MBD1

Chr 18

methyl-CpG binding domain protein 1

Also known as: CXXC3, PCM1, RFT

NCBI Gene: 4152ENSG00000141644UniProt: Q9UIS9

MBD1 encodes a transcriptional repressor that binds to methylated CpG islands in gene promoters and recruits histone-modifying complexes to silence gene expression. Mutations cause autosomal dominant intellectual disability with variable features including developmental delay and behavioral abnormalities. This gene is highly constrained against loss-of-function variants, indicating that such mutations are likely to be pathogenic.

Summary from RefSeq, UniProt
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0
Active trials
7
Pubs (1 yr)
0
P/LP submissions
—
P/LP missense
0.27
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical Summary— MBD1
⚡
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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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.27LOEUF
pLI 0.997
Z-score 5.07
OE 0.13 (0.07–0.27)
Highly constrained

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

Missense Constraint
1.99Z-score
OE missense 0.72 (0.65–0.79)
290 obs / 402.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.13 (0.07–0.27)
0≤0.351.4
Missense OE0.72 (0.65–0.79)
0≤0.61.4
Synonymous OE1.05
0≤1.21.6
LoF obs/exp: 5 / 39.3Missense obs/exp: 290 / 402.5Syn Z: -0.51
DN
0.3892th %ile
GOF
0.3491th %ile
LOF
0.74top 10%

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

LOFprediction above median · LOEUF 0.27

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

ClinVar

Protein Context — Lollipop Plot

MBD1 · 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

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
In silico prediction and interaction of resveratrol on methyl-CpG binding proteins by molecular docking and MD simulations study
Sahu RK et al.·RSC Adv
2022
Optochemical Control of TET Dioxygenases Enables Kinetic Insights into the Domain-Dependent Interplay of TET1 and MBD1 while Oxidizing and Reading 5-Methylcytosine
Lin TC et al.·ACS Chem Biol
2022
The Kinesin-14 Tail: Dual microtubule binding domains drive spindle morphogenesis through tight microtubule cross-linking and robust sliding.
Ems-McClung SC et al.·bioRxiv
2025
Association between forkhead box P3 expression level and gender of Iranian juvenile idiopathic arthritis patients
Ghavidel AA et al.·Reumatologia
2022Cohort
The Kinesin-14 Tail: Dual microtubule binding domains drive spindle morphogenesis through tight microtubule cross-linking and robust sliding.
Ems-McClung SC et al.·Mol Biol Cell
2025
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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