KDM6A
Chr XXLDlysine demethylase 6A
Also known as: KABUK2, UTX, bA386N14.2
The encoded protein is a histone demethylase that catalyzes the demethylation of tri/dimethylated histone H3, functioning as an epigenetic regulator of gene expression. Mutations cause Kabuki syndrome 2, a neurodevelopmental disorder with intellectual disability, distinctive facial features, and multiple congenital anomalies, inherited in an X-linked dominant pattern. The gene is highly intolerant to loss-of-function variants, and disease predominantly occurs through haploinsufficiency mechanisms.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Moderately missense-constrained (top ~2.5%)
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
KDM6A · 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
ARID1A and/or KDM6A Mutation and CXCL13 Expression
ACTIVE NOT RECRUITINGPemetrexed Response in Relation to Tumor Alterations of Gene Status for the Treatment of Patients With Metastatic Urothelial Bladder Cancer and Other Solid Tumors
RECRUITINGExercise to Fight Obesity
RECRUITINGExternal Resources
Links to major genomics databases and tools