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
  • Leucine-Rich Repeat LGI Family Member 3 3 4
  • LGI1-Like Protein 4 3 4
  • LGIL4 3 4
  • Leucine-Rich Repeat LGI Family, Member 3 2
  • LGI3 5

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. Diseases associated with LGI3 include Epilepsy, Familial Temporal Lobe, 3 and Epilepsy, Familial Temporal Lobe, 1. Among its related pathways are Developmental Biology and LGI-ADAM interactions. An important paralog of this gene is LGI1.

UniProtKB/Swiss-Prot Summary for LGI3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LGI3 Gene

Genomics for LGI3 Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH08J022155 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 250.7 +0.2 184 1.4 ZIC2 KLF9 ZKSCAN1 ZNF2 CBX8 ZBTB48 CTCF NRF1 CBX2 GLIS1 LGI3 lnc-BMP1-1 lnc-BMP1-2 SFTPC FGF17 NPM2 REEP4 lnc-LGI3-1 RF00017-6872
GH08J022158 Enhancer 0.3 Ensembl dbSUPER 250.7 -1.8 -1817 0.2 LGI3 lnc-BMP1-1 lnc-BMP1-2 SFTPC NONHSAG049714.2 BMP1 RF00017-6872
GH08J021917 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 9.5 +236.7 236708 4.9 TBP ZBTB10 SIX5 NR2C1 MNT IKZF1 SMAD5 ETS1 IRF2 ZFP64 XPO7 HSALNG0063869 ENSG00000253200 FHIP2B C8orf58 CCAR2 POLR3D FGF17 BMP1 BIN3
GH08J022214 Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.1 -61.1 -61106 6.7 MXD4 CEBPA MNT IKZF1 ZFP64 BHLHE40 ZIC2 KDM6A ZNF395 FOXA2 RF00017-6873 PIWIL2 MIR320A POLR3D SFTPC LOC100507071 LGI3 NPM2 SORBS3 ENSG00000251034
GH08J022176 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 11.3 -21.4 -21402 3.4 ZIC2 VEZF1 SAP130 ZNF341 TEAD3 YY1 SP2 BCL6 JUND ZNF189 LGI3 SFTPC NPM2 FGF17 LOC100507071 PIWIL2 BMP1 LOC101929237 PPP3CC piR-43105-625
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LGI3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LGI3

Top Transcription factor binding sites by QIAGEN in the LGI3 gene promoter:
  • GR
  • GR-alpha
  • GR-beta
  • p53

Genomic Locations for LGI3 Gene

Latest Assembly
10,255 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
9,977 bases
Minus strand

(GRCh37/hg19 by Ensembl)
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

  • Glycosylation at Asn189 and Asn311
  • Modification sites at PhosphoSitePlus

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

Protein Domains for LGI3 Gene

  • Cysteine-rich flanking region, C-terminal

Suggested Antigen Peptide Sequences for LGI3 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich glioma-inactivated protein 3 (LGI3_HUMAN)
genes like me logo Genes that share domains with LGI3: view

No data available for Graphical View of Domain Structure and 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 --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LGI3: view
genes like me logo Genes that share phenotypes with LGI3: view

Animal Models for research

  • Taconic Biosciences Mouse Models for LGI3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGI3

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 4
cytosol 3
plasma membrane 2
cytoskeleton 1
nucleus 1
endosome 1
mitochondrion 0
peroxisome 0
endoplasmic reticulum 0
lysosome 0
golgi apparatus 0

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 IEA,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

PathCards logo

SuperPathways 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

mRNA/cDNA for LGI3 Gene

8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGI3

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

Expression for LGI3 Gene

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

Protein tissue co-expression partners for LGI3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LGI3

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 for research

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 30 31
  • 99.27 (n)
(Monodelphis domestica)
Mammalia LGI3 31
  • 92 (a)
(Canis familiaris)
Mammalia LGI3 30 31
  • 91.89 (n)
(Mus musculus)
Mammalia Lgi3 30 17 31
  • 89.48 (n)
(Rattus norvegicus)
Mammalia Lgi3 30
  • 88.5 (n)
(Bos Taurus)
Mammalia LGI3 30 31
  • 88.44 (n)
(Ornithorhynchus anatinus)
Mammalia LGI3 31
  • 78 (a)
(Danio rerio)
Actinopterygii lgi3 30 31
  • 64.48 (n)
Species where no ortholog for LGI3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Evolutionary constrained regions (ECRs) for LGI3: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LGI3 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs149352514 Benign: not provided 22,148,657(-) C/T
NM_139278.4(LGI3):c.1150G>A (p.Gly384Ser)
rs772786699 Likely Benign: not provided 22,156,508(-) G/A
NM_139278.4(LGI3):c.35C>T (p.Pro12Leu)
rs34112456 - p.Ala524Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LGI3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

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

Disorders for LGI3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LGI3 Gene - From: COP

Disorder Aliases PubMed IDs
epilepsy, familial temporal lobe, 3
  • etl3
epilepsy, familial temporal lobe, 1
  • etl1
li-fraumeni syndrome 1
  • lfs1
benign familial infantile epilepsy
  • benign familial infantile convulsion
- elite association - COSMIC cancer census association via MalaCards
Search LGI3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LGI3

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

No data available for 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 23
  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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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
  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

Products for LGI3 Gene

Sources for LGI3 Gene