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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LRRTM2
leucine rich repeat transmembrane neuronal 2
Chromosome 5 · 5q31.2
NCBI Gene: 26045Ensembl: ENSG00000146006.8HGNC: HGNC:19409UniProt: O43300
18PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingGABA-ergic synapsepostsynaptic specialization membraneGO:0005615atrial fibrillationovarian dysfunctionpreeclampsialagophthalmos
✦AI Summary

LRRTM2 is a postsynaptic cell-adhesion molecule that functions as a key regulator of excitatory glutamatergic synapse development and maintenance 1. Structurally, LRRTM2 contains leucine-rich repeat domains and functions as a ligand for presynaptic neurexins, specifically binding neurexin-1α and neurexin-1β variants lacking a splice site 4 insert in a calcium-dependent manner 2. This binding triggers presynaptic differentiation and instructs the development of functional glutamate release sites at the synapse 1. LRRTM2 cooperates with neuroligin-1 in an additive or synergistic manner to regulate synaptic assembly, and notably exhibits greater potency than neuroligin-1 in promoting synaptic differentiation 3. The gene is nested within the seventh intron of CTNNA1, sharing a bidirectional promoter that regulates alternative transcription of both genes in the nervous system 4. Clinically, microdeletions encompassing LRRTM2 at 5q31.2 have been associated with intellectual disability and developmental delay, identifying LRRTM2 as a candidate gene for neurodevelopmental disorders 5. However, sequencing studies in 330 ID/DD patients revealed no frequent point mutations, suggesting haploinsufficiency rather than loss-of-function mutations drives LRRTM2-related pathology 5.

Sources cited
1
LRRTM2 acts as neurexin ligand to induce excitatory synapses and promotes presynaptic differentiation
PMID: 20064387
2
Crystal structure reveals Ca2+-mediated interactions between Nrxn1β and LRRTM2 and selective binding mechanisms
PMID: 30262834
3
LRRTM2 binds neurexin variants lacking splice site 4 insert and cooperates synergistically with neuroligin-1
PMID: 20519524
4
LRRTM2 shares bidirectional promoter with CTNNA1 and is highly expressed in nervous system
PMID: 21708131
5
5q31.2 microdeletions containing LRRTM2 cause intellectual disability; point mutations are not frequent cause
PMID: 23326251
Disease Associationsⓘ20
atrial fibrillationOpen Targets
0.14Weak
ovarian dysfunctionOpen Targets
0.13Weak
preeclampsiaOpen Targets
0.10Weak
lagophthalmosOpen Targets
0.09Suggestive
metabolic syndromeOpen Targets
0.07Suggestive
goutOpen Targets
0.07Suggestive
Senior-Boichis syndromeOpen Targets
0.05Suggestive
risk-taking behaviourOpen Targets
0.05Suggestive
insomniaOpen Targets
0.05Suggestive
polycystic kidney disease 5Open Targets
0.05Suggestive
breast carcinomaOpen Targets
0.04Suggestive
squamous cell carcinomaOpen Targets
0.04Suggestive
hepatorenocardiac degenerative fibrosisOpen Targets
0.04Suggestive
irritable bowel syndromeOpen Targets
0.04Suggestive
nephronophthisis 3Open Targets
0.04Suggestive
colorectal adenocarcinomaOpen Targets
0.04Suggestive
renal-hepatic-pancreatic dysplasia 1Open Targets
0.04Suggestive
sclerosing cholangitisOpen Targets
0.04Suggestive
renal-hepatic-pancreatic dysplasia 2Open Targets
0.04Suggestive
nephronophthisisOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
LRFN1Shared pathway100%CASKIN1Shared pathway100%NLGN3Protein interaction100%NLGN4XProtein interaction100%NLGN1Protein interaction99%DLG4Protein interaction99%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
6%
Ovary
3%
Heart
2%
Liver
1%
Lung
1%
Gene Interaction Network
Click a node to explore
LRRTM2LRFN1CASKIN1NLGN3NLGN4XNLGN1DLG4
PROTEIN STRUCTURE
Preparing viewer…
PDB5Z8X · 3.15 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.55Moderately Constrained
pLIⓘ
0.88Intermediate
Observed/Expected LoF0.35 [0.23–0.55]
RankingsWhere LRRTM2 stands among ~20K protein-coding genes
  • #14,731of 20,598
    Most Researched18
  • #3,540of 17,882
    Most Constrained (LOEUF)0.55 · top quartile
Genes detectedLRRTM2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Bidirectional transcription from human LRRTM2/CTNNA1 and LRRTM1/CTNNA2 gene loci leads to expression of N-terminally truncated CTNNA1 and CTNNA2 isoforms.
PMID: 21708131
Biochem Biophys Res Commun · 2011
1.00
2
5q31 Microdeletions: Definition of a Critical Region and Analysis of LRRTM2, a Candidate Gene for Intellectual Disability.
PMID: 23326251
Mol Syndromol · 2012
0.90
3
Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction.
PMID: 30262834
Nat Commun · 2018
0.80
4
LRRTM2 functions as a neurexin ligand in promoting excitatory synapse formation.
PMID: 20064387
Neuron · 2009
0.70
5
Crystal Structure of an Engineered LRRTM2 Synaptic Adhesion Molecule and a Model for Neurexin Binding.
PMID: 26785044
Biochemistry · 2016
0.60