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LGI2 leucine rich repeat LGI family member 2 [ Homo sapiens (human) ]

Gene ID: 55203, updated on 7-Apr-2024

Summary

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Official Symbol
LGI2provided by HGNC
Official Full Name
leucine rich repeat LGI family member 2provided by HGNC
Primary source
HGNC:HGNC:18710
See related
Ensembl:ENSG00000153012 MIM:608301; AllianceGenome:HGNC:18710
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LGIL2
Summary
Predicted to be involved in inhibitory synapse assembly. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in gall bladder (RPKM 3.7), appendix (RPKM 3.2) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
4p15.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (24992081..25030946, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (24973998..25012867, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (25000469..25032568, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:24801347-24801847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:24810365-24810945 Neighboring gene coiled-coil domain containing 149 Neighboring gene superoxide dismutase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:24858054-24858554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:24858555-24859055 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:24864823-24866022 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:24870157-24871356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:24918461-24919030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:24919031-24919599 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:24966942-24968141 Neighboring gene uncharacterized LOC102723675 Neighboring gene uncharacterized LOC124900684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:25086876-25087376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:25087377-25087877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25089726-25090269 Neighboring gene uncharacterized LOC105374534 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133175-25133701 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133702-25134228 Neighboring gene Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21370

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. Is LGI2 the candidate gene for partial epilepsy with pericentral spikes? Limviphuvadh V, et al. J Bioinform Comput Biol, 2010 Feb. PMID 20183877
  2. Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2. Limviphuvadh V, et al. BMC Biochem, 2010 Sep 24. PMID 20863412, Free PMC Article
  3. The LGI1 gene involved in lateral temporal lobe epilepsy belongs to a new subfamily of leucine-rich repeat proteins. Gu W, et al. FEBS Lett, 2002 May 22. PMID 12023020
  4. Using gene-history and expression analyses to assess the involvement of LGI genes in human disorders. Gu W, et al. Mol Biol Evol, 2005 Nov. PMID 16014869
  5. A common protein interaction domain links two recently identified epilepsy genes. Scheel H, et al. Hum Mol Genet, 2002 Jul 15. PMID 12095917

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

Genotypes

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

Clone Names

  • FLJ10675, KIAA1916, MGC126808, MGC126810

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in inhibitory synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in inhibitory synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in extracellular region TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
leucine-rich repeat LGI family member 2
Names
LGI1-like protein 2
leucine-rich glioma-inactivated protein 2
leucine-rich, glioma inactivated 2

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.

mRNA and Protein(s)

  1. NM_018176.4 → NP_060646.2  leucine-rich repeat LGI family member 2 precursor

    See identical proteins and their annotated locations for NP_060646.2

    Status: VALIDATED

    Source sequence(s)
    AC113614, BC101761
    Consensus CDS
    CCDS3431.1
    UniProtKB/Swiss-Prot
    Q3MIN2, Q8N0V4, Q8NDW6, Q96PX2, Q9NVK4
    Related
    ENSP00000371548.4, ENST00000382114.9
    Conserved Domains (4) summary
    TIGR00864
    Location:140 → 215
    PCC; polycystin cation channel protein
    sd00031
    Location:111 → 134
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:266 → 304
    EPTP; EPTP domain
    pfam13855
    Location:110 → 169
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    24992081..25030946 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008356.2 → XP_016863845.1  leucine-rich repeat LGI family member 2 isoform X2

  2. XM_011513850.3 → XP_011512152.1  leucine-rich repeat LGI family member 2 isoform X1

    Conserved Domains (5) summary
    sd00031
    Location:111 → 134
    LRR_1; leucine-rich repeat [structural motif]
    pfam03736
    Location:219 → 260
    EPTP; EPTP domain
    pfam12799
    Location:110 → 149
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:110 → 169
    LRR_8; Leucine rich repeat
    cl15307
    Location:167 → 212
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    24973998..25012867 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350374.1 → XP_054206349.1  leucine-rich repeat LGI family member 2 isoform X2

  2. XM_054350373.1 → XP_054206348.1  leucine-rich repeat LGI family member 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N0V4.1 GenPept UniProtKB/Swiss-Prot:Q8N0V4

Gene LinkOut

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