L3MBTL3

Chr 6

L3MBTL histone methyl-lysine binding protein 3

Also known as: MBT-1, MBT1

NCBI Gene: 84456ENSG00000198945UniProt: Q96JM7

This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of this gene has been observed in human patients with medulloblastoma. [provided by RefSeq, Oct 2016]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
9
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.27
LOEUF· LoF intol.
LOF
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.27LOEUF
pLI 0.997
Z-score 5.30
OE 0.14 (0.07–0.27)
Highly constrained

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

Missense Constraint?
1.64Z-score
OE missense 0.78 (0.71–0.85)
333 obs / 428.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.14 (0.07–0.27)
0≤0.351.4
Missense OE?0.78 (0.71–0.85)
0≤0.61.4
Synonymous OE?1.06
0≤1.21.6
LoF obs/exp: 6 / 44.0Missense obs/exp: 333 / 428.3Syn Z: -0.53

ClinVar

No ClinVar data available.

Protein Context — Lollipop Plot

L3MBTL3 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients