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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:AGAT deficiency
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Accession:DOID:0050712 term browser browse the term
Definition: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. (DO)
Synonyms:exact_synonym: CCDS3;   GATM deficiency;   L-Arginine:Glycine Aminidotransferase Deficiency;   arginine:glycine amidinotransferase deficiency;   cerebral creatine deficiency syndrome 3;   creatine deficiency syndrome due to AGAT deficiency
 primary_id: MESH:C567192
 alt_id: OMIM:612718
For additional species annotation, visit the Alliance of Genome Resources.



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AGAT deficiency term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G B2m beta-2 microglobulin ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,095,740...109,101,764
Ensembl chr 3:109,095,729...109,101,766
JBrowse link
G Bloc1s6 biogenesis of lysosomal organelles complex 1 subunit 6 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,816,397...109,826,528
Ensembl chr 3:109,816,366...109,828,308
JBrowse link
G Duox1 dual oxidase 1 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,260,526...109,295,588
Ensembl chr 3:109,262,397...109,295,563
JBrowse link
G Duox2 dual oxidase 2 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,223,809...109,247,023
Ensembl chr 3:109,226,924...109,245,902
JBrowse link
G Duoxa1 dual oxidase maturation factor 1 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,249,815...109,260,511
Ensembl chr 3:109,249,923...109,260,499
JBrowse link
G Duoxa2 dual oxidase maturation factor 2 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,245,476...109,248,844
Ensembl chr 3:109,245,476...109,248,968
JBrowse link
G Gatm glycine amidinotransferase ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency OMIM
ClinVar
PMID:9536098 PMID:10762163 PMID:11555793 PMID:12468279 PMID:17576681 More... NCBI chr 3:109,658,919...109,675,508
Ensembl chr 3:109,658,951...109,684,129
JBrowse link
G MGC105649 hypothetical LOC302884 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,719,952...109,723,507
Ensembl chr 3:109,719,897...109,724,006
Ensembl chr 3:109,719,897...109,724,006
JBrowse link
G Patl2 PAT1 homolog 2 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,072,958...109,087,425
Ensembl chr 3:109,075,290...109,083,253
JBrowse link
G Shf Src homology 2 domain containing F ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,296,517...109,316,315
Ensembl chr 3:109,296,784...109,316,328
JBrowse link
G Slc28a2 solute carrier family 28 member 2 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,324,815...109,387,702
Ensembl chr 3:109,366,996...109,387,702
JBrowse link
G Slc30a4 solute carrier family 30 member 4 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,753,270...109,775,306
Ensembl chr 3:109,753,273...109,775,306
JBrowse link
G Sord sorbitol dehydrogenase ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,184,697...109,216,133
Ensembl chr 3:109,184,676...109,216,133
JBrowse link
G Spata5l1 spermatogenesis associated 5-like 1 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,694,739...109,708,356
Ensembl chr 3:109,694,757...109,707,757
JBrowse link
G Spg11 SPG11 vesicle trafficking associated, spatacsin ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,007,658...109,072,904
Ensembl chr 3:109,008,135...109,072,911
JBrowse link
G Terb2 telomere repeat binding bouquet formation protein 2 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,138,343...109,156,700
Ensembl chr 3:109,138,343...109,156,683
JBrowse link
G Trim69 tripartite motif-containing 69 ISO ClinVar Annotator: match by term: Arginine:glycine amidinotransferase deficiency ClinVar PMID:28492532 NCBI chr 3:109,111,468...109,135,255
Ensembl chr 3:109,111,468...109,132,037
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18203
    syndrome 9805
      cerebral creatine deficiency syndrome 68
        AGAT deficiency 17
Path 2
Term Annotations click to browse term
  disease 18203
    disease of anatomical entity 17561
      nervous system disease 13192
        central nervous system disease 11332
          brain disease 10625
            disease of mental health 7593
              developmental disorder of mental health 4927
                specific developmental disorder 4191
                  communication disorder 315
                    language disorder 146
                      speech disorder 79
                        AGAT deficiency 17
paths to the root