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Aliases for LRRTM3 Gene

Aliases for LRRTM3 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 3 2 3 5
  • Leucine-Rich Repeat Transmembrane Neuronal Protein 3 3

External Ids for LRRTM3 Gene

Previous GeneCards Identifiers for LRRTM3 Gene

  • GC10U900142
  • GC10P068031
  • GC10P068030
  • GC10P068355
  • GC10P068685
  • GC10P062684

Summaries for LRRTM3 Gene

GeneCards Summary for LRRTM3 Gene

LRRTM3 (Leucine Rich Repeat Transmembrane Neuronal 3) is a Protein Coding gene. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. An important paralog of this gene is LRRTM4.

UniProtKB/Swiss-Prot for LRRTM3 Gene

  • Exhibits a limited synaptogenic activity in vitro, restricted to excitatory presynaptic differentiation (By similarity). May play a role in the development and maintenance of the vertebrate nervous system.

Additional gene information for LRRTM3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRTM3 Gene

Genomics for LRRTM3 Gene

GeneHancer (GH) Regulatory Elements for LRRTM3 Gene

Promoters and enhancers for LRRTM3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J066925 Promoter/Enhancer 1.3 EPDnew ENCODE 650.7 +0.0 7 1 CTCF MXI1 PKNOX1 MAX SIN3A BATF IRF4 RAD21 YY1 TEAD3 LRRTM3 LOC101928961 CTNNA3
GH10J066961 Enhancer 0.3 FANTOM5 10 +35.8 35826 0.6 LRRTM3 LOC101928961 CTNNA3
GH10J067043 Enhancer 0.3 FANTOM5 7.9 +117.1 117132 0.7 LRRTM3 GC10P067038 ENSG00000225299 CTNNA3
GH10J066716 Enhancer 0.3 ENCODE 5.3 -208.5 -208519 2.1 MAFK LRRTM3 GC10P066636 ENSG00000277056
GH10J066957 Enhancer 0.4 FANTOM5 ENCODE 3.4 +32.8 32789 2.3 LRRTM3 LOC101928961 CTNNA3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRTM3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRTM3 gene promoter:
  • Lmo2
  • HEN1
  • Bach1
  • LCR-F1
  • C/EBPalpha
  • Evi-1
  • HNF-4alpha1
  • HOXA9
  • HOXA9B
  • Meis-1

Genomic Locations for LRRTM3 Gene

Genomic Locations for LRRTM3 Gene
175,546 bases
Plus strand
175,104 bases
Plus strand

Genomic View for LRRTM3 Gene

Genes around LRRTM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRTM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRTM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRTM3 Gene

Proteins for LRRTM3 Gene

  • Protein details for LRRTM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 3
    Protein Accession:
    Secondary Accessions:
    • A8K2A3
    • Q2NKX7
    • Q6N0A3

    Protein attributes for LRRTM3 Gene

    581 amino acids
    Molecular mass:
    65896 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LRRTM3 Gene


neXtProt entry for LRRTM3 Gene

Post-translational modifications for LRRTM3 Gene

  • Glycosylation at isoforms=2357 and isoforms=2126
  • Modification sites at PhosphoSitePlus

Other Protein References for LRRTM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRRTM3 Gene

Domains & Families for LRRTM3 Gene

Gene Families for LRRTM3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for LRRTM3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the LRRTM family.
  • Belongs to the LRRTM family.
genes like me logo Genes that share domains with LRRTM3: view

Function for LRRTM3 Gene

Molecular function for LRRTM3 Gene

UniProtKB/Swiss-Prot Function:
Exhibits a limited synaptogenic activity in vitro, restricted to excitatory presynaptic differentiation (By similarity). May play a role in the development and maintenance of the vertebrate nervous system.

Phenotypes From GWAS Catalog for LRRTM3 Gene

Gene Ontology (GO) - Molecular Function for LRRTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRRTM3: view
genes like me logo Genes that share phenotypes with LRRTM3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LRRTM3 Gene

Localization for LRRTM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRTM3 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRRTM3 gene
Compartment Confidence
plasma membrane 4
extracellular 2
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for LRRTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LRRTM3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRTM3 Gene

Pathways & Interactions for LRRTM3 Gene

genes like me logo Genes that share pathways with LRRTM3: view

Pathways by source for LRRTM3 Gene

Gene Ontology (GO) - Biological Process for LRRTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0019221 cytokine-mediated signaling pathway IBA --
GO:0046426 negative regulation of JAK-STAT cascade IBA --
GO:0051965 positive regulation of synapse assembly IEA --
GO:1902004 positive regulation of amyloid-beta formation IMP 17098871
genes like me logo Genes that share ontologies with LRRTM3: view

No data available for SIGNOR curated interactions for LRRTM3 Gene

Drugs & Compounds for LRRTM3 Gene

No Compound Related Data Available

Transcripts for LRRTM3 Gene

mRNA/cDNA for LRRTM3 Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(20) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LRRTM3 Gene

Leucine rich repeat transmembrane neuronal 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRTM3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b
SP2: -
SP4: - - -

Relevant External Links for LRRTM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LRRTM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRTM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRTM3 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x6.0), Brain - Nucleus accumbens (basal ganglia) (x5.4), Brain - Anterior cingulate cortex (BA24) (x5.3), Brain - Caudate (basal ganglia) (x4.6), Brain - Putamen (basal ganglia) (x4.5), and Brain - Cortex (x4.4).

Protein differential expression in normal tissues from HIPED for LRRTM3 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRTM3 Gene

Protein tissue co-expression partners for LRRTM3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRTM3 Gene:


SOURCE GeneReport for Unigene cluster for LRRTM3 Gene:


mRNA Expression by UniProt/SwissProt for LRRTM3 Gene:

Tissue specificity: Expressed in neuronal tissues.

Evidence on tissue expression from TISSUES for LRRTM3 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with LRRTM3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRTM3 Gene

Orthologs for LRRTM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRTM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LRRTM3 34 33
  • 99.83 (n)
(Monodelphis domestica)
Mammalia LRRTM3 34
  • 97 (a)
(Canis familiaris)
Mammalia LRRTM3 34 33
  • 96.56 (n)
(Bos Taurus)
Mammalia LRRTM3 34 33
  • 96.35 (n)
(Ornithorhynchus anatinus)
Mammalia LRRTM3 34
  • 95 (a)
(Rattus norvegicus)
Mammalia Lrrtm3 33
  • 91.22 (n)
(Mus musculus)
Mammalia Lrrtm3 16 34 33
  • 91.16 (n)
(Gallus gallus)
Aves LRRTM3 34 33
  • 87.38 (n)
(Anolis carolinensis)
Reptilia LRRTM3 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrtm3 33
  • 72.84 (n)
fruit fly
(Drosophila melanogaster)
Insecta haf 34
  • 9 (a)
Species where no ortholog for LRRTM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LRRTM3 Gene

Gene Tree for LRRTM3 (if available)
Gene Tree for LRRTM3 (if available)
Evolutionary constrained regions (ECRs) for LRRTM3: view image

Paralogs for LRRTM3 Gene

Paralogs for LRRTM3 Gene

(3) SIMAP similar genes for LRRTM3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LRRTM3: view

Variants for LRRTM3 Gene

Sequence variations from dbSNP and Humsavar for LRRTM3 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000041377 -- 67,077,861(+) AAAGAAA/AAA intron_variant
rs1000049278 -- 67,099,054(+) C/T 3_prime_UTR_variant, non_coding_transcript_variant
rs1000052119 -- 66,952,938(+) G/T genic_upstream_transcript_variant, intron_variant
rs1000076433 -- 67,073,394(+) T/A/G intron_variant
rs1000078165 -- 67,015,662(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LRRTM3 Gene

Variant ID Type Subtype PubMed ID
nsv831905 CNV gain 17160897
nsv551413 CNV gain 21841781
nsv551412 CNV loss 21841781
nsv551411 CNV loss 21841781
nsv520745 CNV gain 19592680
nsv467351 CNV loss 19166990
nsv1134021 CNV deletion 24896259
nsv1125503 CNV tandem duplication 24896259
nsv1125335 OTHER inversion 24896259
nsv1050214 CNV loss 25217958
nsv1045134 CNV loss 25217958
nsv1037295 CNV loss 25217958
esv3891851 CNV loss 25118596
esv3623673 CNV loss 21293372
esv3623669 CNV loss 21293372
esv3623667 CNV loss 21293372
esv3623664 CNV loss 21293372
esv3546441 CNV deletion 23714750
esv3382497 CNV insertion 20981092
esv2737995 CNV deletion 23290073
esv2737984 CNV deletion 23290073
esv2676584 CNV deletion 23128226
dgv916n100 CNV gain 25217958
dgv33e55 CNV gain 17911159

Variation tolerance for LRRTM3 Gene

Residual Variation Intolerance Score: 23.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.47; 55.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRTM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRTM3 Gene

Disorders for LRRTM3 Gene

Additional Disease Information for LRRTM3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LRRTM3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRTM3 Gene

Publications for LRRTM3 Gene

  1. A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. (PMID: 12676565) Laurén J … Timmusk T (Genomics 2003) 2 3 4 58
  2. An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3. (PMID: 19105203) Edwards TL … Ritchie MD (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  5. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. (PMID: 29117863) Choudhury NR … Michlewski G (BMC biology 2017) 3 58

Products for LRRTM3 Gene

Sources for LRRTM3 Gene

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