Kleefstra syndrome 2: genes and variants
Kleefstra syndrome 2 is linked to 1 analyzed protein (KMT2C). 2 DNA variants are known to cause it; 186 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Kleefstra syndrome 2
KMT2C: Histone-lysine N-methyltransferase 2C
It helps establish enhancer-associated H3K4 methylation and thereby controls lineage-specific transcription together with other COMPASS-family proteins. Somatic loss-of-function alterations are frequent across cancers, while germline variants can cause neurodevelopmental phenotypes.
2 disease-causing and 186 uncertain variants in KMT2C are linked to Kleefstra syndrome 2.
Known disease-causing variants in Kleefstra syndrome 2
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| KMT2C K1207E | 1207 | Disease-causing (★) | |
| KMT2C G4445D | 4445 | Disease-causing (★) |
Diseases related to Kleefstra syndrome 2
- Multiple myeloma, also linked to KMT2C
- Medulloblastoma, also linked to KMT2C
- KMT2C-related NDD, also linked to KMT2C
Frequently asked questions
Which genes are linked to Kleefstra syndrome 2?
In CATVariant, Kleefstra syndrome 2 is linked to 1 analyzed protein: KMT2C (Histone-lysine N-methyltransferase 2C).
How many genetic variants are linked to Kleefstra syndrome 2?
228 variants: 2 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 186 are of uncertain significance or have conflicting reports.
Which uncertain variants in Kleefstra syndrome 2 look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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