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Undiagnosed metabolic disorders

Gene: PHGDH

Green List (high evidence)

PHGDH (phosphoglycerate dehydrogenase)
EnsemblGeneIds (GRCh38): ENSG00000092621
EnsemblGeneIds (GRCh37): ENSG00000092621
OMIM: 606879, Gene2Phenotype
PHGDH is in 13 panels

1 review

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for both phenotypes. At least 6 variants reported in 6 unrelated cases of Phosphoglycerate dehydrogenase deficiency 601815 and 4 variants reported in 4 unrelated cases of Neu-Laxova syndrome 1 256520.
Created: 19 Aug 2019, 3:15 p.m. | Last Modified: 19 Aug 2019, 3:15 p.m.
Panel Version: 1.233
Comment on phenotypes: Phosphoglycerate dehydrogenase deficiency (Disorders of serine, glycine or glycerate metabolism)
Created: 19 Aug 2019, 3:09 p.m. | Last Modified: 19 Aug 2019, 3:09 p.m.
Panel Version: 1.232
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)
Created: 6 Jan 2017, 2:01 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Unexplained skeletal dysplasia

History Filter Activity

19 Aug 2019, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PHGDH were set to 27604308; 24816252

19 Aug 2019, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: phgdh has been classified as Green List (High Evidence).

19 Aug 2019, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PHGDH were changed from Phosphoglycerate dehydrogenase deficiency (Disorders of serine, glycine or glycerate metabolism); Intellectual disability; Unexplained skeletal dysplasia to Neu-Laxova syndrome 1 256520; Phosphoglycerate dehydrogenase deficiency 601815

27 Feb 2017, Gel status: 2

panel promoted to version 1

Sarah Leigh (Genomics England Curator)

Construction of “Undiagnosed Metabolic Disorders” (UDM) panel • The 614 genes from the neurometabolic gene panel (PMID: 27604308) added • Green genes downloaded from V1 metabolic panels (Cerebral folate deficiency, Congenital disorders of glycosylation, Hyperammonaemia, Ketotic hypoglycaemia, Mitochondrial disorders, Mucopolysaccharideosis, Gaucher, Fabry, Peroxisomal disorders), sources replaced with "Expert review green", then loaded as a review onto UDM panel, resulting in 367 green genes and 333 red (therefore 86 new green genes included from the additional metabolic panels that weren't previously on the UDM panel) • Downloaded green genes from all panels. Removed genes from none V1 panels. Removed genes from the metabolic panels mentioned above. Compared the remaining genes with the red genes from UDM panel. Loaded as an "Expert review Amber" review to the overlapping genes, (the panel name where the genes came from was used as the phenotype) • Used variant information from PMID 27604308 to review the genes on this panel • Reviewed genes on UDM panel with genes from Emory "Inherited Metabolic Disorders: Sequencing Panel" and UKGTN “Inborn Errors of Metabolism 226 panel”, changing status where appropriate, added 14 UKGTN genes that had not be listed before • Review 10 red genes that had not previously been reviewed, 4/10 were reclassified as green • Review the remaining 145 red genes that had not previously been reviewed (shared between reviewers EM, RF, LD, AT, HB, ON & SL), resulting in 60 green, 11 amber, 70 red, 4 I don’t know reviews) • Reviewed genes from PMID: 24816252 as a publication to genes found in the Inborn error or metabolism Genes metabolomics GWAS paper (figure 5). 2 new genes added

6 Jan 2017, Gel status: 2

Set Mode of Inheritance, Added New Source

Sarah Leigh (Genomics England Curator)

PHGDH was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Amber Model of inheritance for gene PHGDH was set to BIALLELIC, autosomal or pseudoautosomal

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

PHGDH was created by sleigh

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

PHGDH was added to Undiagnosed metabolic disorderspanel. Sources: Literature