KMT2D

Chr 12AD

lysine methyltransferase 2D

Also known as: AAD10, ALR, BCAHH, CAGL114, KABUK1, KMS, MLL2, MLL4

This gene encodes a histone methyltransferase that catalyzes H3K4 methylation as part of chromatin remodeling machinery, functioning in transcriptional activation and DNA repair. Mutations cause Kabuki syndrome 1, a multisystem disorder characterized by distinctive facial features, intellectual disability, growth deficiency, and variable anomalies including cardiac defects, hearing loss, and endocrine abnormalities. The gene follows autosomal dominant inheritance and is highly constrained against loss-of-function variants.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.102 OMIM phenotypes
Clinical SummaryKMT2D
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Gene-Disease Validity (ClinGen)
Kabuki syndrome 1 · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
5 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.10LOEUF
pLI 1.000
Z-score 12.95
OE 0.07 (0.040.10)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
3.73Z-score
OE missense 0.81 (0.790.84)
2541 obs / 3127.8 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.07 (0.040.10)
00.351.4
Missense OE0.81 (0.790.84)
00.61.4
Synonymous OE1.05
01.21.6
LoF obs/exp: 15 / 224.4Missense obs/exp: 2541 / 3127.8Syn Z: -1.43
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveKMT2D-related multiple malformations syndrome (BCAHH)OTHERAD
definitiveKMT2D-related Kabuki syndromeLOFAD
DN
0.2698th %ile
GOF
0.09100th %ile
LOF
0.81top 5%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFprediction above median · 1 literature citation · LOEUF 0.10
DN1 literature citation

Literature Evidence

DNUnlike KMT2D haploinsufficiency in KS1, these MVs likely result in disease through a dominant negative mechanism.PMID:31949313
LOFHaploinsufficiency of KMT2D is sufficient to cause Kabuki syndrome and is compatible with life.PMID:31814321

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

KMT2D · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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