AtlasGene
PDP1
pyruvate dehydrogenase phosphatase catalytic subunit 1
- HGNC 9279↗(opens in a new tab)
- Ensembl gene ENSG00000164951↗(opens in a new tab)
- NCBI Gene 54704↗(opens in a new tab)
Summary
- Cytogenetic location
- 8q22.1
- Coordinates
- Chromosome 8: 93,916,923–93,926,068 (GRCh38)
- Exons
- 2 exons across 9.1 kb
- Protein
- 537 amino acids, 61.1 kDa
- Also known as
- PDP, PDH, PPM2A
- Previous symbols
- PPM2C
- MANE Select transcript
- ENST00000297598.5NM_018444.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Get my Genome TestCurated reports relevant to this gene
Pyruvate Dehydrogenase & Pyruvate Carboxylase Deficiency
- Pyruvate Dehydrogenase DeficiencyAutosomal recessive
Caused by variants in PDHA1 (X-linked, often new in the child) or in PDHB, DLAT, PDHX, DLD, PDP1 or LIAS, which can cause lactic acidosis, developmental delay, seizures and movement problems.
- 3 GenCC submitters rate it definitive or strong
▶Actionability
Knowing allows a ketogenic diet, avoidance of high-carbohydrate loads, and thiamine for responsive forms.
Broader groupings
Rare Hereditary Peripheral Neuropathies
- Hereditary Peripheral Neuropathy
One of 233 genes linked to it
Caused by changes in one of many genes needed to keep long nerve fibres healthy. In this report these include IGHMBP2 and PLEKHG5, which are recessive.
- 3 GenCC submitters rate it definitive or strong
▶Actionability
Physiotherapy, orthoses and occupational therapy help maintain mobility, with surgery for foot deformities when needed. Some forms need breathing monitoring. Genetic counselling guides family testing according to the inheritance pattern of the gene involved.
How PDP1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 4.2 kb of the gene's 9.1 kb; 1,614 of those bases code for the protein.
Sequencing PDP1
1Easy
How hard PDP1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of PDP1's exons sit where short reads map cleanly.
What adds to it: the share of PDP1's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. On its own, a gene wholly in this kind of region would score 100.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. On its own, a gene wholly in this kind of region would score 60.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so a read from one may be placed on the other. On its own, a gene wholly in this kind of region would score 60.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. On its own, a gene wholly in this kind of region would score 50.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. On its own, a gene wholly in this kind of region would score 30.2.4%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. On its own, a gene wholly in this kind of region would score 20.3.7%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of PDP1's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
3
positions in PDP1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 9.1 kb of PDP1, introns included, not only the 4.2 kb of exons.
ClinVar pathogenic variants (3)
The PDP1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 1
- Likely pathogenic 2
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_018444.4(PDP1):c.437del (p.His146fs) | pyruvate dehydrogenase phosphatase deficiency | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018444.4(PDP1):c.48dup (p.Leu17fs) | pyruvate dehydrogenase phosphatase deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018444.4(PDP1):c.500dup (p.Leu167fs) | pyruvate dehydrogenase phosphatase deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
- DLATdihydrolipoamide S-acetyltransferaseShares 2 conditions
- DLDdihydrolipoamide dehydrogenaseShares 2 conditions
- LIASlipoic acid synthetaseShares 2 conditions
- PDHA1pyruvate dehydrogenase E1 subunit alpha 1Shares 2 conditions
- PDHBpyruvate dehydrogenase E1 subunit betaShares 2 conditions
- PDHXpyruvate dehydrogenase complex component XShares 2 conditions
- AARS1alanyl-tRNA synthetase 1Shares 1 condition
- ABHD12abhydrolase domain containing 12, lysophospholipaseShares 1 condition
- AIFM1apoptosis inducing factor mitochondria associated 1Shares 1 condition
- APOA1apolipoprotein A1Shares 1 condition
- ARSAarylsulfatase AShares 1 condition
- ATL1atlastin GTPase 1Shares 1 condition
Traits linked to PDP1
The Human Phenotype Ontology lists these as features of the rare conditions PDP1 can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-21: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.21-311f020e.
Cite this page
Dante Labs. (n.d.). PDP1 gene: pyruvate dehydrogenase phosphatase catalytic subunit 1. Retrieved 21 October 2026, from https://dantelabs.com/genes/pdp1
Dante Labs. PDP1 gene: pyruvate dehydrogenase phosphatase catalytic subunit 1 [Internet]. [cited 21 October 2026]. Available from: https://dantelabs.com/genes/pdp1
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