LIMD1
Chr 3LIM domain containing 1
LIMD1 encodes an adapter protein that functions as a transcriptional corepressor, regulates microRNA-mediated gene silencing, and is essential for P-body formation while also modulating multiple signaling pathways including Hippo and Wnt signaling. Mutations cause autosomal recessive intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely not tolerated.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
The highest-scoring mechanism for this gene is gain-of-function.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
127 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 6 | 0 | 6 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 93 | 2 | 0 | 95 |
Likely Benign | 0 | 6 | 0 | 0 | 6 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 99 | 9 | 1 | 109 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
LIMD1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools