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Aliases for LGI2 Gene

Aliases for LGI2 Gene

  • Leucine Rich Repeat LGI Family Member 2 2 3 5
  • Leucine-Rich Glioma-Inactivated Protein 2 3 4
  • LGI1-Like Protein 2 3 4
  • LGIL2 3 4
  • Leucine-Rich Repeat LGI Family, Member 2 2
  • Leucine-Rich Repeat LGI Family Member 2 3
  • Leucine-Rich, Glioma Inactivated 2 3
  • KIAA1916 4

External Ids for LGI2 Gene

Previous GeneCards Identifiers for LGI2 Gene

  • GC04M025125
  • GC04M024688
  • GC04M024754
  • GC04M024679
  • GC04M024341

Summaries for LGI2 Gene

GeneCards Summary for LGI2 Gene

LGI2 (Leucine Rich Repeat LGI Family Member 2) is a Protein Coding gene. Diseases associated with LGI2 include Deafness, Autosomal Recessive 98. Among its related pathways are Developmental Biology and LGI-ADAM interactions. An important paralog of this gene is LGI1.

Gene Wiki entry for LGI2 Gene

Additional gene information for LGI2 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LGI2 Gene

Genomics for LGI2 Gene

GeneHancer (GH) Regulatory Elements for LGI2 Gene

Promoters and enhancers for LGI2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J025030 Promoter 1.4 EPDnew Ensembl 650.7 +0.1 78 0.8 KLF17 ZNF398 ZBTB8A ZNF335 NFIC ZNF341 PATZ1 ZBTB26 EZH2 LGI2 LOC102723675 GC04M024941
GH04J025098 Enhancer 0.9 Ensembl ENCODE 15.7 -68.9 -68871 2 TEAD4 TAL1 TCF12 ZNF366 POLR2A NCOR1 CBFA2T2 SOX6 RNF2 MTA2 LGI2 GC04M025099 LOC105374534 GC04M024941
GH04J024657 Enhancer 1.1 Ensembl ENCODE dbSUPER 9.7 +371.8 371807 2.7 USF1 FOXA2 MAX SIN3A ZIC2 ZNF335 POLR2A RBAK ZNF366 ZSCAN5C LINC02473 GC04M024658 ATP5MGP3 ANAPC4 DHX15 ZCCHC4 LGI2
GH04J025088 Enhancer 0.8 Ensembl 11.4 -57.8 -57822 0.6 HDAC1 PKNOX1 TCF12 EGR1 ATF7 MEF2D SMARCA4 GMEB1 IKZF1 KDM1A CCDC149 LGI2 SEL1L3 GC04M024941 LOC105374534
GH04J024855 Enhancer 0.9 Ensembl ENCODE 9.5 +173.4 173365 3 BATF IRF4 POLR2A EED ETV6 FOS BCLAF1 IKZF2 RUNX3 CREM SOD3 LGI2 GC04M024806 GC04P024947 CCDC149
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LGI2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LGI2 gene promoter:
  • RP58
  • Nkx2-5
  • AP-1
  • Pax-5
  • HEN1
  • RSRFC4
  • Egr-2
  • CUTL1
  • E4BP4
  • POU6F1 (c2)

Genomic Locations for LGI2 Gene

Genomic Locations for LGI2 Gene
chr4:24,998,847-25,030,879
(GRCh38/hg38)
Size:
32,033 bases
Orientation:
Minus strand
chr4:25,000,469-25,032,501
(GRCh37/hg19)
Size:
32,033 bases
Orientation:
Minus strand

Genomic View for LGI2 Gene

Genes around LGI2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LGI2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LGI2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LGI2 Gene

Proteins for LGI2 Gene

  • Protein details for LGI2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N0V4-LGI2_HUMAN
    Recommended name:
    Leucine-rich repeat LGI family member 2
    Protein Accession:
    Q8N0V4
    Secondary Accessions:
    • Q3MIN2
    • Q8NDW6
    • Q96PX2
    • Q9NVK4

    Protein attributes for LGI2 Gene

    Size:
    545 amino acids
    Molecular mass:
    62298 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91746.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LGI2 Gene

Post-translational modifications for LGI2 Gene

  • Glycosylation at posLast=402402, isoforms=271, isoforms=186, and posLast=7070
  • Modification sites at PhosphoSitePlus

Other Protein References for LGI2 Gene

No data available for DME Specific Peptides for LGI2 Gene

Domains & Families for LGI2 Gene

Gene Families for LGI2 Gene

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

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LGI2: view

No data available for UniProtKB/Swiss-Prot for LGI2 Gene

Function for LGI2 Gene

Phenotypes From GWAS Catalog for LGI2 Gene

genes like me logo Genes that share phenotypes with LGI2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LGI2

CRISPR Products

miRNA for LGI2 Gene

miRTarBase miRNAs that target LGI2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGI2

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LGI2 Gene

Localization for LGI2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LGI2 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
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 LGI2 gene
Compartment Confidence
extracellular 5
cytoskeleton 2
golgi apparatus 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LGI2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA --
genes like me logo Genes that share ontologies with LGI2: view

Pathways & Interactions for LGI2 Gene

genes like me logo Genes that share pathways with LGI2: view

Pathways by source for LGI2 Gene

2 Reactome pathways for LGI2 Gene

Interacting Proteins for LGI2 Gene

Gene Ontology (GO) - Biological Process for LGI2 Gene

None

No data available for SIGNOR curated interactions for LGI2 Gene

Drugs & Compounds for LGI2 Gene

No Compound Related Data Available

Transcripts for LGI2 Gene

mRNA/cDNA for LGI2 Gene

Unigene Clusters for LGI2 Gene

Leucine-rich repeat LGI family, member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGI2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LGI2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1:
SP2: - -

Relevant External Links for LGI2 Gene

GeneLoc Exon Structure for
LGI2
ECgene alternative splicing isoforms for
LGI2

Expression for LGI2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LGI2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LGI2 Gene

This gene is overexpressed in Nerve - Tibial (x4.6).

Protein differential expression in normal tissues from HIPED for LGI2 Gene

This gene is overexpressed in Amniocyte (68.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LGI2 Gene



Protein tissue co-expression partners for LGI2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LGI2 Gene:

LGI2

SOURCE GeneReport for Unigene cluster for LGI2 Gene:

Hs.12488

mRNA Expression by UniProt/SwissProt for LGI2 Gene:

Q8N0V4-LGI2_HUMAN
Tissue specificity: Brain, heart and placenta.

Evidence on tissue expression from TISSUES for LGI2 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with LGI2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LGI2 Gene

Orthologs for LGI2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LGI2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LGI2 34 33
  • 99.45 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LGI2 34
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LGI2 34 33
  • 92.9 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LGI2 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lgi2 16 34 33
  • 90.63 (n)
dog
(Canis familiaris)
Mammalia LGI2 34 33
  • 90.59 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lgi2 33
  • 90.23 (n)
chicken
(Gallus gallus)
Aves LGI2 34 33
  • 81.5 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LGI2 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lgi2 33
  • 76.06 (n)
zebrafish
(Danio rerio)
Actinopterygii lgi2a 34
  • 70 (a)
OneToMany
lgi2b 34
  • 59 (a)
OneToMany
Species where no ortholog for LGI2 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)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LGI2 Gene

ENSEMBL:
Gene Tree for LGI2 (if available)
TreeFam:
Gene Tree for LGI2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LGI2: view image

Paralogs for LGI2 Gene

Paralogs for LGI2 Gene

(6) SIMAP similar genes for LGI2 Gene using alignment to 3 proteins:

  • LGI2_HUMAN
  • H0YA65_HUMAN
  • L0R890_HUMAN
genes like me logo Genes that share paralogs with LGI2: view

Variants for LGI2 Gene

Sequence variations from dbSNP and Humsavar for LGI2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000062768 -- 25,020,687(-) G/A intron_variant
rs1000093391 -- 25,020,430(-) G/A intron_variant
rs1000108086 -- 24,992,902(-) C/G genic_downstream_transcript_variant, intron_variant
rs10001303 -- 25,032,553(-) T/C upstream_transcript_variant
rs1000153694 -- 25,014,254(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LGI2 Gene

Variant ID Type Subtype PubMed ID
nsv1073313 CNV deletion 25765185
nsv829887 CNV gain+loss 17160897
nsv829888 CNV gain 17160897
nsv958244 CNV deletion 24416366

Variation tolerance for LGI2 Gene

Residual Variation Intolerance Score: 11.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.16; 84.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LGI2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LGI2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LGI2 Gene

Disorders for LGI2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LGI2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 98
  • dfnb98
- elite association - COSMIC cancer census association via MalaCards
Search LGI2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LGI2

genes like me logo Genes that share disorders with LGI2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LGI2 Gene

Publications for LGI2 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. Using gene-history and expression analyses to assess the involvement of LGI genes in human disorders. (PMID: 16014869) Gu W … Begemann G (Molecular biology and evolution 2005) 2 3 22 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. A common protein interaction domain links two recently identified epilepsy genes. (PMID: 12095917) Scheel H … Hofmann K (Human molecular genetics 2002) 3 4 58

Products for LGI2 Gene

Sources for LGI2 Gene

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