KDM1B
Chr 6lysine demethylase 1B
Also known as: AOF1, C6orf193, LSD2
The KDM1B protein is a histone demethylase that removes methyl groups from lysine-4 of histone H3, acting as a transcriptional corepressor and playing a critical role in DNA methylation of imprinted genes during oogenesis. Loss-of-function mutations in KDM1B cause autosomal recessive intellectual disability with microcephaly through disruption of epigenetic gene regulation. The low pLI score (0.001) and moderate LOEUF score (0.53) indicate this gene is relatively tolerant to heterozygous loss-of-function but pathogenic when both copies are affected.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
ClinVar Variant Classifications
105 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 14 | 0 | 14 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 63 | 4 | 0 | 67 |
Likely Benign | 0 | 1 | 0 | 1 | 2 |
Benign | 0 | 0 | 1 | 0 | 1 |
| Total | 0 | 64 | 19 | 1 | 84 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
KDM1B · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
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