Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	9211
Gene name Gene Name - the full gene name approved by the HGNC.	Leucine rich glioma inactivated 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	LGI1
Synonyms (NCBI Gene) Gene synonyms aliases	ADLTE, ADPAEF, ADPEAF, EPITEMPIN, EPT, ETL1, IB1099
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10q23.33
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28937874	A>C	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant, intron variant
rs28939075	T>G	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant, intron variant
rs104894167	T>C	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs146425212	A>C,G	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, missense variant, non coding transcript variant, synonymous variant
rs148862146	C>T	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, non coding transcript variant, synonymous variant
rs797044997	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs797044998	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant
rs797044999	C>T	Pathogenic	Coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs869025201	T>C	Pathogenic	Coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs886039496	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant
rs934556455	C>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, intron variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs1060502053	G>A	Pathogenic	Stop gained, non coding transcript variant, intron variant, genic downstream transcript variant, coding sequence variant
rs1060502054	C>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1064794249	G>A	Likely-pathogenic	Non coding transcript variant, intron variant, genic downstream transcript variant, coding sequence variant, missense variant
rs1064797149	C>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1364913665	AT>-	Pathogenic	Frameshift variant, intron variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs1554907767	->AATAGTCAGAA	Pathogenic	Intron variant, non coding transcript variant, inframe indel, stop gained, coding sequence variant, genic downstream transcript variant
rs1554907787	T>G	Pathogenic	Intron variant, non coding transcript variant, stop gained, coding sequence variant, genic downstream transcript variant
rs1564851314	G>T	Likely-pathogenic	Splice acceptor variant

Show/Hide all(27)

miRTarBase ID	miRNA	Experiments
MIRT1108339	hsa-miR-1269	CLIP-seq
MIRT1108340	hsa-miR-1269b	CLIP-seq
MIRT1108341	hsa-miR-1288	CLIP-seq
MIRT1108342	hsa-miR-3654	CLIP-seq
MIRT1108343	hsa-miR-378	CLIP-seq
MIRT1108344	hsa-miR-378b	CLIP-seq
MIRT1108345	hsa-miR-378c	CLIP-seq
MIRT1108346	hsa-miR-378d	CLIP-seq
MIRT1108347	hsa-miR-378e	CLIP-seq
MIRT1108348	hsa-miR-378f	CLIP-seq
MIRT1108349	hsa-miR-378h	CLIP-seq
MIRT1108350	hsa-miR-378i	CLIP-seq
MIRT1108351	hsa-miR-422a	CLIP-seq
MIRT1108352	hsa-miR-4477b	CLIP-seq
MIRT1108353	hsa-miR-4515	CLIP-seq
MIRT1108354	hsa-miR-4520a-3p	CLIP-seq
MIRT1108355	hsa-miR-4638-3p	CLIP-seq
MIRT1108356	hsa-miR-4740-5p	CLIP-seq
MIRT1108357	hsa-miR-499-3p	CLIP-seq
MIRT1108358	hsa-miR-499a-3p	CLIP-seq
MIRT2260819	hsa-miR-889	CLIP-seq
MIRT2430724	hsa-miR-30a	CLIP-seq
MIRT2430725	hsa-miR-30b	CLIP-seq
MIRT2430726	hsa-miR-30c	CLIP-seq
MIRT2430727	hsa-miR-30d	CLIP-seq
MIRT2430728	hsa-miR-30e	CLIP-seq
MIRT2430729	hsa-miR-4495	CLIP-seq

Show/Hide all(27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005102	Function	Signaling receptor binding	IPI	20463223
GO:0005102	Function	Signaling receptor binding	IPI	20463223
GO:0005515	Function	Protein binding	IPI	20463223, 27066583
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IDA	17067999
GO:0005615	Component	Extracellular space	IDA	17067999
GO:0005615	Component	Extracellular space	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0007165	Process	Signal transduction	IEA
GO:0007399	Process	Nervous system development	TAS	9879993
GO:0007411	Process	Axon guidance	IMP	20463223
GO:0030307	Process	Positive regulation of cell growth	IMP	20463223
GO:0030425	Component	Dendrite	IEA
GO:0031175	Process	Neuron projection development	IMP	20463223
GO:0043083	Component	Synaptic cleft	IEA
GO:0043194	Component	Axon initial segment	IEA
GO:0045202	Component	Synapse	IEA
GO:0048018	Function	Receptor ligand activity	ISS
GO:0050806	Process	Positive regulation of synaptic transmission	IEA
GO:0050806	Process	Positive regulation of synaptic transmission	ISS
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099645	Process	Neurotransmitter receptor localization to postsynaptic specialization membrane	IEA

MIM	HGNC	e!Ensembl
604619	6572	ENSG00000108231

Protein

UniProt ID

O95970

Protein name

Leucine-rich glioma-inactivated protein 1 (Epitempin-1)

Protein 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

PDB

5Y2Z , 5Y30 , 5Y31 , 8HPY , 8HQ1 , 8HQ2 , 8Y6B

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13855	LRR_8	69 → 127	Leucine rich repeat	Repeat
PF13855	LRR_8	115 → 175	Leucine rich repeat	Repeat
PF03736	EPTP	225 → 266	EPTP domain	Repeat
PF03736	EPTP	271 → 312	EPTP domain	Repeat
PF03736	EPTP	317 → 363	EPTP domain	Repeat
PF03736	EPTP	366 → 414	EPTP domain	Repeat
PF03736	EPTP	419 → 461	EPTP domain	Repeat
PF03736	EPTP	464 → 505	EPTP domain	Repeat
PF03736	EPTP	510 → 550	EPTP domain	Repeat

Tissue specificity

TISSUE SPECIFICITY: Predominantly expressed in neural tissues, especially in brain. Expression is reduced in low-grade brain tumors and significantly reduced or absent in malignant gliomas. {ECO:0000269|PubMed:16518856}.; TISSUE SPECIFICITY: [Isoform 1]:

Sequence

MESERSKRMGNACIPLKRIAYFLCLLSALLLTEGKKPAKPKCPAVCTCTKDNALCENARS
IPRTVPPDVISLSFVRSGFTEISEGSFLFTPSLQLLLFTSNSFDVISDDAFIGLPHLEYL
FIENNNIKSISRHTFRGLKSLIHLSLANNNLQTLPKDIFKGLDSLTNVDLRGNSFNCDCK
LKWLVEWLGHTNATVEDIYCEGPPEYKKRKINSLSSKDFDCIITEFAKSQDLPYQSLSID
TFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDNITGTSTVVCKPIVIETQLYVIVA
QLFGGSHIYKRDSFANKFIKIQDIEILKIRKPNDIETFKIENNWYFVVADSSKAGFTTIY
KWNGNGFYSHQSLHAWYRDTDVEYLEIVRTPQTLRTPHLILSSSSQRPVIYQWNKATQLF
TNQTDIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKVMKWGGSSFQDIQRMPSRGSMVFQ
PLQINNYQYAILGSDYSFTQVYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASS
FKGNTQIYKHVIVDLSA

Sequence length

557

Interactions

View interactions

	Reactome
			LGI-ADAM interactions

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Epilepsy	Epilepsy, familial temporal lobe, 1	rs119488100, rs869025201, rs28937874, rs797044999, rs1589762127, rs104894166, rs797044998, rs28939075, rs1364913665, rs2134001459, rs104894167, rs119488099	N/A
Epilepsy With Auditory Features	autosomal dominant epilepsy with auditory features	rs119488099, rs1064794249, rs1554907787, rs1554907767, rs1564845068, rs797044999, rs1564851314, rs1589776148, rs104894166, rs1364913665, rs797044998, rs1060502054, rs1060502053	N/A
seizure	Seizure	rs797044999, rs886039496	N/A

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Aphasia	Associate	19064878
Autoimmune Diseases of the Nervous System	Associate	36621173, 37217310
Autosomal Dominant Lateral Temporal Lobe Epilepsy	Associate	12023020, 12446220, 15079011, 15660777, 15946341, 16707245, 18711109, 19064878, 19780791, 22323750, 24177143
Bohring syndrome	Associate	12023020
Brain Neoplasms	Associate	18575738
Developmental Disabilities	Associate	26993267
Drug Resistant Epilepsy	Associate	19552651
Encephalitis	Associate	30253786, 32849520, 35115410, 36973076, 37217310, 37644514
Epilepsies Partial	Associate	20659151, 31327507
Epilepsy	Associate	15660777, 15946341, 16707245, 19835947, 20863412, 21504429, 24177143, 31020005
Epilepsy Generalized	Associate	15079011
Epilepsy Idiopathic Generalized	Associate	15079011
Epilepsy Temporal Lobe	Associate	12023020, 14510822, 15009222, 19552651, 20863412, 21479274, 21504429, 22496201, 23621105, 25243798, 28633043, 29034879
Facial Asymmetry	Associate	30253786
Frontotemporal Dementia	Associate	19552651
Glioma	Inhibit	15047712
Glioma	Associate	19835947
Hearing Disorders	Associate	15079011, 19064878, 22323750
Immunologic Deficiency Syndromes	Associate	29788256
Limbic Encephalitis	Associate	29272336
Lipodystrophy Familial Partial	Associate	21479274
Neoplasm Metastasis	Inhibit	15047712
Neoplasm Metastasis	Associate	19835947
Neoplasms	Associate	19835947
Nerve Degeneration	Associate	33843981
Neurologic Manifestations	Associate	15660777
Paraneoplastic Syndromes Nervous System	Associate	33843981
Seizures	Associate	15009222, 15946341, 16707245, 19780791, 21504429, 29272336, 33453592
Status Epilepticus	Associate	19552651
Temporal epilepsy familial	Associate	15079011, 15660777
Warts	Associate	31892232

LGI1 (leucine rich glioma inactivated 1)