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Inborn errors of metabolism

Gene: PDK3

Amber List (moderate evidence)

PDK3 (pyruvate dehydrogenase kinase 3)
EnsemblGeneIds (GRCh38): ENSG00000067992
EnsemblGeneIds (GRCh37): ENSG00000067992
OMIM: 300906, Gene2Phenotype
PDK3 is in 6 panels

4 reviews

Sarah Leigh (Genomics England Curator)

Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 2 variants reported in at least three unrelated cases, together with functional studies.
Created: 27 Sep 2019, 4:28 p.m. | Last Modified: 27 Sep 2019, 4:28 p.m.
Panel Version: 1.313
Comment on mode of pathogenicity: A gain of function mechanism has been reported for the p.R158H variant, resulting in a more activity than the wild-type kinase (PMID: 23297365).
Created: 27 Sep 2019, 3:54 p.m. | Last Modified: 27 Sep 2019, 3:54 p.m.
Panel Version: 1.312
Comment on phenotypes: Pyruvate dehydrogenase kinase deficiency (Disorders of pyruvate metabolism)
Created: 27 Sep 2019, 2:41 p.m. | Last Modified: 27 Sep 2019, 2:41 p.m.
Panel Version: 1.309

Zornitza Stark (Australian Genomics)

I don't know

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
Charcot-Marie-Tooth disease, X-linked dominant, 6, MIM#300905

Publications

Variants in this GENE are reported as part of current diagnostic practice

Olivia Niblock (Genomics England Curator)

Red List (low evidence)

At least 1 variant reported. Phenotype associated with Charcot-Marie-Tooth Disease in humans, not in G2P. Cellular response to glucose in rats only
Created: 23 Feb 2017, 5:15 p.m.

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
?Charcot-Marie-Tooth disease, X-linked dominant, 6 300905

Publications

Shamima Rahman (UCL Institute of Child Health)

Green List (high evidence)

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert Review Amber
  • London North GLH
  • NHS GMS
Phenotypes
  • ?Charcot-Marie-Tooth disease, X-linked dominant, 6 300905
OMIM
300906
Clinvar variants
Variants in PDK3
Penetrance
None
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

27 Sep 2019, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: pdk3 has been classified as Amber List (Moderate Evidence).

27 Sep 2019, Gel status: 1

Set mode of pathogenicity

Sarah Leigh (Genomics England Curator)

Mode of pathogenicity for gene: PDK3 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

27 Sep 2019, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PDK3 were set to 27604308; 26801680; 28902413

27 Sep 2019, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PDK3 were set to 27604308

27 Sep 2019, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PDK3 were changed from ?Charcot-Marie-Tooth disease, X-linked dominant, 6 300905; ?Charcot-Marie-Tooth disease, X-linked dominant, 6, 300905; Pyruvate dehydrogenase kinase deficiency (Disorders of pyruvate metabolism) to ?Charcot-Marie-Tooth disease, X-linked dominant, 6 300905

13 Feb 2019, Gel status: 1

Added New Source, Added New Source

Ivone Leong (Genomics England Curator)

Source NHS GMS was added to PDK3. Source London North GLH was added to PDK3.

8 Jan 2019, Gel status: 1

Panel promoted to version 1.0

Ellen McDonagh (Genomics England Curator)

Sarah Leigh: Associated with phenotype in O

16 Dec 2018, Gel status: 1

Set Phenotypes, Set publications

Ellen McDonagh (Genomics England Curator)

Added phenotypes ?Charcot-Marie-Tooth disease, X-linked dominant, 6 300905; Pyruvate dehydrogenase kinase deficiency (Disorders of pyruvate metabolism) for gene: PDK3 Publications for gene PDK3 were changed from to 27604308

16 Dec 2018, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: PDK3 was added gene: PDK3 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: PDK3 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: PDK3 were set to ?Charcot-Marie-Tooth disease, X-linked dominant, 6, 300905