LGI1

protein-coding

leucine rich glioma inactivated 1, the group of LGI family

Gene 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]

Previous symbols:
  • EPT

MANE transcript

NM_005097.4

Inheritance

AD

ClinVar variants

P:74U:262B:148

Top phenotype

Epilepsy, familial temporal lobe, 1

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr10:93,757,840-93,806,272

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~48.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epilepsy, familial temporal lobe, 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700090

Submitter: Labcorp Genetics (formerly Invitae)

autosomal dominant epilepsy with auditory featuresSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010898

Submitter: Orphanet

autosomal dominant epilepsy with auditory featuresSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010898

Submitter: PanelApp Australia

autosomal dominant epilepsy with auditory featuresDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010898

Submitter: ClinGen

Autosomal Dominant Epilepsy with Auditory Features (ADEAF), also known as familial temporal lobe epilepsy, is characterized by seizures originating in the temporal lobe associated with auditory symptoms (ringing, buzzing, and distortion of sounds) and receptive aphasia. The condition can also be associated with non-auditory seizures, including tonic-clonic seizures. Onset can occur from early childhood through the 5th decade, typically during adolescence or early adulthood, and seizures tend to be well-controlled. ADEAF is inherited in an autosomal dominant pattern with incomplete penetrance, estimated at approximately 60%. Rare de novo mutations have been reported and ADEAF is associated with intrafamilial variability. LGI1 is the primary gene implicated in ADEAF and was initially described in 2002 (Kalichov et al, PMID 11810107). Since that time, numerous families have been reported in the literature, with over 40 disease-causing mutations reported, typically unique to individual families. The mutation spectrum includes nonsense, frameshift, splice site, missense and large deletions with loss of function as the mechanism of disease (Kalichov et al, PMID 11810107; Morante-Redolat et al, PMID 11978770; Chabrol et al, PMID 17296837; Sadleir et al, PMID: 24206907; Hedera et al, PubMed 15009222; Michelucci et al, PMID 14510822; Fanciulli et al, PMID 22496201; Kesim et al, PMID 26773249). Supporting experimental evidence includes functional alteration in non-patient cells (Yokoi et al, PMID 25485908), expression (Fukata et al, PMID 16990550; Fukata et al, 20133599), non-human model organism (Yu et al, 20130004; Baulac et al, 22589250; Teng et al, 20819949; Chabrol et al, 20659958; Fukata et al, 20133599), and rescue in non-human model organism (Fukata et al, 20133599). A genetic evidence score of 12 and experimental evidence score of 6 results in a total score of 18. Evidence supporting an association between LGI1 and ADEAF has been replicated over time; therefore, the gene-disease validity has been classified as DEFINITIVE.

Clinical Genomic Database (CGD)

Epilepsy, familial temporal lobe, 1AD

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 8773604; 11906506; 12205652; 11810107; 15079010; 15079011; 17562837; 19064878; 20301709; 21444903; 21504429; 22496201Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LGI1 variants in ClinVar

13 Conditions Cataloged
Autosomal dominant epilepsy with auditory featuresTotal: 399
not providedTotal: 146
Inborn genetic diseasesTotal: 79
Epilepsy, familial temporal lobe, 1Total: 60
not specifiedTotal: 20
LGI1-related disorderTotal: 6
Developmental and epileptic encephalopathy 121Total: 5
SeizureTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005097.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
130
clinvar
134
missense
9
clinvar
8
clinvar
254
clinvar
17
clinvar
288
nonsense
17
clinvar
3
clinvar
1
clinvar
21
start loss
1
clinvar
1
frameshift
14
clinvar
13
clinvar
2
clinvar
29
splice donor/acceptor (+/-2bp)
9
clinvar
2
clinvar
11
Total41332621480484

Highest pathogenic variant AF is 0.0000018598654

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005097.4RefSeqNP_005088.18MANE Select
ENST00000371418.9EnsemblENSP00000360472.48MANE Select
NM_001308275.2RefSeqNP_001295204.18Standard
NM_001308276.2RefSeqNP_001295205.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lgi1bDanio rerio

Structure: tectal ventricle

Quality: hydrocephalic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Developmental Biology
  • LGI-ADAM interactions

Biological Process

  • nervous system development
  • axon guidance
  • cell population proliferation
  • positive regulation of cell growth
  • neuron projection development

Molecular Function

  • signaling receptor binding
  • protein binding

Cellular Component

  • extracellular region
  • extracellular space
  • membrane
  • cell junction
  • synaptic cleft

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000371418
Coding exons
8
Length
40351
Individuals with no LoFs
125730
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125733
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.781582920.5420.00001543682
Missense (PolyPhen)30117.610.255091574
Synonymous0.6981031120.9160.000006601034
Loss of Function4.43124.80.04030.00000123320

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Regulates voltage-gated potassium channels assembled from KCNA1, KCNA4 and KCNAB1. It slows down channel inactivation by precluding channel closure mediated by the KCNAB1 subunit. Ligand for ADAM22 that positively regulates synaptic transmission mediated by AMPA-type glutamate receptors (By similarity). Plays a role in suppressing the production of MMP1/3 through the phosphatidylinositol 3-kinase/ERK pathway. May play a role in the control of neuroblastoma cell survival. {ECO:0000250, ECO:0000269|PubMed:15047712, ECO:0000269|PubMed:16518856}.;
Disease
DISEASE: Epilepsy, familial temporal lobe, 1 (ETL1) [MIM:600512]: A focal form of epilepsy characterized by recurrent seizures that arise from foci within the temporal lobe. Seizures are usually accompanied by sensory symptoms, most often auditory in nature. {ECO:0000269|PubMed:11810107, ECO:0000269|PubMed:12205652, ECO:0000269|PubMed:12601709, ECO:0000269|PubMed:12771268, ECO:0000269|PubMed:15079010, ECO:0000269|PubMed:17067999, ECO:0000269|PubMed:17296837, ECO:0000269|PubMed:17562837, ECO:0000269|PubMed:18625862, ECO:0000269|PubMed:19552651}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.326

Intolerance Scores

RVIS EVS
-0.71
RVIS percentile EVS
14.4

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.784

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.