LGI1
protein-codingleucine 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]
- EPT
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~48.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0700090
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0010898
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0010898
Submitter: PanelApp Australia
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)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LGI1 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 130 | 134 | ||
| missense | 9 | 8 | 254 | 17 | 288 | |
| nonsense | 17 | 3 | 1 | 21 | ||
| start loss | 1 | 1 | ||||
| frameshift | 14 | 13 | 2 | 29 | ||
| splice donor/acceptor (+/-2bp) | 9 | 2 | 11 | |||
| Total | 41 | 33 | 262 | 148 | 0 | 484 |
Highest pathogenic variant AF is 0.0000018598654
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005088.1 | 8 | MANE Select | |
| Ensembl | ENSP00000360472.4 | 8 | MANE Select | |
| RefSeq | NP_001295204.1 | 8 | Standard | |
| RefSeq | NP_001295205.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lgi1b | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.78 | 158 | 292 | 0.542 | 0.0000154 | 3682 |
| Missense (PolyPhen) | 30 | 117.61 | 0.25509 | 1574 | ||
| Synonymous | 0.698 | 103 | 112 | 0.916 | 0.00000660 | 1034 |
| Loss of Function | 4.43 | 1 | 24.8 | 0.0403 | 0.00000123 | 320 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |