Gene
LGI1
leucine rich glioma inactivated 1
- HGNC 6572(opens in a new tab)
- Ensembl gene ENSG00000108231(opens in a new tab)
- NCBI Gene 9211(opens in a new tab)
Summary
- Cytogenetic location
- 10q23.33
- Coordinates
- Chromosome 10: 93,757,936–93,798,159 (GRCh38)
- Exons
- 8 exons across 40.2 kb
- Protein
- 557 amino acids
- Also known as
- IB1099, ETL1, EPITEMPIN
- Previous symbols
- EPT
- MANE Select transcript
- ENST00000371418.9NM_005097.4
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Epilepsy (Full Panel)
- Epilepsy
One of 171 genes linked to it
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
- ClinGen rates the link definitive
- 3 GenCC submitters rate it definitive or strong
How LGI1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 2.2 kb of the gene's 40.2 kb; 1,674 of those bases code for the protein.
How a genome test reads LGI1
46
positions in LGI1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 40.2 kb of LGI1, introns included, not only the 2.2 kb of exons.
Traits linked to LGI1
The Human Phenotype Ontology lists these as features of the rare conditions LGI1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Absent speech development
- Bilateral tonic-clonic seizure with focal onset
- Delayed ability to sit
- Delayed ability to walk
- Delayed speech and language development
- EEG with focal epileptiform discharges
- Epilepsy
- Generalized clonic seizure
Show 78 more traits
- Grand mal seizures
- Inability to walk by childhood/adolescence
- Motor delay
- Poor eye contact
- Severe global developmental delay
- Bilateral tonic-clonic seizure with generalized onset
- Epileptic encephalopathy
- Focal motor seizure
- Generalized myoclonic seizure
- Global developmental delay
- Hallucinations of sound
- Increased reflexes
- Intellectual disability
- Repeated seizures without recovery between them
- Seizure affecting one half of brain
- Degeneration of cerebrum
- Difficulty finding words
- Difficulty sleeping
- EEG abnormality
- EEG with burst suppression
- Focal autonomic seizure with epigastric sensation/nausea/vomiting/other gastrointestinal phenomena
- Focal aware seizure
- Focal aware sensory seizure with auditory features
- Focal impaired awareness seizure
- Focal sensory seizure with auditory features
- Focal tonic seizure
- Hypsarrhythmia
- Interictal epileptiform activity
- Lethargy
- Multifocal epileptiform discharges
- Abnormal autonomic nervous system physiology
- Autism spectrum disorder
- Brief seizures with staring spells
- Choreoathetosis
- CNS hypomyelination
- Degeneration of cerebellum
- Deja vu
- Delayed CNS myelination
- Delayed myelination
- Diffuse cerebral atrophy
- Diffuse white matter abnormalities
- Disorder of involuntary muscle movements
- EEG with abnormally slow frequencies
- EEG with generalized epileptiform discharges
- EEG with spike-wave complexes
- Episodic ataxia
- Febrile seizure (within the age range of 3 months to 6 years)
- Fewer and broader ridges in brain
- Focal automatism seizure
- Focal autonomic seizure
- Focal autonomic seizure with palpitations/tachycardia/bradycardia/asystole
- Focal clonic seizure
- Focal sensory seizure with cephalic sensation
- Focal sensory seizure with vestibular features
- Focal sensory seizure with visual features
- Generalized tonic seizure
- Infantile spasms
- Intellectual disability, mild
- Jerking
- Loss of developmental milestones
- More active than typical
- Nocturnal seizures
- Self-injurious behavior
- Sudden loss of muscle tone
- Teeth grinding
- Thin corpus callosum
- Tremor
- Underdevelopment of part of brain called corpus callosum
- Uni- and bilateral multifocal epileptiform discharges
- Ventriculomegaly
- Visual hallucinations
- Behavioral abnormality
- Depression
- Dystonia
- Generalized-onset seizure
- Impulsivity
- Migraine
- Brain imaging abnormality
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). LGI1 gene: leucine rich glioma inactivated 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/lgi1
Dante Labs. LGI1 gene: leucine rich glioma inactivated 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/lgi1
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