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Aliases for LGI3 Gene

Aliases for LGI3 Gene

  • Leucine Rich Repeat LGI Family Member 3 2 3 5
  • Leucine-Rich Glioma-Inactivated Protein 3 3 4
  • LGI1-Like Protein 4 3 4
  • LGIL4 3 4
  • Leucine-Rich Repeat LGI Family, Member 3 2
  • Leucine-Rich Repeat LGI Family Member 3 3

External Ids for LGI3 Gene

Previous GeneCards Identifiers for LGI3 Gene

  • GC08M021762
  • GC08M022356
  • GC08M021824
  • GC08M022026
  • GC08M022060
  • GC08M020546

Summaries for LGI3 Gene

GeneCards Summary for LGI3 Gene

LGI3 (Leucine Rich Repeat LGI Family Member 3) is a Protein Coding gene. Among its related pathways are LGI-ADAM interactions and Developmental Biology. An important paralog of this gene is LGI1.

UniProtKB/Swiss-Prot for LGI3 Gene

  • May participate in the regulation of neuronal exocytosis.

Additional gene information for LGI3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LGI3 Gene

Genomics for LGI3 Gene

GeneHancer (GH) Regulatory Elements for LGI3 Gene

Promoters and enhancers for LGI3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08I022155 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.7 662 1.6 MXI1 SUZ12 EBF1 ZIC2 ZNF2 ZKSCAN1 HIC1 ZNF335 ZFHX2 GLIS2 SFTPC LGI3 REEP4
GH08I022177 Enhancer 1 ENCODE dbSUPER 11.3 -21.7 -21679 2.8 FOXA2 ARID4B KLF17 SIN3A ZNF121 GLIS2 EGR1 FOS EGR2 SP3 LGI3 SFTPC XPO7 NPM2 FGF17 LOC100507071 PIWIL2 CCAR2 BMP1 LOC101929237
GH08I022202 Enhancer 1 ENCODE dbSUPER 10.8 -47.7 -47665 3.8 BCOR KLF1 FOXA2 SAP130 ZNF644 RAD21 RARA ZNF121 CTBP1 GATA3 PHYHIP MIR320A POLR3D BMP1 SFTPC LGI3 NPM2 LOC105379319
GH08I022545 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 3.3 -393.1 -393099 10 PKNOX1 FOXA2 ZFP64 ARID4B SIN3A DMAP1 IRF4 GLIS2 FOS SP5 SORBS3 GC08M022549 PPP3CC RNU6-336P PDLIM2 ENSG00000248235 CCAR2 ENSG00000253200 XPO7 SLC39A14
GH08I022214 Enhancer 0.6 ENCODE 10.7 -58.9 -58935 2.4 L3MBTL2 TEAD4 CBFA2T3 MNT ZNF592 ZFHX2 EGR1 POLR2A MGA EGR2 PIWIL2 MIR320A POLR3D SFTPC LOC100507071 LGI3 PHYHIP LOC105379319
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LGI3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LGI3 gene promoter:

Genomic Locations for LGI3 Gene

Genomic Locations for LGI3 Gene
10,260 bases
Minus strand

Genomic View for LGI3 Gene

Genes around LGI3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LGI3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LGI3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LGI3 Gene

Proteins for LGI3 Gene

  • Protein details for LGI3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Leucine-rich repeat LGI family member 3
    Protein Accession:
    Secondary Accessions:
    • A5PLP2
    • Q86TL4
    • Q8N296

    Protein attributes for LGI3 Gene

    548 amino acids
    Molecular mass:
    61704 Da
    Quaternary structure:
    • Interacts with STX1A.
    • Sequence=BAC03553.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for LGI3 Gene


neXtProt entry for LGI3 Gene

Post-translational modifications for LGI3 Gene

No Post-translational modifications

Other Protein References for LGI3 Gene

No data available for DME Specific Peptides for LGI3 Gene

Domains & Families for LGI3 Gene

Gene Families for LGI3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for LGI3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LGI3: view

No data available for UniProtKB/Swiss-Prot for LGI3 Gene

Function for LGI3 Gene

Molecular function for LGI3 Gene

UniProtKB/Swiss-Prot Function:
May participate in the regulation of neuronal exocytosis.

Phenotypes From GWAS Catalog for LGI3 Gene

Gene Ontology (GO) - Molecular Function for LGI3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
genes like me logo Genes that share ontologies with LGI3: view
genes like me logo Genes that share phenotypes with LGI3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LGI3 Gene

Localization for LGI3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LGI3 Gene

Secreted. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle. Cell junction, synapse, synaptosome. Note=Found in the synaptosomal membrane fraction. {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LGI3 gene
Compartment Confidence
extracellular 5
cytosol 3
plasma membrane 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LGI3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0008021 synaptic vesicle IEA --
GO:0030054 cell junction IEA --
GO:0031410 cytoplasmic vesicle IEA --
GO:0043005 neuron projection IEA --
genes like me logo Genes that share ontologies with LGI3: view

Pathways & Interactions for LGI3 Gene

genes like me logo Genes that share pathways with LGI3: view

Pathways by source for LGI3 Gene

2 Reactome pathways for LGI3 Gene

Gene Ontology (GO) - Biological Process for LGI3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IEA --
GO:0017157 regulation of exocytosis IEA --
genes like me logo Genes that share ontologies with LGI3: view

No data available for SIGNOR curated interactions for LGI3 Gene

Drugs & Compounds for LGI3 Gene

No Compound Related Data Available

Transcripts for LGI3 Gene

Unigene Clusters for LGI3 Gene

Leucine-rich repeat LGI family, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LGI3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP1: -

Relevant External Links for LGI3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LGI3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LGI3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LGI3 Gene

This gene is overexpressed in Brain - Cortex (x5.6), Brain - Spinal cord (cervical c-1) (x5.4), Brain - Frontal Cortex (BA9) (x5.0), Brain - Substantia nigra (x4.8), and Brain - Putamen (basal ganglia) (x4.8).

Protein differential expression in normal tissues from HIPED for LGI3 Gene

This gene is overexpressed in Frontal cortex (51.3) and Spinal cord (16.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LGI3 Gene

Protein tissue co-expression partners for LGI3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LGI3 Gene:


SOURCE GeneReport for Unigene cluster for LGI3 Gene:


mRNA Expression by UniProt/SwissProt for LGI3 Gene:

Tissue specificity: Widely expressed, with highest levels in brain and lung.

Evidence on tissue expression from TISSUES for LGI3 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with LGI3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LGI3 Gene

Orthologs for LGI3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LGI3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LGI3 33 34
  • 99.27 (n)
(Monodelphis domestica)
Mammalia LGI3 34
  • 92 (a)
(Canis familiaris)
Mammalia LGI3 33 34
  • 91.89 (n)
(Mus musculus)
Mammalia Lgi3 33 16 34
  • 89.48 (n)
(Rattus norvegicus)
Mammalia Lgi3 33
  • 88.5 (n)
(Bos Taurus)
Mammalia LGI3 33 34
  • 88.44 (n)
(Ornithorhynchus anatinus)
Mammalia LGI3 34
  • 78 (a)
(Danio rerio)
Actinopterygii lgi3 33 34
  • 64.48 (n)
Species where no ortholog for LGI3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LGI3 Gene

Gene Tree for LGI3 (if available)
Gene Tree for LGI3 (if available)

Paralogs for LGI3 Gene

Paralogs for LGI3 Gene

(5) SIMAP similar genes for LGI3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LGI3: view

Variants for LGI3 Gene

Sequence variations from dbSNP and Humsavar for LGI3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000063065 -- 22,148,077(-) C/T 3_prime_UTR_variant
rs1000634636 -- 22,146,573(-) C/G/T downstream_transcript_variant
rs1000909861 -- 22,157,383(-) A/C upstream_transcript_variant
rs1001574006 -- 22,147,354(-) C/G 3_prime_UTR_variant
rs1001643674 -- 22,158,410(-) A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LGI3 Gene

Variant ID Type Subtype PubMed ID
nsv831264 CNV gain+loss 17160897
nsv831263 CNV loss 17160897
nsv610771 CNV loss 21841781
nsv610765 CNV loss 21841781
nsv528590 CNV loss 19592680
nsv527293 CNV loss 19592680
nsv524720 CNV loss 19592680
nsv470204 CNV loss 18288195
nsv465613 CNV loss 19166990
esv3572630 CNV loss 25503493
esv2759604 CNV loss 17122850
dgv881n27 CNV loss 19166990
dgv2060e212 CNV loss 25503493
dgv12055n54 CNV loss 21841781
dgv12054n54 CNV loss 21841781

Variation tolerance for LGI3 Gene

Residual Variation Intolerance Score: 24.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.11; 61.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LGI3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LGI3 Gene

Disorders for LGI3 Gene

Additional Disease Information for LGI3

No disorders were found for LGI3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LGI3 Gene

Publications for LGI3 Gene

  1. The LGI1 gene involved in lateral temporal lobe epilepsy belongs to a new subfamily of leucine-rich repeat proteins. (PMID: 12023020) Gu W … Steinlein OK (FEBS letters 2002) 2 3 4 22 58
  2. Leucine-rich glioma inactivated 3 is involved in amyloid beta peptide uptake by astrocytes and endocytosis itself. (PMID: 18628660) Okabayashi S … Kimura N (Neuroreport 2008) 2 3 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58

Products for LGI3 Gene

Sources for LGI3 Gene

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