KDM1A
Chr 1ADlysine demethylase 1A
Also known as: AIMAH3, AOF2, BHC110, CPRF, KDM1, LSD1
This protein functions as a histone demethylase and component of histone deacetylase complexes that silences gene expression. Loss-of-function mutations cause autosomal dominant cleft palate with psychomotor retardation and distinctive facial features, as well as ACTH-independent macronodular adrenal hyperplasia. The high constraint scores (pLI 0.997, LOEUF 0.276) support haploinsufficiency as the pathogenic mechanism.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Highly missense-constrained (top ~0.1%)
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
KDM1A · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools