PDHX

Chr 11AR

pyruvate dehydrogenase complex component X

Also known as: DLDBP, E3BP, OPDX, PDHXD, PDX1, proX

The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to Krebs cycle. The PDH complex contains three catalytic subunits, E1, E2, and E3, two regulatory subunits, E1 kinase and E1 phosphatase, and a non-catalytic subunit, E3 binding protein (E3BP). This gene encodes the E3 binding protein subunit; also known as component X of the pyruvate dehydrogenase complex. This protein tethers E3 dimers to the E2 core of the PDH complex. Defects in this gene are a cause of pyruvate dehydrogenase deficiency which results in neurological dysfunction and lactic acidosis in infancy and early childhood. This protein is also a minor antigen for antimitochondrial antibodies. These autoantibodies are present in nearly 95% of patients with the autoimmune liver disease primary biliary cirrhosis (PBC). In PBC, activated T lymphocytes attack and destroy epithelial cells in the bile duct where this protein is abnormally distributed and overexpressed. PBC eventually leads to cirrhosis and liver failure. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]

GeneReviewsOMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 0.721 OMIM phenotype
Clinical SummaryPDHX
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Gene-Disease Validity (ClinGen)
Leigh syndrome · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

2 total gene-disease associations curated

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
47 unique Pathogenic / Likely Pathogenic· 199 VUS of 468 total submissions
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GeneReview available — PDHX
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.72LOEUF
pLI 0.000
Z-score 2.64
OE 0.43 (0.270.72)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-0.20Z-score
OE missense 1.03 (0.941.14)
289 obs / 279.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.43 (0.270.72)
00.351.4
Missense OE?1.03 (0.941.14)
00.61.4
Synonymous OE?1.02
01.21.6
LoF obs/exp: 11 / 25.4Missense obs/exp: 289 / 279.4Syn Z: -0.15
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitivePDHX-related lacticacidemia due to PDX1 deficiencyLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6743th %ile
GOF
0.5758th %ile
LOF
0.4038th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

468 submitted variants in ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic24
VUS199
Likely Benign111
Benign67
Conflicting23
23
Pathogenic
24
Likely Pathogenic
199
VUS
111
Likely Benign
67
Benign
23
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
18
0
5
0
23
Likely Pathogenic
18
1
5
0
24
VUS
2
165
29
3
199
Likely Benign
0
5
58
48
111
Benign
0
6
49
12
67
Conflicting
23
Total3817714663447

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

18 pathogenic / likely-pathogenic (of 29) ClinVar copy-number / structural variants overlap PDHX — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

PDHX · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →