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LGI1 leucine rich glioma inactivated 1 [ Homo sapiens (human) ]

Gene ID: 9211, updated on 2-Nov-2024

Summary

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Official Symbol
LGI1provided by HGNC
Official Full Name
leucine rich glioma inactivated 1provided by HGNC
Primary source
HGNC:HGNC:6572
See related
Ensembl:ENSG00000108231 MIM:604619; AllianceGenome:HGNC:6572
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EPT; ETL1; ADLTE; ADPAEF; ADPEAF; IB1099; EPITEMPIN
Summary
This gene encodes a member of the secreted leucine-rich repeat (LRR) superfamily and shares homology with members of the SLIT protein family. The encoded protein may regulate the activity of voltage-gated potassium channels and may be involved in neuronal growth regulation and cell survival. This gene is rearranged as a result of translocations in glioblastoma cell lines, and it is frequently down-regulated or rearranged in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Expression
Biased expression in brain (RPKM 13.8), esophagus (RPKM 1.7) and 3 other tissues See more
Orthologs
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Genomic context

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See LGI1 in Genome Data Viewer
Location:
10q23.33
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (93757936..93798159)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (94637831..94677073)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (95517693..95557916)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene FRA10A associated CGG repeat 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3786 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95474242-95474394 Neighboring gene fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) Neighboring gene uncharacterized LOC101927013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:95505761-95506512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:95508859-95509841 Neighboring gene uncharacterized LOC105378437 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:95550082-95550640 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:95609025-95609669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2630 Neighboring gene RAB11A, member RAS oncogene family pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2631 Neighboring gene solute carrier family 35 member G1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Investigation of LGI1 as the antigen in limbic encephalitis previously attributed to potassium channels: a case series. Lai M, et al. Lancet Neurol, 2010 Aug. PMID 20580615, Free PMC Article
  2. A novel loss-of-function LGI1 mutation linked to autosomal dominant lateral temporal epilepsy. Striano P, et al. Arch Neurol, 2008 Jul. PMID 18625862
  3. Penetrance of LGI1 mutations in autosomal dominant partial epilepsy with auditory features. Rosanoff MJ, et al. Neurology, 2008 Aug 19. PMID 18711109, Free PMC Article
  4. LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy. Nobile C, et al. Hum Mutat, 2009 Apr. PMID 19191227
  5. A novel three base-pair LGI1 deletion leading to loss of function in a family with autosomal dominant lateral temporal epilepsy and migraine-like episodes. de Bellescize J, et al. Epilepsy Res, 2009 Jul. PMID 19268539

See all (85) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Activity-driven synaptic translocation of LGI1 controls excitatory neurotransmission.
    Title: Activity-driven synaptic translocation of LGI1 controls excitatory neurotransmission.
  2. Familial mesial temporal lobe epilepsy phenotype is associated with novel LGI1 variants: A report of two families.
    Title: Familial mesial temporal lobe epilepsy phenotype is associated with novel LGI1 variants: A report of two families.
  3. The downregulation of Kv1 channels in Lgi1[-/-]mice is accompanied by a profound modification of its interactome and a parallel decrease in Kv2 channels.
    Title: The downregulation of Kv(1) channels in Lgi1(-/-)mice is accompanied by a profound modification of its interactome and a parallel decrease in Kv(2) channels.
  4. Leucine-Rich Glioma-Inactivated 1 (LGI1) Protein Stimulates Proliferation and IL-10 Production in Peripheral Blood Mononuclear Cells of Patients with LGI1 Antibody-Mediated Autoimmune Encephalitis In Vitro.
    Title: Leucine-Rich Glioma-Inactivated 1 (LGI1) Protein Stimulates Proliferation and IL-10 Production in Peripheral Blood Mononuclear Cells of Patients with LGI1 Antibody-Mediated Autoimmune Encephalitis In Vitro.
  5. Characterization of cardiac bradyarrhythmia associated with LGI1-IgG autoimmune encephalitis.
    Title: Characterization of cardiac bradyarrhythmia associated with LGI1-IgG autoimmune encephalitis.
  6. Autosomal dominant lateral temporal epilepsy in a family exhibiting a rare heterozygous mutation and deletion in the leucine-rich glioma inactivated 1 gene.
    Title: Autosomal dominant lateral temporal epilepsy in a family exhibiting a rare heterozygous mutation and deletion in the leucine-rich glioma inactivated 1 gene.
  7. A novel LGI1 mutation causing autosomal dominant lateral temporal lobe epilepsy confirmed by a precise knock-in mouse model.
    Title: A novel LGI1 mutation causing autosomal dominant lateral temporal lobe epilepsy confirmed by a precise knock-in mouse model.
  8. Clinical features of nine cases of leucine-rich glioma inactivated 1 protein antibody-associated encephalitis.
    Title: Clinical features of nine cases of leucine-rich glioma inactivated 1 protein antibody-associated encephalitis.
  9. Serum and CSF cytokine levels mirror different neuroimmunological mechanisms in patients with LGI1 and Caspr2 encephalitis.
    Title: Serum and CSF cytokine levels mirror different neuroimmunological mechanisms in patients with LGI1 and Caspr2 encephalitis.
  10. Clinical characteristics of patients double positive for CASPR2 and LGI1-antibodies.
    Title: Clinical characteristics of patients double positive for CASPR2 and LGI1-antibodies.
Submit: New GeneRIF Correction See all GeneRIFs (67)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
NOT enables signaling receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in axon guidance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neurotransmitter receptor localization to postsynaptic specialization membrane IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in axon initial segment IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in synaptic cleft IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich glioma-inactivated protein 1
Names
epitempin-1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011832.2 RefSeqGene

    Range
    5002..45225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308275.2 → NP_001295204.1  leucine-rich glioma-inactivated protein 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001295204.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which leads to a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL157396, AL358154
    Consensus CDS
    CCDS76325.1
    UniProtKB/TrEMBL
    A0A0S2Z4X3, A0A1B0GV33
    Related
    ENSP00000360467.3, ENST00000371413.4
    Conserved Domains (4) summary
    TIGR00864
    Location:146 → 221
    PCC; polycystin cation channel protein
    sd00031
    Location:71 → 92
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:225 → 264
    EPTP; EPTP domain
    pfam13855
    Location:91 → 151
    LRR_8; Leucine rich repeat

  2. NM_001308276.2 → NP_001295205.1  leucine-rich glioma-inactivated protein 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001295205.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AL157396, AL358154
    Consensus CDS
    CCDS81490.1
    UniProtKB/Swiss-Prot
    O95970
    Related
    ENSP00000485917.1, ENST00000630047.2
    Conserved Domains (3) summary
    TIGR00864
    Location:98 → 173
    PCC; polycystin cation channel protein
    sd00031
    Location:93 → 116
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:462 → 502
    EPTP; EPTP domain

  3. NM_005097.4 → NP_005088.1  leucine-rich glioma-inactivated protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_005088.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL157396, AL358154
    Consensus CDS
    CCDS7431.1
    UniProtKB/Swiss-Prot
    A8K0Z1, B4E1S0, O95970, Q5W001, Q5W002, Q8NI23, Q96LF5
    UniProtKB/TrEMBL
    A0A0S2Z4S7
    Related
    ENSP00000360472.4, ENST00000371418.9
    Conserved Domains (4) summary
    TIGR00864
    Location:146 → 221
    PCC; polycystin cation channel protein
    sd00031
    Location:71 → 92
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:510 → 549
    EPTP; EPTP domain
    pfam13855
    Location:91 → 151
    LRR_8; Leucine rich repeat

RNA

  1. NR_131777.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two internal exons and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL157396, AL358154
    Related
    ENST00000627420.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    93757936..93798159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016911.3 → XP_016872400.1  leucine-rich glioma-inactivated protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A1B0GUD3, A0A1B0GV33
    Related
    ENSP00000490058.1, ENST00000635953.1
    Conserved Domains (4) summary
    TIGR00864
    Location:146 → 221
    PCC; polycystin cation channel protein
    sd00031
    Location:71 → 92
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:225 → 266
    EPTP; EPTP domain
    pfam13855
    Location:91 → 151
    LRR_8; Leucine rich repeat

  2. XM_017016912.3 → XP_016872401.1  leucine-rich glioma-inactivated protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5G1
    Conserved Domains (5) summary
    smart00370
    Location:91 → 113
    LRR; Leucine-rich repeats, outliers
    smart00082
    Location:125 → 173
    LRRCT; Leucine rich repeat C-terminal domain
    sd00031
    Location:93 → 116
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:177 → 218
    EPTP; EPTP domain
    pfam13855
    Location:71 → 127
    LRR_8; Leucine rich repeat

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    94637831..94677073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367142.1 → XP_054223117.1  leucine-rich glioma-inactivated protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A1B0GUD3

  2. XM_054367143.1 → XP_054223118.1  leucine-rich glioma-inactivated protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5G1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95970.1 GenPept UniProtKB/Swiss-Prot:O95970

Gene LinkOut

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