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

    Gene ID: 9211, updated on 27-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
    mouse all
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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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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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    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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