Seroatlas · Human Serome Atlas

LDB3

LIM domain-binding protein 3

Also known as: CMD1C, KIAA0613, LDB3_HUMAN, PDLIM6, ZASP

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

Protein identityUniProt · HPA

UniProt accession: O75112
Gene: LDB3
Ensembl: ENSG00000122367
Chromosome: 10
Canonical length: 727 aa
Protein class: Disease related genes, Human disease related genes, Plasma proteins, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Focal adhesion sites,Cytosol

OverviewNCBI Gene

This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]

Canonical amino-acid sequenceUniProt

727 residues, UniProt reviewed canonical sequence.

>O75112|LDB3
     1  MSYSVTLTGP GPWGFRLQGG KDFNMPLTIS RITPGSKAAQ SQLSQGDLVV AIDGVNTDTM
    61  THLEAQNKIK SASYNLSLTL QKSKRPIPIS TTAPPVQTPL PVIPHQKDPA LDTNGSLVAP
   121  SPSPEARASP GTPGTPELRP TFSPAFSRPS AFSSLAEASD PGPPRASLRA KTSPEGARDL
   181  LGPKALPGSS QPRQYNNPIG LYSAETLREM AQMYQMSLRG KASGVGLPGG SLPIKDLAVD
   241  SASPVYQAVI KSQNKPEDEA DEWARRSSNL QSRSFRILAQ MTGTEFMQDP DEEALRRSST
   301  PIEHAPVCTS QATTPLLPAS AQPPAAASPS AASPPLATAA AHTAIASAST TAPASSPADS
   361  PRPQASSYSP AVAASSAPAT HTSYSEGPAA PAPKPRVVTT ASIRPSVYQP VPASTYSPSP
   421  GANYSPTPYT PSPAPAYTPS PAPAYTPSPV PTYTPSPAPA YTPSPAPNYN PAPSVAYSGG
   481  PAEPASRPPW VTDDSFSQKF APGKSTTSIS KQTLPRGGPA YTPAGPQVPP LARGTVQRAE
   541  RFPASSRTPL CGHCNNVIRG PFLVAMGRSW HPEEFTCAYC KTSLADVCFV EEQNNVYCER
   601  CYEQFFAPLC AKCNTKIMGE VMHALRQTWH TTCFVCAACK KPFGNSLFHM EDGEPYCEKD
   661  YINLFSTKCH GCDFPVEAGD KFIEALGHTW HDTCFICAVC HVNLEGQPFY SKKDRPLCKK
   721  HAHTINL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LDB3 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): 0.55
Highest tissue expression: 2,718 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 2,718 nTPM
tongue: 1,686 nTPM
heart muscle: 1,171 nTPM
blood vessel: 77 nTPM
spinal cord: 60 nTPM
esophagus: 51 nTPM

Single-cell type

myonuclei: 924 nCPM
cardiomyocytes: 570 nCPM
oligodendrocytes: 297 nCPM
vascular smooth muscle cells: 148 nCPM
thymic myoid cells: 102 nCPM
pericytes: 94 nCPM

Immune cell

basophil: 0.3 nTPM
neutrophil: 0.1 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

white matter: 136 nTPM
medulla oblongata: 103 nTPM
pons: 78 nTPM
basal ganglia: 74 nTPM
thalamus: 73 nTPM
midbrain: 70 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LDB3.

Disease | AllUniProt

Conditions LDB3 is implicated in, by any mechanism.

Cardiomyopathy, dilated, 1C, with or without left ventricular non-compaction (CMD1C) MIM:601493
Left ventricular non-compaction 3 (LVNC3) MIM:601493
Myopathy, myofibrillar, 4 (MFM4) MIM:609452
Cardiomyopathy, familial hypertrophic, 24 (CMH24) MIM:601493
Cardiomyopathy, dilated, 2L (CMD2L) MIM:621237

Disease | GeneticClinVar

39 pathogenic / likely-pathogenic of 1,597 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Myofibrillar myopathy 4
Dilated cardiomyopathy 1C
Cardiomyopathy, dilated, 2l
Cardiomyopathy
Neuromuscular disease

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): 0.68
gnomAD pLI: 0
gnomAD missense Z: 0.29
DepMap mean gene effect: -0.07
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 2% 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 LDB3 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 LDB3 as an antibody target. Whether an autoantibody or antibody against LDB3 could matter depends on whether native LDB3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LDB3 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 LDB3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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