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LGI4

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Summary

LGI4 (leucine rich repeat LGI family member 4, HGNC:18712) is a protein-coding gene on chromosome 19q13.12, encoding Leucine-rich repeat LGI family member 4 (Q8N135). Component of Schwann cell signaling pathway(s) that controls axon segregation and myelin formation.

Involved in regulation of myelination. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Implicated in arthrogryposis multiplex congenita-1 and childhood absence epilepsy.

Source: NCBI Gene 163175 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): arthrogryposis multiplex congenita 1, neurogenic, with myelin defect (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 1
  • Clinical variants (ClinVar): 157 total — 8 pathogenic, 10 likely-pathogenic
  • Phenotypes (HPO): 35
  • MANE Select transcript: NM_139284

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18712
Approved symbolLGI4
Nameleucine rich repeat LGI family member 4
Location19q13.12
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000153902
Ensembl biotypeprotein_coding
OMIM608303
Entrez163175

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000310123, ENST00000392225, ENST00000473160, ENST00000493050, ENST00000587780, ENST00000591633, ENST00000591840, ENST00000592346, ENST00000593248, ENST00000874487, ENST00000874488, ENST00000874489

RefSeq mRNA: 1 — MANE Select: NM_139284 NM_139284

CCDS: CCDS12444

Canonical transcript exons

ENST00000310123 — 9 exons

ExonStartEnd
ENSE000034770723513369335133764
ENSE000035151073513197135132042
ENSE000035463003512685335127017
ENSE000035571143513178935131860
ENSE000035605723512627035126775
ENSE000035723453513138635131555
ENSE000036319053512451335125507
ENSE000036602573513403335134104
ENSE000038490413513451135135059

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 99.55.

FANTOM5 (CAGE): breadth broad, TPM avg 17.1284 / max 6187.2534, expressed in 418 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
18048613.3450381
1804872.8238256
1804880.5003187
1804850.304391
1804840.093155
2087800.061829

Top tissues by expression

247 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
peripheral nervous systemUBERON:000001099.55gold quality
nerveUBERON:000102199.55gold quality
tibial nerveUBERON:000132399.55gold quality
sural nerveUBERON:001548898.67gold quality
endocervixUBERON:000045897.67gold quality
muscle layer of sigmoid colonUBERON:003580597.32gold quality
lower esophagus muscularis layerUBERON:003583396.98gold quality
lower esophagusUBERON:001347396.93gold quality
esophagogastric junction muscularis propriaUBERON:003584196.65gold quality
mucosa of stomachUBERON:000119996.50gold quality
right frontal lobeUBERON:000281096.30gold quality
C1 segment of cervical spinal cordUBERON:000646996.26gold quality
left uterine tubeUBERON:000130395.78gold quality
ectocervixUBERON:001224995.65gold quality
Brodmann (1909) area 9UBERON:001354095.64gold quality
anterior cingulate cortexUBERON:000983595.35gold quality
spinal cordUBERON:000224095.25gold quality
amygdalaUBERON:000187694.82gold quality
subcutaneous adipose tissueUBERON:000219094.41gold quality
tibial arteryUBERON:000761094.37gold quality
popliteal arteryUBERON:000225094.36gold quality
transverse colonUBERON:000115793.89gold quality
putamenUBERON:000187493.84gold quality
right atrium auricular regionUBERON:000663193.69gold quality
nucleus accumbensUBERON:000188293.59gold quality
right coronary arteryUBERON:000162593.52gold quality
caudate nucleusUBERON:000187393.50gold quality
body of uterusUBERON:000985393.47gold quality
cardiac atriumUBERON:000208193.14gold quality
left coronary arteryUBERON:000162692.91gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-GEOD-135922yes1144.09
E-MTAB-10287yes57.06
E-HCAD-11yes39.06
E-MTAB-8410yes31.84
E-CURD-46yes15.69
E-ANND-3yes11.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting LGI4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-365899.9673.874379
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-19898.7067.32920
HSA-MIR-219B-5P97.9165.80531
HSA-MIR-64797.7367.79927
HSA-MIR-6802-3P97.2965.42613
HSA-MIR-1250-5P94.3264.7478
HSA-MIR-319794.0263.4785

Literature-anchored findings (GeneRIF, showing 7)

  • has seven copies of the EPTP repeat, a unifying protein sequence motif of a heterogenous group of proteins linked to epileptic diseases. The EPTP repeat probably forms a beta-propeller structure. (PMID:12217514)
  • Screening of the LGI4 coding region in BFIC and childhood absence epilepsy (CAE) revealed several frequent exonic polymorphisms. (PMID:14505228)
  • The positive genotypic association between benign familial infantile convulsions (BFIC)and c.1722G/A polymorphism suggests that LGI4 might contribute to the susceptibility to BFIC. (PMID:19815358)
  • Schwann cells are the principal cellular source of Lgi4 in the developing nerve; transgenic Lgi4 binds directly to Adam22 without a requirement for additional membrane associated factors. (PMID:20220021)
  • Intratumoral heterogeneity of ADAM23 promotes tumor growth and metastasis through LGI4 and nitric oxide signals. (PMID:24662834)
  • in four unrelated multiplex families presenting with severe arthrogryposis multiplex congenital, identified biallelic loss-of-function mutations in LGI4; functional tests showed these germline mutations caused aberrant splicing of the endogenous LGI4 transcript and in a cell-based assay impaired the secretion of truncated LGI4 protein (PMID:28318499)
  • Characterizing the molecular etiology of arthrogryposis multiplex congenita in patients with LGI4 mutations. (PMID:34288120)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriolgi1aENSDARG00000020493
danio_reriolgi1bENSDARG00000058421
danio_reriosi:ch211-191d15.2ENSDARG00000092834
mus_musculusLgi4ENSMUSG00000036560
rattus_norvegicusLgi4ENSRNOG00000021087
drosophila_melanogasterConFBGN0005775
drosophila_melanogasterkek3FBGN0028370
drosophila_melanogasterCG18095FBGN0028872
drosophila_melanogasterCG7509FBGN0035575
caenorhabditis_eleganslron-9WBGENE00011971
caenorhabditis_elegansWBGENE00020649
caenorhabditis_elegansWBGENE00022789

Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LRIG3 (ENSG00000139263), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRRTM2 (ENSG00000146006), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRIT3 (ENSG00000183423), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), ELFN1 (ENSG00000225968), LRRC24 (ENSG00000254402), TRIL (ENSG00000255690)

Protein

Protein identifiers

Leucine-rich repeat LGI family member 4 — Q8N135 (reviewed: Q8N135)

Alternative names: LGI1-like protein 3, Leucine-rich glioma-inactivated protein 4

All UniProt accessions (3): Q8N135, A8MVC2, K7ENQ0

UniProt curated annotations — full annotation on UniProt →

Function. Component of Schwann cell signaling pathway(s) that controls axon segregation and myelin formation.

Subunit / interactions. Can bind to ADAM11, ADAM22 and ADAM23.

Subcellular location. Secreted.

Tissue specificity. Widely expressed, with highest expression in brain.

Disease relevance. Arthrogryposis multiplex congenita 1, neurogenic, with myelin defect (AMC1) [MIM:617468] A form of arthrogryposis multiplex congenita, a developmental condition characterized by multiple joint contractures resulting from reduced or absent fetal movements. AMC1 is an autosomal recessive severe form with onset in utero. Most affected individuals die in utero. Those who survive have generalized contractures and hypotonia. The disorder is caused by a neurogenic defect and poor or absent myelin formation around peripheral nerves rather than by a muscular defect. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N135-11yes
Q8N135-22

RefSeq proteins (1): NP_644813* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000483Cys-rich_flank_reg_CDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR005492EPTPRepeat
IPR009039EARRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR051295LGI_relatedFamily

Pfam: PF03736, PF13855

UniProt features (20 total): repeat 11, sequence variant 3, splice variant 2, signal peptide 1, chain 1, glycosylation site 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N135-F192.800.88

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 177

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-5682910LGI-ADAM interactions
R-HSA-1266738Developmental Biology

MSigDB gene sets: 186 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_BEHAVIOR, GOBP_NEURON_MATURATION, GOBP_ADULT_BEHAVIOR, GOBP_GLIAL_CELL_DEVELOPMENT, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_MYELINATION, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_ADULT_LOCOMOTORY_BEHAVIOR, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, COUP_01, GOBP_ANATOMICAL_STRUCTURE_MATURATION, GOBP_ENSHEATHMENT_OF_NEURONS, GOBP_CELL_MATURATION

GO Biological Process (9): adult locomotory behavior (GO:0008344), glial cell proliferation (GO:0014009), myelination in peripheral nervous system (GO:0022011), regulation of myelination (GO:0031641), neuron maturation (GO:0042551), Schwann cell development (GO:0014044), glial cell development (GO:0021782), gliogenesis (GO:0042063), myelination (GO:0042552)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
myelination2
locomotory behavior1
adult behavior1
cell population proliferation1
gliogenesis1
Schwann cell development1
peripheral nervous system axon ensheathment1
regulation of cellular process1
regulation of nervous system development1
cell maturation1
neuron development1
Schwann cell differentiation1
glial cell development1
glial cell differentiation1
cell development1
neurogenesis1
axon ensheathment1
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

878 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LGI4ADAM22Q9P0K1886
LGI4ADAM23O75077590
LGI4ADGRG6Q86SQ4444
LGI4DLG2Q15700442
LGI4EFHC2Q5JST6435
LGI4ADAM28Q9UKQ2431
LGI4LGI2Q8N0V4411
LGI4ADAM11O75078401
LGI4LGI1O95970381
LGI4EFHC1Q5JVL4376
LGI4PLEKHG2Q9H7P9366
LGI4MECRQ9BV79360
LGI4CNTNAP1P78357360
LGI4POU3F1Q03052360
LGI4GJC3Q8NFK1360

IntAct

0 interactions, top by confidence:

BioGRID (1): LGI4 (Synthetic Growth Defect)

ESM2 similar proteins: A0JND9, D3YTS9, O19058, O35795, O55026, O75173, P08648, P11117, P17405, P20611, P21217, P24638, P29376, P56433, Q04519, Q0P5F0, Q0V8G3, Q0VD19, Q11128, Q11131, Q32M88, Q4R5N9, Q4R942, Q5MY95, Q5NVF6, Q5RFQ8, Q62994, Q63148, Q6IY74, Q8BH73, Q8HYJ3, Q8HYJ4, Q8HYJ5, Q8HYJ7, Q8HZR3, Q8K1S1, Q8N135, Q923W9, Q9BZG2, Q9H3T2

Diamond homologs: O95970, P24014, Q1EGL0, Q1EGL1, Q1EGL2, Q4R4H3, Q5E9T6, Q5R945, Q6EMK4, Q8K1S1, Q8K406, Q8K4Y5, Q8K4Z0, Q8N0V4, Q8N135, Q8N145, Q9CZT5, Q9JIA1, Q9WVC1, P70193, O88279, Q80TR4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

157 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic8
Likely pathogenic10
Uncertain significance84
Likely benign21
Benign28

Top pathogenic / likely-pathogenic (18)

Variant IDHGVSClassification
424865NM_139284.3(LGI4):c.793G>A (p.Ala265Thr)Pathogenic
424866NM_139284.3(LGI4):c.863G>A (p.Trp288Ter)Pathogenic
424867NM_139284.3(LGI4):c.793+5G>CPathogenic
424868NM_139284.3(LGI4):c.1301T>A (p.Val434Asp)Pathogenic
424869NM_139284.3(LGI4):c.1299+5G>TPathogenic
424870NM_139284.3(LGI4):c.773G>C (p.Arg258Pro)Pathogenic
549679NM_139284.3(LGI4):c.1153C>T (p.Gln385Ter)Pathogenic
585241NM_139284.3(LGI4):c.2T>C (p.Met1Thr)Pathogenic
1252057NM_139284.3(LGI4):c.961G>A (p.Glu321Lys)Likely pathogenic
2441163NM_139284.3(LGI4):c.312C>A (p.Tyr104Ter)Likely pathogenic
2444227NM_139284.3(LGI4):c.774_778dup (p.Glu260fs)Likely pathogenic
4845822NM_139284.3(LGI4):c.869dup (p.Ser291fs)Likely pathogenic
524105NM_139284.3(LGI4):c.830del (p.Gly277fs)Likely pathogenic
549680NM_139284.3(LGI4):c.200T>G (p.Leu67Arg)Likely pathogenic
692278NM_139284.3(LGI4):c.1031T>A (p.Leu344Gln)Likely pathogenic
800799NM_139284.3(LGI4):c.834del (p.Ser279fs)Likely pathogenic
974840NM_139284.3(LGI4):c.1272C>A (p.Cys424Ter)Likely pathogenic
974841NM_139284.3(LGI4):c.263_265del (p.Phe88del)Likely pathogenic

SpliceAI

2465 predictions. Top by Δscore:

VariantEffectΔscore
19:35126864:T:TAdonor_gain1.0000
19:35127013:CAGCT:Cacceptor_gain1.0000
19:35127014:AGCT:Aacceptor_gain1.0000
19:35127015:GCT:Gacceptor_gain1.0000
19:35127016:CT:Cacceptor_gain1.0000
19:35127016:CTC:Cacceptor_gain1.0000
19:35127017:TC:Tacceptor_loss1.0000
19:35127017:TCT:Tacceptor_gain1.0000
19:35127018:C:Aacceptor_gain1.0000
19:35127018:C:CAacceptor_loss1.0000
19:35127018:C:CCacceptor_gain1.0000
19:35131788:CA:Cdonor_gain1.0000
19:35133994:C:CAdonor_gain1.0000
19:35141108:C:Gacceptor_gain1.0000
19:35141115:T:TAacceptor_gain1.0000
19:35141120:T:TAacceptor_gain1.0000
19:35141123:T:TAacceptor_gain1.0000
19:35141127:CACAG:Cacceptor_loss1.0000
19:35141128:ACAGA:Aacceptor_loss1.0000
19:35141129:C:Gacceptor_gain1.0000
19:35141130:A:AGacceptor_gain1.0000
19:35141131:G:GGacceptor_gain1.0000
19:35141131:GAC:Gacceptor_gain1.0000
19:35141202:GC:Gdonor_gain1.0000
19:35141202:GCTGA:Gdonor_gain1.0000
19:35141203:C:Gdonor_gain1.0000
19:35141204:TGA:Tdonor_gain1.0000
19:35141205:GA:Gdonor_gain1.0000
19:35141205:GAG:Gdonor_gain1.0000
19:35141206:AG:Adonor_loss1.0000

AlphaMissense

3443 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:35131971:A:GL129P0.998
19:35132039:G:CF106L0.998
19:35132039:G:TF106L0.998
19:35132040:A:CF106C0.998
19:35132041:A:GF106L0.998
19:35125379:G:CS476R0.997
19:35125379:G:TS476R0.997
19:35125381:T:GS476R0.997
19:35131857:G:CS130R0.997
19:35131857:G:TS130R0.997
19:35131859:T:GS130R0.997
19:35133693:A:GL105P0.997
19:35125482:A:GF442S0.996
19:35126299:A:GC424R0.996
19:35131510:C:AW168C0.996
19:35131510:C:GW168C0.996
19:35131845:G:CN134K0.996
19:35131845:G:TN134K0.996
19:35133720:A:CF96C0.996
19:35133720:A:GF96S0.996
19:35126486:C:AW361C0.995
19:35126486:C:GW361C0.995
19:35131540:G:CN158K0.995
19:35131540:G:TN158K0.995
19:35131855:A:GL131P0.995
19:35134033:A:GL81P0.995
19:35125496:C:AW437C0.994
19:35125496:C:GW437C0.994
19:35126297:G:CC424W0.994
19:35131980:A:TL126H0.994

dbSNP variants (sampled 300 via entrez): RS1000170996 (19:35134398 C>A), RS1000219608 (19:35128627 C>T), RS1000253211 (19:35124699 G>A), RS1000357117 (19:35129765 G>A,T), RS1000368540 (19:35130103 C>G,T), RS1000550566 (19:35129924 G>A,T), RS1000603176 (19:35130200 C>T), RS1000616306 (19:35135412 G>A,T), RS1000687788 (19:35128581 T>C), RS1000857292 (19:35134117 G>A), RS1000911485 (19:35135368 T>C), RS1001054745 (19:35124967 G>C), RS1001546442 (19:35125124 A>G), RS1002268951 (19:35133230 T>G), RS1002623006 (19:35132943 T>A)

Disease associations

OMIM: gene MIM:608303 | disease phenotypes: MIM:617468, MIM:208100, MIM:208150

GenCC curated gene-disease

DiseaseClassificationInheritance
arthrogryposis multiplex congenita 1, neurogenic, with myelin defectStrongAutosomal recessive
hypomyelination neuropathy-arthrogryposis syndromeSupportiveAutosomal recessive

Mondo (5): arthrogryposis multiplex congenita 1, neurogenic, with myelin defect (MONDO:0060486), arthrogryposis multiplex congenita 2, neurogenic type (MONDO:0008823), arthrogryposis multiplex congenita (MONDO:0015168), fetal akinesia deformation sequence 1 (MONDO:0100101), (MONDO:0017049)

Orphanet (3): Neurogenic arthrogryposis multiplex congenita (Orphanet:1143), Arthrogryposis multiplex congenita (Orphanet:1037), Fetal akinesia deformation sequence (Orphanet:994)

HPO phenotypes

35 total (30 of 35 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000218High palate
HP:0000278Retrognathia
HP:0000341Narrow forehead
HP:0000347Micrognathia
HP:0000411Protruding ear
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000565Esotropia
HP:0000678Dental crowding
HP:0001252Hypotonia
HP:0001284Areflexia
HP:0001315Reduced tendon reflexes
HP:0001371Flexion contracture
HP:0001376Limitation of joint mobility
HP:0001558Decreased fetal movement
HP:0001762Talipes equinovarus
HP:0001989Fetal akinesia sequence
HP:0002069Bilateral tonic-clonic seizure
HP:0002089Pulmonary hypoplasia
HP:0002098Respiratory distress
HP:0002384Focal impaired awareness seizure
HP:0002421Poor head control
HP:0002804Arthrogryposis multiplex congenita
HP:0002987Elbow flexion contracture
HP:0003273Hip contracture
HP:0003457EMG abnormality
HP:0003691Scapular winging
HP:0003826Stillbirth
HP:0005684Distal arthrogryposis

GWAS associations

1 associations (top):

StudyTraitp-value
GCST012335_24Hodgkin’s lymphoma3.000000e-11

MeSH disease descriptors (1)

DescriptorNameTree numbers
C536614Arthrogryposis multiplex congenita neurogenic type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenincreases expression2
Tobacco Smoke Pollutionincreases expression2
aristolochic acid Iincreases expression1
bisphenol Aincreases methylation1
butyraldehydeincreases expression1
obeticholic acidincreases expression1
clothianidinincreases expression1
licochalcone Bincreases expression1
Sunitinibdecreases expression1
Nickeldecreases expression1
Triclosandecreases expression1
Antirheumatic Agentsincreases expression1
Palmitic Acidincreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

4 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05393375Not specifiedCOMPLETEDArthrogryposis Multiplex Congenita in Pediatric Age: Correlation Between MUScular MRI and Functional Evaluation
NCT05673265Not specifiedUNKNOWNPediatric and Adult Registry for Patients With ARThrogryposis
NCT06130592Not specifiedUNKNOWNTechnical Feasibility Study of Ultrasound Muscle Imaging in Antenatal Ultrasound
NCT07360574Not specifiedNOT_YET_RECRUITINGPiezo2-related Arthrogryposis & physiopathOLOgy 3

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

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This page pulls from 75 datasets indexed by BioBTree:

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