LRRTM4

gene
On this page

Also known as FLJ12568

Summary

LRRTM4 (leucine rich repeat transmembrane neuronal 4, HGNC:19411) is a protein-coding gene on chromosome 2p12, encoding Leucine-rich repeat transmembrane neuronal protein 4 (Q86VH4). May play a role in the development and maintenance of the vertebrate nervous system.

Predicted to enable heparan sulfate proteoglycan binding activity. Predicted to be involved in regulation of synapse assembly. Predicted to act upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Predicted to be located in postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in several cellular components, including GABA-ergic synapse; photoreceptor ribbon synapse; and postsynaptic density membrane.

Source: NCBI Gene 80059 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 83 total
  • MANE Select transcript: NM_001134745

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19411
Approved symbolLRRTM4
Nameleucine rich repeat transmembrane neuronal 4
Location2p12
Locus typegene with protein product
StatusApproved
AliasesFLJ12568
Ensembl geneENSG00000176204
Ensembl biotypeprotein_coding
OMIM610870
Entrez80059

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000409088, ENST00000409093, ENST00000409282, ENST00000409884, ENST00000409911, ENST00000456154, ENST00000491242

RefSeq mRNA: 5 — MANE Select: NM_001134745 NM_001134745, NM_001282924, NM_001282928, NM_001330370, NM_024993

CCDS: CCDS46346, CCDS46347, CCDS74530, CCDS82475

Canonical transcript exons

ENST00000409884 — 4 exons

ExonStartEnd
ENSE000015855047752166877521818
ENSE000015883127674768576748916
ENSE000015883367752210977522376
ENSE000015896067751831877519864

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 97.42.

FANTOM5 (CAGE): breadth broad, TPM avg 3.4776 / max 401.9012, expressed in 295 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
293011.3577166
293000.7558156
292980.4692142
292990.3989121
292960.2985104
293020.144269
292970.02709
292920.02047
292930.00402
292940.00191

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065597.42gold quality
oocyteCL:000002390.12gold quality
cortical plateUBERON:000534388.90gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.58gold quality
prefrontal cortexUBERON:000045181.28gold quality
dorsolateral prefrontal cortexUBERON:000983479.19gold quality
ganglionic eminenceUBERON:000402378.31gold quality
frontal cortexUBERON:000187077.86gold quality
neocortexUBERON:000195077.54gold quality
Brodmann (1909) area 9UBERON:001354076.38gold quality
ventricular zoneUBERON:000305376.24gold quality
right frontal lobeUBERON:000281075.71gold quality
anterior cingulate cortexUBERON:000983575.68gold quality
primary visual cortexUBERON:000243675.59gold quality
cingulate cortexUBERON:000302775.58gold quality
middle temporal gyrusUBERON:000277175.33silver quality
cerebral cortexUBERON:000095675.26gold quality
Brodmann (1909) area 23UBERON:001355474.77gold quality
occipital lobeUBERON:000202173.34gold quality
superior frontal gyrusUBERON:000266173.26gold quality
telencephalonUBERON:000189372.57gold quality
buccal mucosa cellCL:000233672.50silver quality
postcentral gyrusUBERON:000258171.47gold quality
forebrainUBERON:000189070.45gold quality
parietal lobeUBERON:000187270.41silver quality
nucleus accumbensUBERON:000188269.49gold quality
orbitofrontal cortexUBERON:000416769.31silver quality
caudate nucleusUBERON:000187368.88gold quality
Brodmann (1909) area 46UBERON:000648368.73silver quality
temporal lobeUBERON:000187168.43gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-35yes7602.48
E-HCAD-25yes5311.07
E-GEOD-180759yes4129.24
E-ANND-3yes3.99
E-HCAD-30no6078.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting LRRTM4, 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-3613-3P100.0076.367965
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-1252-5P100.0069.802774
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4682100.0068.891258
HSA-MIR-4533100.0069.482758
HSA-MIR-4455100.0065.481587
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5692A100.0074.406850
HSA-MIR-607799.9968.042299
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-570-3P99.9672.414910
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-651-3P99.9473.485177
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-381-3P99.9371.872854
HSA-MIR-205-3P99.9269.923165
HSA-MIR-30099.9271.762856
HSA-MIR-10527-5P99.9172.283754

Literature-anchored findings (GeneRIF, showing 2)

  • Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. (PMID:31854516)
  • LRRTM4 Terminal Exon Duplicated in Family with Tourette Syndrome, Autism and ADHD. (PMID:35052406)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioLRRTM4ENSDARG00000078839
danio_reriolrrtm4l1ENSDARG00000080015
danio_reriolrrtm4l2ENSDARG00000099386
danio_rerioLRRTM4ENSDARG00000106522
mus_musculusLrrtm4ENSMUSG00000052581
rattus_norvegicusLrrtm4ENSRNOG00000021938

Paralogs (22): DCN (ENSG00000011465), RTN4R (ENSG00000040608), ASPN (ENSG00000106819), FLRT3 (ENSG00000125848), FLRT1 (ENSG00000126500), LRRC4 (ENSG00000128594), LRRC4B (ENSG00000131409), PODNL1 (ENSG00000132000), LRTM1 (ENSG00000144771), LRRC4C (ENSG00000148948), LRRTM1 (ENSG00000162951), LRRC15 (ENSG00000172061), PODN (ENSG00000174348), BGN (ENSG00000182492), LRRC19 (ENSG00000184434), FLRT2 (ENSG00000185070), GP1BA (ENSG00000185245), RTN4RL1 (ENSG00000185924), RTN4RL2 (ENSG00000186907), NYX (ENSG00000188937), LRRC66 (ENSG00000188993), LRRTM3 (ENSG00000198739)

Protein

Protein identifiers

Leucine-rich repeat transmembrane neuronal protein 4Q86VH4 (reviewed: Q86VH4)

All UniProt accessions (4): B8ZZ84, C9JM64, Q86VH4, Q4KMX1

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the development and maintenance of the vertebrate nervous system. Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation.

Subunit / interactions. Peripherally associated with AMPAR complex. AMPAR complex consists of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complex is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents, including LRRTM4. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complex and profoundly impact their biogenesis and protein processing.

Subcellular location. Cell membrane. Postsynaptic cell membrane.

Tissue specificity. Expressed in neuronal tissues.

Similarity. Belongs to the LRRTM family.

Isoforms (2)

UniProt IDNamesCanonical?
Q86VH4-11yes
Q86VH4-22

RefSeq proteins (5): NP_001128217, NP_001269853, NP_001269857, NP_001317299, NP_079269 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR050333SLRPFamily

Pfam: PF13855

UniProt features (22 total): repeat 10, glycosylation site 3, domain 2, topological domain 2, splice variant 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86VH4-F174.450.55

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 (3): 58, 126, 291

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6794361Neurexins and neuroligins
R-HSA-112316Neuronal System
R-HSA-6794362Protein-protein interactions at synapses

MSigDB gene sets: 148 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, 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, GGGTGGRR_PAX4_03, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, ATGTTAA_MIR302C, SRF_Q5_01, IRF7_01, CEBP_Q2, NKX62_Q2, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION

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 (4): plasma membrane (GO:0005886), postsynaptic membrane (GO:0045211), membrane (GO:0016020), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Protein-protein interactions at synapses1
Neuronal System1

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
synaptic membrane1
postsynapse1
cellular anatomical structure1
cell junction1

Protein interactions and networks

STRING

1630 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRRTM4GPC4O75487947
LRRTM4CNPY2Q9Y2B0854
LRRTM4PTPRSQ13332853
LRRTM4CTNNA2P26232822
LRRTM4GPC1P35052722
LRRTM4TRAPPC10P48553636
LRRTM4GPC3P51654583
LRRTM4NRXN1Q9ULB1554
LRRTM4NRXN2Q9P2S2529
LRRTM4CPQQ9Y646491
LRRTM4CCDC167Q9P0B6489
LRRTM4ARFGEF3Q5TH69479
LRRTM4LLPHQ9BRT6460
LRRTM4RFX8Q6ZV50457
LRRTM4NLGN2Q8NFZ4449

IntAct

9 interactions, top by confidence:

ABTypeScore
LRRTM4AP3B1psi-mi:“MI:0914”(association)0.530
LRRTM4SGPL1psi-mi:“MI:0914”(association)0.530
LRRTM4Dlg4psi-mi:“MI:0407”(direct interaction)0.440
SCRIBCHD2psi-mi:“MI:0914”(association)0.350
ZNF426ABLIM3psi-mi:“MI:0914”(association)0.350
PILRANID2psi-mi:“MI:0914”(association)0.350
LRRTM3URB1psi-mi:“MI:0914”(association)0.350

BioGRID (32): LRRTM4 (Affinity Capture-MS), LRRTM4 (Affinity Capture-MS), LRRTM4 (Affinity Capture-MS), LRRTM4 (Affinity Capture-Western), LRRTM4 (Proximity Label-MS), LRRTM4 (Affinity Capture-RNA), LRRTM4 (Affinity Capture-RNA), CDK11B (Affinity Capture-MS), AFF4 (Affinity Capture-MS), CNPY4 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CXXC1 (Affinity Capture-MS), CENPB (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), BLK (Affinity Capture-MS)

ESM2 similar proteins: A0N0X6, A4IIW9, B0BLW3, B1H134, B1H234, B4F7C5, D3ZAL8, D3ZTV3, D4A7P2, E5DHB5, F1NUK7, F7D3V9, O43155, O43300, O94898, P58681, Q32Q07, Q3SXY7, Q3URE9, Q504C1, Q50L44, Q52KR2, Q5R482, Q5R6T0, Q5RDJ4, Q61809, Q66HV9, Q6RKD8, Q6UXK5, Q70AK3, Q7L985, Q80XG9, Q80ZD7, Q80ZD8, Q80ZD9, Q86VH4, Q86VH5, Q8BGA3, Q8BGT1, Q8BLU0

Diamond homologs: A1A4H9, B4F7C5, D3ZAL8, D4A6D8, D4A7P2, O43300, O75093, P58874, Q5R6B1, Q80XG9, Q86UE6, Q86VH4, Q86VH5, Q8BGA3, Q8BZ81, Q8C2S7, Q8K377, Q920A0, Q9BGP6, Q9UBM4, O88279, P70186, Q1ENI8, Q3ZBN5, Q80TR4, Q99MQ4, Q9BXN1, O02678, Q80ZD7, Q80ZD8, A3KNN3, A6H789, A6H793, A6NJW4, A8WHP9, D4AC13, G5EFX6, O00468, O19045, O35367

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2883 predictions. Top by Δscore:

VariantEffectΔscore
2:76748923:A:Cacceptor_gain1.0000
2:76748914:CAT:Cacceptor_gain0.9900
2:76748915:ATCTG:Aacceptor_loss0.9900
2:76748916:TC:Tacceptor_loss0.9900
2:76748918:T:Aacceptor_loss0.9900
2:76748923:A:ACacceptor_gain0.9900
2:77024359:ATTT:Adonor_gain0.9900
2:77109390:C:Adonor_gain0.9900
2:77121661:A:ATdonor_gain0.9900
2:77227074:TGC:Tdonor_gain0.9900
2:76748912:GGCAT:Gacceptor_gain0.9800
2:76748913:GCAT:Gacceptor_gain0.9800
2:76748914:CATC:Cacceptor_gain0.9800
2:76748915:AT:Aacceptor_gain0.9800
2:76748917:C:CCacceptor_gain0.9800
2:76748921:A:ACacceptor_gain0.9800
2:76748921:A:Cacceptor_gain0.9800
2:76923367:CAT:Cacceptor_gain0.9800
2:77004734:A:ACdonor_gain0.9800
2:77004735:C:CCdonor_gain0.9800
2:77043975:ATT:Adonor_gain0.9800
2:77121660:C:CTdonor_gain0.9800
2:76822900:CCATA:Cacceptor_gain0.9700
2:77011789:T:Cdonor_gain0.9700
2:77024341:T:TAdonor_gain0.9700
2:77114556:T:Cacceptor_gain0.9700
2:76791046:A:ACdonor_gain0.9600
2:76791047:C:CCdonor_gain0.9600
2:76984007:C:CTdonor_gain0.9600
2:76984008:T:TTdonor_gain0.9600

AlphaMissense

3891 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:77518568:A:GL434P1.000
2:77518574:A:GL432P1.000
2:77518574:A:TL432H1.000
2:77518577:G:TA431D1.000
2:77518582:A:CS429R1.000
2:77518582:A:TS429R1.000
2:77518584:T:GS429R1.000
2:77518586:C:TG428E1.000
2:77518587:C:GG428R1.000
2:77518587:C:TG428R1.000
2:77518852:A:CC339W1.000
2:77518853:C:GC339S1.000
2:77518853:C:TC339Y1.000
2:77518854:A:GC339R1.000
2:77518854:A:TC339S1.000
2:77518924:G:CC315W1.000
2:77518925:C:GC315S1.000
2:77518926:A:GC315R1.000
2:77518926:A:TC315S1.000
2:77518930:C:AW313C1.000
2:77518930:C:GW313C1.000
2:77518932:A:GW313R1.000
2:77518932:A:TW313R1.000
2:77518936:A:CN311K1.000
2:77518936:A:TN311K1.000
2:77519080:A:CN263K1.000
2:77519080:A:TN263K1.000
2:77519224:G:CN215K1.000
2:77519224:G:TN215K1.000
2:77519234:A:GL212P1.000

dbSNP variants (sampled 300 via entrez): RS1000000707 (2:77135057 A>G), RS1000002136 (2:77006138 C>T), RS1000002662 (2:77065054 GAAT>G), RS1000003156 (2:76781750 G>A,C), RS1000004667 (2:77051714 G>T), RS1000006784 (2:77039776 T>C), RS1000012402 (2:77249581 T>A,C), RS1000013847 (2:77498256 A>T), RS1000015034 (2:77139019 T>A), RS1000016376 (2:77277456 C>A,T), RS1000020914 (2:76776567 T>C), RS1000023142 (2:77287447 T>G), RS1000027975 (2:76762618 G>A,T), RS1000032144 (2:77460633 G>A,C), RS1000032469 (2:77208840 C>T)

Disease associations

OMIM: gene MIM:610870 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

StudyTraitp-value
GCST002337_174Amyotrophic lateral sclerosis (sporadic)2.000000e-08
GCST002701_36Verbal declarative memory5.000000e-06
GCST002985_1Middle childhood and early adolescence aggressive behavior6.000000e-07
GCST002986_1Childhood and early adolescence aggressive behavior5.000000e-08
GCST003657_6Attention deficit hyperactivity disorder symptom score6.000000e-06
GCST003901_12Cognitive decline (age-related)3.000000e-06
GCST007006_2Logical memory (delayed recall) in normal cognition7.000000e-08
GCST007201_24Schizophrenia1.000000e-07
GCST007201_409Schizophrenia1.000000e-06
GCST007323_13Risk-taking tendency (4-domain principal component model)7.000000e-09
GCST007326_39Number of sexual partners7.000000e-10
GCST007565_186Morning person6.000000e-19
GCST007565_70Morning person5.000000e-24
GCST007576_269Chronotype2.000000e-10
GCST007576_315Chronotype5.000000e-24
GCST007576_369Chronotype5.000000e-11
GCST008144_1Fasting plasma glucose8.000000e-06
GCST008368_17Plasma anti-thyroid peroxidase levels5.000000e-06
GCST009464_33Facial morphology4.000000e-08
GCST010057_2Lung function1.000000e-06
GCST010135_23Oily fish consumption8.000000e-10
GCST010140_15Pork consumption8.000000e-10
GCST010292_1Response to lamotrigine and valproic acid in genetic generalized epilepsy8.000000e-07
GCST010396_61Gut microbiota (bacterial taxa, hurdle binary method)8.000000e-06
GCST010536_6Carotid plaque maximum area3.000000e-06
GCST010538_7Sum of carotid plaque area3.000000e-07
GCST010762_1Hypotension and cognitive impairment6.000000e-06
GCST010989_204Body size at age 104.000000e-15

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004874memory performance
EFO:0006805word list delayed recall measurement
EFO:0007860ADHD symptom measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0004312vital capacity
EFO:0008111diet measurement
EFO:0007874gut microbiome measurement
EFO:0006501carotid plaque build
EFO:0009819comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression4
trichostatin Aaffects cotreatment, decreases expression2
Cadmiumdecreases expression, increases abundance2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphindecreases expression, affects cotreatment1
Temozolomidedecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arbutindecreases expression1
Benzo(a)pyrenedecreases methylation1
Diethylhexyl Phthalatedecreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Okadaic Aciddecreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

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