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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 4:101,314,710...101,316,974
Ensembl chr 4:101,314,710...101,316,893
JBrowse link
G HAO2 hydroxyacid oxidase 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 4:101,588,510...101,787,818
Ensembl chr 4:101,588,861...101,732,304
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 4:101,420,941...101,440,302
Ensembl chr 4:101,420,872...101,438,126
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 4:101,565,229...101,574,110 JBrowse link
G NOTCH2 notch receptor 2 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 4:100,951,522...101,152,348
Ensembl chr 4:100,981,636...101,150,195
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 chr 4:101,445,977...101,478,144
Ensembl chr 4:101,444,693...101,478,144
JBrowse link
G REG4 regenerating family member 4 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:28492532 NCBI chr 4:101,337,295...101,354,550
Ensembl chr 4:101,337,282...101,357,025
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 4:101,918,891...102,032,280 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 4:101,787,585...101,881,231
Ensembl chr 4:101,787,583...101,883,070
JBrowse link
G ZNF697 zinc finger protein 697 ISO ClinVar Annotator: match by term: PHGDH deficiency ClinVar PMID:14645240 PMID:24836451 PMID:28492532 NCBI chr 4:101,520,252...101,552,266
Ensembl chr 4:101,521,763...101,552,753
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15430
    physical disorder 5064
      congenital nervous system abnormality 1520
        microcephaly 1131
          PHGDH deficiency 10
Path 2
Term Annotations click to browse term
  disease 15430
    Developmental Disease 13490
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 12612
        genetic disease 12321
          monogenic disease 10535
            autosomal genetic disease 10088
              autosomal dominant disease 6582
                complex cortical dysplasia with other brain malformations 1617
                  Malformations of Cortical Development, Group I 1374
                    microcephaly 1131
                      PHGDH deficiency 10
paths to the root