SUV39H1

Chr X

SUV39H1 histone lysine methyltransferase

Also known as: H3-K9-HMTase 1, KMT1A, MG44, SUV39H

The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, resulting in transcriptional gene silencing and heterochromatin formation at pericentric and telomeric regions. Mutations cause an autosomal dominant neurodevelopmental disorder characterized by intellectual disability, developmental delay, and behavioral abnormalities. This gene is highly constrained against loss-of-function variants (pLI = 0.99), indicating that haploinsufficiency is likely not tolerated in the general population.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.22
Clinical SummarySUV39H1
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.22LOEUF
pLI 0.990
Z-score 3.43
OE 0.00 (0.000.22)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
3.49Z-score
OE missense 0.32 (0.260.39)
65 obs / 205.8 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.00 (0.000.22)
00.351.4
Missense OE0.32 (0.260.39)
00.61.4
Synonymous OE0.91
01.21.6
LoF obs/exp: 0 / 13.7Missense obs/exp: 65 / 205.8Syn Z: 0.64
DN
0.2698th %ile
GOF
0.4085th %ile
LOF
0.67top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.22

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

SUV39H1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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