LEMD3

Chr 12AD

LEM domain containing 3

Also known as: MAN1

The protein functions as a specific repressor of TGF-beta, activin, and BMP signaling pathways at the inner nuclear membrane through interaction with R-SMAD proteins. Mutations cause Buschke-Ollendorff syndrome and osteopoikilosis with or without melorheostosis, which are skeletal disorders affecting bone development and connective tissue. The gene follows autosomal dominant inheritance and is highly constrained against loss-of-function variants.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.252 OMIM phenotypes
Clinical SummaryLEMD3
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.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.25LOEUF
pLI 0.999
Z-score 5.25
OE 0.12 (0.060.25)
Highly constrained

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

Missense Constraint
-0.26Z-score
OE missense 1.03 (0.961.11)
485 obs / 469.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.12 (0.060.25)
00.351.4
Missense OE1.03 (0.961.11)
00.61.4
Synonymous OE1.12
01.21.6
LoF obs/exp: 5 / 41.5Missense obs/exp: 485 / 469.1Syn Z: -1.22
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveLEMD3-related Buschke-Ollendorff syndromeLOFAD
DN
0.2897th %ile
GOF
0.3491th %ile
LOF
0.74top 10%

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

LOFprediction above median · 1 literature citation · LOEUF 0.25

Literature Evidence

LOFWe have previously shown that LEMD3 haploinsufficiency is responsible for the Buschke-Ollendorff lesions and now provide strong evidence that a heterozygous deletion of HMGA2 is causing the growth failure observed in this disorder.PMID:19298872

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

LEMD3 · 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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