L2HGDH

Chr 14AR

L-2-hydroxyglutarate dehydrogenase

Also known as: C14orf160, L2HGA

L-2-hydroxyglutarate dehydrogenase is a FAD-dependent enzyme that oxidizes L-2-hydroxyglutarate to alpha-ketoglutarate in mammalian tissues. Mutations cause L-2-hydroxyglutaric aciduria, an autosomal recessive neurometabolic disorder resulting in moderate to severe cognitive disability. The gene is highly constrained against loss-of-function variants (pLI near 0, LOEUF 0.787), indicating intolerance to protein-disrupting mutations.

OMIMResearchSummary from RefSeq, OMIM
LOFmechanismARLOEUF 0.791 OMIM phenotype
Clinical SummaryL2HGDH
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Gene-Disease Validity (ClinGen)
mitochondrial disease · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.79LOEUF
pLI 0.000
Z-score 2.34
OE 0.48 (0.300.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.42Z-score
OE missense 0.93 (0.831.03)
235 obs / 254.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.48 (0.300.79)
00.351.4
Missense OE0.93 (0.831.03)
00.61.4
Synonymous OE0.90
01.21.6
LoF obs/exp: 11 / 23.1Missense obs/exp: 235 / 254.0Syn Z: 0.70
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveL2HGDH-related L-2-hydroxyglutaric aciduriaLOFAR

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

DN
0.6743th %ile
GOF
0.5661th %ile
LOF
0.3744th %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

L2HGDH · 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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