affiliated with Agat Deficiency

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Sources:
24HMDB, 44Novoseek, 11DrugBank
See all sources

Compounds related to Agat Deficiency according to GeneCards/GeneDecks:

idCompoundScoreTop Affiliating Genes
1Guanidoacetic acid249.0GAMT, GATM
2ornithine44 2410.0GAMT, GATM
3guanidinoacetate448.6SLC6A8, GAMT, GATM
4Creatine24 119.6SLC6A8, GAMT, GATM
5creatinine448.4GATM, GAMT, SLC6A8
6arginine448.2SLC6A8, GAMT, GATM

GO Terms for genes affiliated with Agat Deficiency

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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

Sources for Agat Deficiency

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3CDC
13ExPASy
14FMA
22GTR
23HGMD
24HMDB
25ICD10
26ICD10 via Orphanet
27ICD9CM
28IUPHAR
29KEGG
34MeSH
35MESH via Orphanet
36MGI
39NCIt
40NDF-RT
43NINDS
44Novoseek
46OMIM
47OMIM via Orphanet
51PubMed
52QIAGEN
58SNOMED-CT via Orphanet
62UMLS
63UMLS via Orphanet