BCL9
Chr 1BCL9 transcription coactivator
Also known as: LGS
BCL9 encodes a protein that promotes beta-catenin transcriptional activity in Wnt signaling pathways and is highly constrained against loss-of-function variants (LOEUF 0.381). Mutations in BCL9 cause neurodevelopmental disorders with intellectual disability, though the specific phenotypic spectrum and inheritance patterns are detailed in GeneReviews. The gene's high constraint score suggests that heterozygous loss-of-function variants are likely pathogenic in the neurodevelopmental context.
Limited evidence — not for standalone diagnostic reporting
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
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
BCL9 · 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