D2HGDH

Chr 2AR

D-2-hydroxyglutarate dehydrogenase

Also known as: D2HGD

This mitochondrial enzyme catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate and is most active in liver and kidney but also functions in heart and brain. Mutations cause D-2-hydroxyglutaric aciduria, an autosomal recessive neurometabolic disorder presenting with developmental delay, epilepsy, hypotonia, and dysmorphic features. The gene is highly constrained against loss-of-function variants (LOEUF 0.58), reflecting its essential metabolic role.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.581 OMIM phenotype
Clinical SummaryD2HGDH
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Gene-Disease Validity (ClinGen)
mitochondrial disease · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.29) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.58LOEUF
pLI 0.054
Z-score 2.95
OE 0.29 (0.160.58)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.72Z-score
OE missense 0.89 (0.810.98)
300 obs / 337.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.29 (0.160.58)
00.351.4
Missense OE0.89 (0.810.98)
00.61.4
Synonymous OE1.05
01.21.6
LoF obs/exp: 6 / 20.4Missense obs/exp: 300 / 337.1Syn Z: -0.54
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedD2HGDH-related D-2-hydroxyglutaric aciduriaLOFAR

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

DN
0.77top 25%
GOF
0.6541th %ile
LOF
0.2873th %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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

D2HGDH · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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