LDB1
LIM domain-binding protein 1
Also known as: CLIM2, LDB1_HUMAN, NLI
Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene
Protein identityUniProt · HPA
- UniProt accession
- Q86U70
- Gene
- LDB1
- Ensembl
- ENSG00000198728
- Chromosome
- 10
- Canonical length
- 411 aa
- Protein class
- Predicted intracellular proteins
- Subcellular location
- Nucleoplasm
- Quaternary structure
- Homodimer
OverviewNCBI Gene
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]
Canonical amino-acid sequenceUniProt
411 residues, UniProt reviewed canonical sequence.
>Q86U70|LDB1
1 MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP TYLEPGIGRH
61 TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED DAMLTITFCL EDGPKRYTIG
121 RTLIPRYFRS IFEGGATELY YVLKHPKEAF HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG
181 RLYLEFMFDD MMRIKTWHFS IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL
241 NYLRLCVILE PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPTR QQPSKRRKRK
301 MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF GDEDERLITR
361 LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES KSENPTSQAS QLocalizationUniProt · AlphaFold · HPA
Whether an antibody against LDB1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.
- Antibody reachability
- Intracellular
- Secreted
- No
- Transmembrane segments
- 0
- Mean surface accessibility (rSASA)
- 0.5
- Highest tissue expression
- 142 nTPM
Expression across tissuesHPA
Tissue
- ovary: 142 nTPM
- skin: 142 nTPM
- bone marrow: 116 nTPM
- cervix: 113 nTPM
- colon: 95 nTPM
- endometrium: 91 nTPM
Single-cell type
- erythrocyte progenitors: 132 nCPM
- megakaryocyte-erythroid progenitors: 91 nCPM
- megakaryocyte progenitors: 41 nCPM
- choroid plexus epithelial cells: 36 nCPM
- basal keratinocytes: 29 nCPM
- suprabasal keratinocytes: 28 nCPM
Immune cell
- neutrophil: 4.9 nTPM
- non-classical monocyte: 4.9 nTPM
- basophil: 2.9 nTPM
- intermediate monocyte: 2.9 nTPM
- naive B-cell: 2.4 nTPM
- gdT-cell: 2.1 nTPM
Brain region
- cerebral cortex: 100 nTPM
- choroid plexus: 92 nTPM
- basal ganglia: 81 nTPM
- hippocampal formation: 74 nTPM
- white matter: 74 nTPM
- amygdala: 73 nTPM
DiseaseUniProt · ClinVar · IEDB · PubMed
Four sources answering four different questions about LDB1.
Disease | GeneticClinVar
11 pathogenic / likely-pathogenic of 59 ClinVar records.
Conditions with pathogenic or likely-pathogenic variants.
Genetic constraint and essentialitygnomAD · DepMap
Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.
- gnomAD LOEUF (loss-of-function intolerance)
- 0.29
- gnomAD pLI
- 0.99
- gnomAD missense Z
- 2.81
- DepMap mean gene effect
- -0.27
- DepMap dependency class
- selective
Cancer expressionTCGA
Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).
OntologyGO
Biological processes
- anterior/posterior axis specification
- cell adhesion
- cerebellar Purkinje cell differentiation
- epithelial structure maintenance
- gastrulation with mouth forming second
- hair follicle development
- negative regulation of DNA-templated transcription
- negative regulation of erythrocyte differentiation
- negative regulation of transcription by RNA polymerase II
- nervous system development
- neuron differentiation
- positive regulation of cell adhesion
- positive regulation of hemoglobin biosynthetic process
- positive regulation of transcription by RNA polymerase II
- positive regulation of transcription elongation by RNA polymerase II
- regulation of cell migration
- regulation of focal adhesion assembly
- regulation of kinase activity
- somatic stem cell population maintenance
- transcription by RNA polymerase II
- transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery
- Wnt signaling pathway
Molecular functions
- chromatin binding
- DNA binding
- DNA-binding transcription factor binding
- enzyme binding
- LIM domain binding
- protein homodimerization activity
- RNA polymerase II-specific DNA-binding transcription factor binding
- transcription coactivator activity
- transcription coregulator activity
Cellular components
Protein domainsUniProt · Pfam · InterPro
KeywordsUniProt
InteractionsUniProt · HPA
Protein binding partners of LDB1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.
Antibody and autoantibody relevanceSeroatlas analysis
Seroatlas reads LDB1 as an antibody target. Whether an autoantibody or antibody against LDB1 could matter depends on whether native LDB1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.
LDB1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.
Annotation status
The present source text does not explicitly label LDB1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.
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