LDB1

Chr 10

LIM domain binding 1

Also known as: CLIM-2, CLIM2, LDB-1, NLI

NCBI Gene: 8861ENSG00000198728UniProt: Q86U70OMIM: 603451

Enables LIM domain binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and enzyme binding activity. Involved in negative regulation of DNA-templated transcription and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIMResearchGenerating 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
23
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.29
LOEUF· LoF intol.
LOF
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.29LOEUF
pLI 0.985
Z-score 3.91
OE 0.09 (0.04–0.29)
Highly constrained

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

Missense Constraint?
2.81Z-score
OE missense 0.51 (0.44–0.59)
132 obs / 259.4 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.09 (0.04–0.29)
0≤0.351.4
Missense OE?0.51 (0.44–0.59)
0≤0.61.4
Synonymous OE?0.99
0≤1.21.6
LoF obs/exp: 2 / 21.6Missense obs/exp: 132 / 259.4Syn Z: 0.05

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

LDB1 · 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