LINGO4

gene
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Summary

LINGO4 (leucine rich repeat and Ig domain containing 4, HGNC:31814) is a protein-coding gene on chromosome 1q21.3, encoding Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4 (Q6UY18).

Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space.

Source: NCBI Gene 339398 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 101 total
  • MANE Select transcript: NM_001004432

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:31814
Approved symbolLINGO4
Nameleucine rich repeat and Ig domain containing 4
Location1q21.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000213171
Ensembl biotypeprotein_coding
OMIM609794
Entrez339398

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000368820

RefSeq mRNA: 1 — MANE Select: NM_001004432 NM_001004432

CCDS: CCDS30855

Canonical transcript exons

ENST00000368820 — 2 exons

ExonStartEnd
ENSE00001448024151800264151802717
ENSE00001448025151805230151805419

Expression profiles

Bgee: expression breadth broad, 87 present calls, max score 90.13.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.13gold quality
gastrocnemiusUBERON:000138886.71gold quality
muscle of legUBERON:000138384.11gold quality
skeletal muscle tissueUBERON:000113480.56gold quality
hindlimb stylopod muscleUBERON:000425279.92gold quality
right hemisphere of cerebellumUBERON:001489071.39gold quality
cerebellumUBERON:000203771.13gold quality
cerebellar cortexUBERON:000212970.97gold quality
cerebellar hemisphereUBERON:000224570.90gold quality
muscle tissueUBERON:000238569.52gold quality
right uterine tubeUBERON:000130267.84gold quality
pituitary glandUBERON:000000757.47gold quality
islet of LangerhansUBERON:000000657.17gold quality
apex of heartUBERON:000209857.07gold quality
heart left ventricleUBERON:000208457.00gold quality
liverUBERON:000210755.98gold quality
right lobe of liverUBERON:000111455.90gold quality
olfactory segment of nasal mucosaUBERON:000538655.12gold quality
adenohypophysisUBERON:000219653.44gold quality
skin of legUBERON:000151151.60gold quality
pancreasUBERON:000126451.22gold quality
prostate glandUBERON:000236750.92gold quality
lymph nodeUBERON:000002949.44gold quality
thyroid glandUBERON:000204649.37gold quality
saliva-secreting glandUBERON:000104449.32gold quality
zone of skinUBERON:000001449.10gold quality
tonsilUBERON:000237248.88silver quality
heartUBERON:000094848.79gold quality
left lobe of thyroid glandUBERON:000112048.74gold quality
minor salivary glandUBERON:000183048.61gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting LINGO4, 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-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-391999.8769.452489
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-6762-3P99.6666.941188
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-486-5P99.5170.39707
HSA-MIR-65799.4866.02848
HSA-MIR-608199.4866.071446
HSA-MIR-468899.4864.68828
HSA-MIR-942-5P99.4168.401977
HSA-MIR-312599.1468.492269
HSA-MIR-125399.1267.081688
HSA-MIR-877-3P99.0968.101637
HSA-MIR-465199.0667.572002
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-391698.9968.042155
HSA-MIR-6859-5P98.9968.072049
HSA-MIR-143-5P98.9868.87946
HSA-MIR-60898.9367.832013
HSA-MIR-487A-5P98.8569.37993
HSA-MIR-487B-5P98.8569.48987
HSA-MIR-445198.8268.171455
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-449098.5168.47943
HSA-MIR-4722-5P98.4666.341611

Literature-anchored findings (GeneRIF, showing 1)

  • variants in coding region of the LINGO4 gene may play little or no role in the risk of Essential tremor susceptibility (PMID:22104011)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriolrtm2bENSDARG00000045811
danio_reriolingo3aENSDARG00000061970
danio_rerioENSDARG00000067815
danio_reriosi:dkey-182i3.11ENSDARG00000069270
danio_reriosi:dkey-1j5.4ENSDARG00000073747
danio_reriowu:fc23c09ENSDARG00000088002
mus_musculusLingo4ENSMUSG00000044505
rattus_norvegicusLingo4ENSRNOG00000022863
drosophila_melanogasterCG5819FBGN0034717
drosophila_melanogasterCG4781FBGN0035043
caenorhabditis_elegansWBGENE00006366

Paralogs (10): EPYC (ENSG00000083782), OGN (ENSG00000106809), ECM2 (ENSG00000106823), FMOD (ENSG00000122176), OMG (ENSG00000126861), OMD (ENSG00000127083), LUM (ENSG00000139329), KERA (ENSG00000139330), PRELP (ENSG00000188783), LINGO3 (ENSG00000220008)

Protein

Protein identifiers

Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4Q6UY18 (reviewed: Q6UY18)

Alternative names: Leucine-rich repeat neuronal protein 6D

All UniProt accessions (1): Q6UY18

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001004432* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000372LRRNTDomain
IPR000483Cys-rich_flank_reg_CDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013098Ig_I-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR032675LRR_dom_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050467LRFNFamily

Pfam: PF07679, PF13855

UniProt features (26 total): repeat 11, glycosylation site 6, domain 3, topological domain 2, signal peptide 1, chain 1, disulfide bond 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UY18-F185.700.70

Functional residue map

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

Disulfide bonds (1): 435–484

Glycosylation sites (6): 191, 253, 263, 492, 508, 515

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GOBP_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, chr1q21

GO Biological Process (1): positive regulation of synapse assembly (GO:0051965)

GO Molecular Function (2): signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
synapse assembly1
positive regulation of nervous system development1
regulation of synapse assembly1
positive regulation of cell junction assembly1
molecular transducer activity1
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LINGO4THEM5Q8N1Q8495
LINGO4HS1BP3Q53T59452
LINGO4CRCT1Q9UGL9440
LINGO4TCHHL1Q5QJ38405
LINGO4CENPPQ6IPU0373
LINGO4STK32BQ9NY57365
LINGO4CRNNQ9UBG3348
LINGO4RPTNQ6XPR3341
LINGO4INTS3Q68E01333
LINGO4PGLYRP4Q96LB8331
LINGO4BNIPLQ7Z465328
LINGO4GIGYF1O75420323
LINGO4RIT2Q99578306
LINGO4ADAT3Q96EY9305
LINGO4OGNP20774302

IntAct

2 interactions, top by confidence:

ABTypeScore
Mpsi-mi:“MI:0914”(association)0.350

BioGRID (2): LINGO4 (Proximity Label-MS), LINGO4 (Proximity Label-MS)

ESM2 similar proteins: A1A4H9, A2ARI4, A2VDH3, A6H793, D4A6D8, E9Q7T7, F1MLX5, F1MT22, O75325, P59034, P59035, Q13641, Q149C3, Q3URE9, Q3UVD5, Q3UY51, Q4KLL3, Q4R8Y9, Q50LG9, Q5M8M9, Q5PQV5, Q5R6B1, Q5RDJ4, Q5VT99, Q6GQU6, Q6UY18, Q6ZSA7, Q7M6Z0, Q7TQ62, Q80WD1, Q86UE6, Q86UN2, Q86UN3, Q86WK6, Q8BHA1, Q8K0S5, Q8K377, Q8N7C0, Q91ZV8, Q96FE5

Diamond homologs: A0N0X6, A1KZ92, A2A8L5, A3KNN3, A4IFW2, A4IGL7, A4IIW9, A6H793, A7MBJ4, A8WGA3, B0BNK7, B0V2N1, B3MH43, B3NS99, B4GBH0, B4HNW4, B4KPU0, B4MR28, B4P5Q9, B4QC63, D2HFT7, D3YXG0, D4A1J9, D4ABX8, E9Q7T7, F1MLX5, F1NWE3, F1NY98, O55005, O60469, O75325, O89026, O94779, O95428, P0C6S8, P0C7J6, P10586, P16621, P59034, P59035

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance96
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

294 predictions. Top by Δscore:

VariantEffectΔscore
1:151805223:CACTT:Cdonor_loss0.9800
1:151805224:ACTTA:Adonor_loss0.9800
1:151805225:CTTA:Cdonor_loss0.9800
1:151805226:TTA:Tdonor_loss0.9800
1:151805227:TACCG:Tdonor_loss0.9800
1:151805228:A:ACdonor_gain0.9800
1:151805228:A:ATdonor_loss0.9800
1:151805229:C:CCdonor_gain0.9800
1:151802793:T:Cacceptor_gain0.9300
1:151805229:CCG:Cdonor_gain0.8700
1:151805228:AC:Adonor_gain0.8500
1:151805229:CC:Cdonor_gain0.8500
1:151805222:GCACT:Gdonor_loss0.8300
1:151805229:CCGGA:Cdonor_gain0.7900
1:151802785:GGCCC:Gacceptor_gain0.7600
1:151802787:CCCTT:Cacceptor_gain0.7300
1:151802788:CCTTC:Cacceptor_gain0.7300
1:151805229:CCGG:Cdonor_gain0.7300
1:151802793:T:TCacceptor_gain0.7100
1:151802793:T:TGacceptor_gain0.7100
1:151802585:C:Aacceptor_gain0.7000
1:151802630:TCCAG:Tacceptor_gain0.7000
1:151802442:T:TAdonor_gain0.6700
1:151802789:CTTCT:Cacceptor_gain0.6600
1:151802790:TTCTT:Tacceptor_gain0.6600
1:151802565:C:Aacceptor_gain0.6300
1:151802789:CTT:Cacceptor_gain0.6300
1:151805326:C:Adonor_gain0.6200
1:151802819:T:Aacceptor_gain0.6000
1:151802791:T:Gacceptor_gain0.5900

AlphaMissense

3784 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:151801364:C:AW447C0.998
1:151801364:C:GW447C0.998
1:151801254:C:GC484S0.996
1:151801255:A:TC484S0.996
1:151801241:A:CN488K0.995
1:151801241:A:TN488K0.995
1:151801253:A:CC484W0.994
1:151801255:A:GC484R0.994
1:151801254:C:TC484Y0.993
1:151801631:G:CN358K0.993
1:151801631:G:TN358K0.993
1:151801703:G:CN334K0.993
1:151801703:G:TN334K0.993
1:151802280:T:AN142I0.993
1:151801209:A:GL499P0.992
1:151801847:A:CN286K0.992
1:151801847:A:TN286K0.992
1:151802423:G:CN94K0.992
1:151802423:G:TN94K0.992
1:151801242:T:AN488I0.991
1:151801261:A:CY482D0.991
1:151801299:A:GL469P0.991
1:151801366:A:GW447R0.991
1:151801366:A:TW447R0.991
1:151801401:C:GC435S0.991
1:151801402:A:TC435S0.991
1:151801704:T:AN334I0.991
1:151801857:A:GL283P0.991
1:151802424:T:AN94I0.991
1:151801791:A:GL305P0.990

dbSNP variants (sampled 300 via entrez): RS1001398538 (1:151805067 T>A), RS1001899209 (1:151800404 T>C), RS1002271177 (1:151804374 G>A,C,T), RS1002353033 (1:151799998 G>A), RS1002436952 (1:151806300 T>C), RS1004887199 (1:151799877 C>A), RS1005006403 (1:151806400 G>A,C,T), RS1005802102 (1:151803178 A>G), RS1005999733 (1:151804812 G>C), RS1006073054 (1:151803591 T>G), RS1007818480 (1:151805342 C>A,G), RS1008099961 (1:151805740 C>T), RS1008966534 (1:151806698 G>A), RS1009071032 (1:151800135 C>T), RS1009094370 (1:151800725 C>T)

Disease associations

OMIM: gene MIM:609794 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorderStrongAutosomal recessive

Mondo (2): polymicrogyria (MONDO:0000087), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): Polymicrogyria (Orphanet:35981)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST005195_138Coronary artery disease3.000000e-11
GCST008916_130Asthma1.000000e-12
GCST008916_88Asthma1.000000e-25
GCST010866_19Coronary artery disease5.000000e-12
GCST90002383_333Hematocrit7.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004348hematocrit

MeSH disease descriptors (2)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625
D065706PolymicrogyriaC10.500.507.500.500; C16.131.666.507.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation2
lasiocarpinedecreases expression1
methyleugenoldecreases expression1
CGP 52608affects binding, increases reaction1
Rosiglitazonedecreases expression1
Leflunomideincreases expression1
Vehicle Emissionsdecreases methylation1
N-Nitrosopyrrolidinedecreases expression1
Valproic Aciddecreases methylation1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedACTIVE_NOT_RECRUITINGEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928Not specifiedCOMPLETEDClinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489Not specifiedUNKNOWNStudy for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice
  • Associated diseases: neurodevelopmental disorder
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): polymicrogyria