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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:PHGDH deficiency
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Accession:DOID:0050722 term browser browse the term
Definition:A serine deficiency that has_material_basis_in deficiency of phosphoglycerate dehydrogenase which results in a disruption of L-serine biosynthesis. (DO)
Synonyms:exact_synonym: PHGDHD;   phosphoglycerate dehydrogenase deficiency
 primary_id: MESH:C566618
 alt_id: MIM:601815;   RDO:0014928

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PHGDH deficiency term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADAM30 ADAM metallopeptidase domain 30 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr20:13,887,509...13,890,543
Ensembl chr20:13,887,666...13,890,095 		JBrowse link
G HAO2 hydroxyacid oxidase 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr20:14,376,096...14,408,753
Ensembl chr20:14,374,543...14,407,992 		JBrowse link
G HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:25741868 PMID:28492532 NCBI chr20:14,018,669...14,040,934
Ensembl chr20:14,019,692...14,041,016 		JBrowse link
G NOTCH2 notch receptor 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr20:13,712,140...13,871,777
Ensembl chr20:13,712,292...13,871,784 		JBrowse link
G PHGDH phosphoglycerate dehydrogenase ISO ClinVar Annotator: match by term: PHGDH deficiency | ClinVar Annotator: match by term: Phosphoglycerate dehydrogenase deficiency OMIM
ClinVar		 PMID:9536098 PMID:11034457 PMID:11055895 PMID:11751922 PMID:14645240 More... NCBI chr20:14,045,395...14,075,935
Ensembl chr20:14,045,346...14,076,177 		JBrowse link
G REG4 regenerating family member 4 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr20:13,975,721...13,995,645
Ensembl chr20:13,978,512...13,993,678 		JBrowse link
G TBX15 T-box transcription factor 15 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr20:14,762,073...14,870,417
Ensembl chr20:14,818,525...14,871,196 		JBrowse link
G WARS2 tryptophanyl tRNA synthetase 2, mitochondrial ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr20:14,614,902...14,726,630
Ensembl chr20:14,615,349...14,726,780 		JBrowse link
G ZNF697 zinc finger protein 697 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr20:14,144,704...14,173,417
Ensembl chr20:14,144,990...14,170,099 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15342
    physical disorder 5030
      congenital nervous system abnormality 1510
        microcephaly 1134
          PHGDH deficiency 9
Path 2
Term Annotations click to browse term
  disease 15342
    Developmental Disease 13376
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 12500
        genetic disease 12198
          monogenic disease 10363
            autosomal genetic disease 9600
              autosomal dominant disease 6361
                complex cortical dysplasia with other brain malformations 1622
                  Malformations of Cortical Development, Group I 1378
                    microcephaly 1134
                      PHGDH deficiency 9
paths to the root