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Undiagnosed metabolic disorders

Gene: PCK1

Green List (high evidence)

PCK1 (phosphoenolpyruvate carboxykinase 1)
EnsemblGeneIds (GRCh38): ENSG00000124253
EnsemblGeneIds (GRCh37): ENSG00000124253
OMIM: 614168, Gene2Phenotype
PCK1 is in 3 panels

2 reviews

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in unrelated cases.
Created: 19 Aug 2019, 2:08 p.m. | Last Modified: 19 Aug 2019, 2:08 p.m.
Panel Version: 1.223
Comment on phenotypes: Phosphoenolpyruvate carboxykinase deficiency (Disorders of gluconeogenesis);Cytosolic phosphoenolpyruvate carboxykinase (PEPCK))
Created: 19 Aug 2019, 2:03 p.m. | Last Modified: 19 Aug 2019, 2:03 p.m.
Panel Version: 1.221

Louise Daugherty (NIHR BioResource - Rare Diseases Study (NIHRBR-RD), University of Cambridge & NHS Blood and Transplant)

gene: PCK1 review by Louise Daugherty

PCK1 is responsible for the cytosolic (soluble) form of PEPCK deficiency. PMID: 24863970 (2014) 1 family (2 sibs affected); PMID:26971250 (2016) 1 affected homozygous 12-bp deletion in PCK1, together with supporting functional studies.
Created: 23 Feb 2017, 5:15 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
?Phosphoenolpyruvate carboxykinase-1, cytosolic, deficiency; (PCK1 DEFICIENCY, Cytosolic phosphoenolpyruvate carboxykinase (PEPCK))

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Literature
Phenotypes
  • ?Phosphoenolpyruvate carboxykinase deficiency, cytosolic 261680
OMIM
614168
Clinvar variants
Variants in PCK1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

19 Aug 2019, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: pck1 has been classified as Green List (High Evidence).

19 Aug 2019, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PCK1 were set to 27604308

19 Aug 2019, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PCK1 were changed from Phosphoenolpyruvate carboxykinase deficiency (Disorders of gluconeogenesis); ?Phosphoenolpyruvate carboxykinase-1, cytosolic, deficiency; (PCK1 DEFICIENCY, Cytosolic phosphoenolpyruvate carboxykinase (PEPCK)) to ?Phosphoenolpyruvate carboxykinase deficiency, cytosolic 261680

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

24 Feb 2017, Gel status: 2

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

PCK1 was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Amber PCK1 was added to Undiagnosed metabolic disorderspanel. Source: Illumina TruGenome Clinical Sequencing Services Model of inheritance for gene PCK1 was set to BIALLELIC, autosomal or pseudoautosomal

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

PCK1 was created by sleigh

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

PCK1 was added to Undiagnosed metabolic disorderspanel. Sources: Literature