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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 chr 2:185,752,183...185,755,623
Ensembl chr 2:185,752,072...185,755,599 		JBrowse link
G Hao2 hydroxyacid oxidase 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 2:186,200,137...186,232,997
Ensembl chr 2:186,200,504...186,224,425 		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 chr 2:185,875,609...185,903,505
Ensembl chr 2:185,875,616...185,902,130 		JBrowse link
G Hsd3b1 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 2:186,169,864...186,175,984
Ensembl chr 2:186,169,863...186,175,999 		JBrowse link
G Hsd3b2 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 2:186,095,897...186,105,354
Ensembl chr 2:186,095,897...186,101,852 		JBrowse link
G Notch2 notch receptor 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 2:185,610,594...185,744,088
Ensembl chr 2:185,610,589...185,744,088 		JBrowse link
G Phgdh phosphoglycerate dehydrogenase ISO 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 2:185,906,962...185,936,054
Ensembl chr 2:185,906,966...185,935,944 		JBrowse link
G Reg4 regenerating family member 4 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 2:185,818,946...185,833,252
Ensembl chr 2:185,821,210...185,833,353 		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 chr 2:186,576,650...186,687,748
Ensembl chr 2:186,576,676...186,687,663 		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 chr 2:186,459,744...186,543,581
Ensembl chr 2:186,459,444...186,543,571 		JBrowse link
G Zfp697 zinc finger protein 697 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 2:185,970,562...186,003,884
Ensembl chr 2:185,970,576...186,001,041 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19099
    physical disorder 5180
      congenital nervous system abnormality 1530
        microcephaly 1142
          PHGDH deficiency 11
Path 2
Term Annotations click to browse term
  disease 19099
    Developmental Disease 14598
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 13613
        genetic disease 13275
          monogenic disease 10822
            autosomal genetic disease 10303
              autosomal dominant disease 6647
                complex cortical dysplasia with other brain malformations 1633
                  Malformations of Cortical Development, Group I 1393
                    microcephaly 1142
                      PHGDH deficiency 11
paths to the root