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

Gene ID: 9211, updated on 14-Oct-2019

Summary

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
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

Genomic context

See LGI1 in Genome Data Viewer
Location:
10q23.33
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (93757809..93798174)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (95517566..95557916)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene FRA10A associated CGG repeat 1 Neighboring gene FRA10A repeat instability region Neighboring gene uncharacterized LOC101927013 Neighboring gene uncharacterized LOC105378437 Neighboring gene RAB11A, member RAS oncogene family pseudogene 1 Neighboring gene solute carrier family 35 member G1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • LGI-ADAM interactions, organism-specific biosystem (from REACTOME)
    LGI-ADAM interactions, organism-specific biosystemSynapse formation and maturation require multiple interactions between presynaptic and postsynaptic neurons. These interactions are mediated by a diverse set of synaptogenic proteins (Kegel et al. 20...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neurotransmitter receptor localization to postsynaptic specialization membrane IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
protein homooligomerization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
synaptic cleft IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_011832.1 RefSeqGene

    Range
    5001..45366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308275.1NP_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)
    AF473548, DB546258, DC326684, H05384
    Consensus CDS
    CCDS76325.1
    UniProtKB/Swiss-Prot
    O95970
    UniProtKB/TrEMBL
    A0A0S2Z4X3
    Related
    ENSP00000360467.3, ENST00000371413.4
    Conserved Domains (4) summary
    TIGR00864
    Location:146221
    PCC; polycystin cation channel protein
    sd00031
    Location:7192
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:225266
    EPTP; EPTP domain
    pfam13855
    Location:91151
    LRR_8; Leucine rich repeat
  2. NM_001308276.1NP_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)
    AF055636, AK303956, DB546258, DC326684, H05384
    Consensus CDS
    CCDS81490.1
    UniProtKB/Swiss-Prot
    O95970
    Related
    ENSP00000485917.1, ENST00000630047.2
    Conserved Domains (3) summary
    TIGR00864
    Location:98173
    PCC; polycystin cation channel protein
    sd00031
    Location:93116
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:462502
    EPTP; EPTP domain
  3. NM_005097.4NP_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
    O95970
    UniProtKB/TrEMBL
    A0A0S2Z4S7
    Related
    ENSP00000360472.4, ENST00000371418.9
    Conserved Domains (4) summary
    TIGR00864
    Location:146221
    PCC; polycystin cation channel protein
    sd00031
    Location:7192
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:510550
    EPTP; EPTP domain
    pfam13855
    Location:91151
    LRR_8; Leucine rich repeat

RNA

  1. NR_131777.1 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)
    AF055636, AK309416, DB546258, DC326684, H05384
    Related
    ENST00000627420.2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    93757809..93798174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0S2Z5G1
    Conserved Domains (5) summary
    smart00370
    Location:91113
    LRR; Leucine-rich repeats, outliers
    smart00082
    Location:125173
    LRRCT; Leucine rich repeat C-terminal domain
    sd00031
    Location:93116
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:177218
    EPTP; EPTP domain
    pfam13855
    Location:71127
    LRR_8; Leucine rich repeat
  2. XM_017016911.2XP_016872400.1  leucine-rich glioma-inactivated protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A1B0GUD3
    Related
    ENSP00000490058.1, ENST00000635953.1
    Conserved Domains (4) summary
    TIGR00864
    Location:146221
    PCC; polycystin cation channel protein
    sd00031
    Location:7192
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:225266
    EPTP; EPTP domain
    pfam13855
    Location:91151
    LRR_8; Leucine rich repeat
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