Seroatlas · Human Serome Atlas

LDB2

LIM domain-binding protein 2

Also known as: CLIM1, LDB1, LDB2_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
O43679
Gene
LDB2
Ensembl
ENSG00000169744
Chromosome
4
Canonical length
373 aa
Protein class
Predicted intracellular proteins
Subcellular location
Nucleoplasm,Nucleoli,Plasma membrane

OverviewNCBI Gene

The protein encoded by this gene belongs to the LIM-domain binding family. Members of this family are characterized by a conserved nuclear localization sequence, an amino-terminal homodimerization domain and a carboxy-terminal LIM interaction domain. These proteins function as adapter molecules to allow assembly of transcriptional regulatory complexes. Genetic association studies suggest functions for this gene in rhegmatogenous retinal detachment and coronary artery disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

Canonical amino-acid sequenceUniProt

373 residues, UniProt reviewed canonical sequence.

>O43679|LDB2
     1  MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE
    61  DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC
   121  DQCTMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD
   181  PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ
   241  RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNNANSTG SKKKTTAANL SLSSQVPDVM
   301  VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ
   361  ETKSENPPPQ ASQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LDB2 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)
0.47
Highest tissue expression
61 nTPM

Expression across tissuesHPA

Tissue

  • endometrium: 61 nTPM
  • cerebral cortex: 57 nTPM
  • adipose tissue: 56 nTPM
  • placenta: 55 nTPM
  • lung: 55 nTPM
  • breast: 51 nTPM

Single-cell type

  • vascular endothelial cells: 2,327 nCPM
  • lymphatic endothelial cells: 1,917 nCPM
  • fibro-adipogenic progenitors: 599 nCPM
  • brain excitatory neurons: 583 nCPM
  • brain inhibitory neurons: 409 nCPM
  • pituicytes/fscs: 406 nCPM

Immune cell

  • NK-cell: 2 nTPM
  • total PBMC: 0.2 nTPM
  • neutrophil: 0.1 nTPM
  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM

Brain region

  • cerebral cortex: 79 nTPM
  • white matter: 36 nTPM
  • basal ganglia: 36 nTPM
  • hippocampal formation: 26 nTPM
  • midbrain: 18 nTPM
  • amygdala: 18 nTPM

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)
0.34
gnomAD pLI
0.95
gnomAD missense Z
2.37
DepMap mean gene effect
0.05
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

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LDB2 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 LDB2 as an antibody target. Whether an autoantibody or antibody against LDB2 could matter depends on whether native LDB2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LDB2 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 LDB2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/LDB2. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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