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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: OMIM: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 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 1:119,893,533...119,896,515
Ensembl chr 1:119,893,533...119,896,515 		JBrowse link
G HAO2 hydroxyacid oxidase 2 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:119,368,785...119,394,130
Ensembl chr 1:119,368,779...119,394,130 		JBrowse link
G HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 1:119,747,996...119,768,932
Ensembl chr 1:119,748,002...119,768,905 		JBrowse link
G HSD3B1 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:119,507,203...119,515,058
Ensembl chr 1:119,507,198...119,515,054 		JBrowse link
G HSD3B2 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:119,414,931...119,423,034
Ensembl chr 1:119,414,931...119,423,035 		JBrowse link
G NOTCH2 notch receptor 2 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 1:119,911,553...120,069,662
Ensembl chr 1:119,911,553...120,100,779 		JBrowse link
G PHGDH phosphoglycerate dehydrogenase IAGP
EXP		 ClinVar Annotator: match by term: PHGDH deficiency
ClinVar Annotator: match by term: PHGDH deficiency | ClinVar Annotator: match by term: Phosphoglycerate dehydrogenase deficiency
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:9536098 PMID:11034457 PMID:11055895 PMID:11751922 PMID:14645240 More... NCBI chr 1:119,711,934...119,744,215
Ensembl chr 1:119,648,411...119,744,218 		JBrowse link
G REG4 regenerating family member 4 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 1:119,794,017...119,811,460
Ensembl chr 1:119,794,017...119,811,580 		JBrowse link
G TBX15 T-box transcription factor 15 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:118,883,047...118,989,510
Ensembl chr 1:118,883,046...118,989,556 		JBrowse link
G WARS2 tryptophanyl tRNA synthetase 2, mitochondrial IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:119,031,216...119,140,672
Ensembl chr 1:119,031,216...119,140,654 		JBrowse link
G ZNF697 zinc finger protein 697 IAGP ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 1:119,619,377...119,648,266
Ensembl chr 1:119,619,377...119,648,266 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 35754
    physical disorder 7158
      congenital nervous system abnormality 1976
        microcephaly 1528
          PHGDH deficiency 11
Path 2
Term Annotations click to browse term
  disease 35754
    Developmental Disease 28610
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 24646
        genetic disease 23840
          monogenic disease 18586
            autosomal genetic disease 16857
              autosomal dominant disease 10967
                complex cortical dysplasia with other brain malformations 2181
                  Malformations of Cortical Development, Group I 1869
                    microcephaly 1528
                      PHGDH deficiency 11
paths to the root