Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LRRTM1 Gene

Aliases for LRRTM1 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 1 2 3 5
  • Leucine-Rich Repeat Transmembrane Neuronal 1 Protein 3
  • Leucine-Rich Repeat Transmembrane Neuronal Protein 1 3

External Ids for LRRTM1 Gene

Previous GeneCards Identifiers for LRRTM1 Gene

  • GC02U900202
  • GC02M080490
  • GC02M080499
  • GC02M080427
  • GC02M080382

Summaries for LRRTM1 Gene

GeneCards Summary for LRRTM1 Gene

LRRTM1 (Leucine Rich Repeat Transmembrane Neuronal 1) is a Protein Coding gene. Diseases associated with LRRTM1 include Schizophrenia. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. An important paralog of this gene is LRRTM2.

UniProtKB/Swiss-Prot for LRRTM1 Gene

  • Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation, acting at both pre- and postsynaptic level.

Gene Wiki entry for LRRTM1 Gene

Additional gene information for LRRTM1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRTM1 Gene

Genomics for LRRTM1 Gene

GeneHancer (GH) Regulatory Elements for LRRTM1 Gene

Promoters and enhancers for LRRTM1 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
GH02J080304 Promoter 0.7 EPDnew 650.7 +0.3 294 0.1 SUZ12 SIN3A EZH2 LRRTM1 LOC100420108 GC02P080062
GH02J080306 Promoter 0.7 EPDnew 650.7 +0.0 19 0.1 POLR2A SIN3A LRRTM1 LOC100420108 GC02P080062
GH02J080305 Promoter 0.5 EPDnew 650.7 -0.4 -350 0.1 LRRTM1 LOC105374824 GC02P080062
GH02J080303 Enhancer 0.4 ENCODE 650.7 +1.3 1268 0.1 USF1 SUZ12 POLR2A LRRTM1 LOC100420108 GC02P080062
GH02J080301 Enhancer 0.2 FANTOM5 2.1 +3.3 3340 0.4 LRRTM1 LOC100420108 GC02P080062
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRTM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRTM1 gene promoter:
  • E47
  • COMP1
  • Hand1
  • Pax-2
  • Zic1
  • TGIF
  • Pax-2a
  • Pbx1a
  • C/EBPalpha
  • AP-4

Genomic Locations for LRRTM1 Gene

Genomic Locations for LRRTM1 Gene
16,470 bases
Minus strand
16,392 bases
Minus strand

Genomic View for LRRTM1 Gene

Genes around LRRTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRTM1 Gene

Proteins for LRRTM1 Gene

  • Protein details for LRRTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 1
    Protein Accession:
    Secondary Accessions:
    • A8K397
    • D6W5K1
    • Q96DN1

    Protein attributes for LRRTM1 Gene

    522 amino acids
    Molecular mass:
    58641 Da
    Quaternary structure:
    No Data Available
    • This gene is imprinted, being predominantly expressed from the paternal allele and showing a variable pattern of maternal down-regulation. May be associated paternally with handedness and schizophrenia.

neXtProt entry for LRRTM1 Gene

Post-translational modifications for LRRTM1 Gene

  • Glycosylation at isoforms=380, isoforms=130, posLast=6363, and posLast=5656
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LRRTM1 Gene

Domains & Families for LRRTM1 Gene

Gene Families for LRRTM1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for LRRTM1 Gene

Suggested Antigen Peptide Sequences for LRRTM1 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 LRRTM1: view

Function for LRRTM1 Gene

Molecular function for LRRTM1 Gene

UniProtKB/Swiss-Prot Function:
Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation, acting at both pre- and postsynaptic level.

Gene Ontology (GO) - Molecular Function for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0004860 protein kinase inhibitor activity IBA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRRTM1: view
genes like me logo Genes that share phenotypes with LRRTM1: view

Animal Models for LRRTM1 Gene

MGI Knock Outs for LRRTM1:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRRTM1

miRNA for LRRTM1 Gene

miRTarBase miRNAs that target LRRTM1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRTM1 Gene

Localization for LRRTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRTM1 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 LRRTM1 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 4
extracellular 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 17667961
GO:0005886 plasma membrane IEA --
GO:0009986 NOT cell surface IDA 17667961
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRRTM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRTM1 Gene

Pathways & Interactions for LRRTM1 Gene

genes like me logo Genes that share pathways with LRRTM1: view

Pathways by source for LRRTM1 Gene

Gene Ontology (GO) - Biological Process for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002091 negative regulation of receptor internalization IEA --
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0007626 locomotory behavior IEA --
GO:0008150 biological_process ND --
GO:0019221 cytokine-mediated signaling pathway IBA --
genes like me logo Genes that share ontologies with LRRTM1: view

No data available for SIGNOR curated interactions for LRRTM1 Gene

Drugs & Compounds for LRRTM1 Gene

No Compound Related Data Available

Transcripts for LRRTM1 Gene

mRNA/cDNA for LRRTM1 Gene

Unigene Clusters for LRRTM1 Gene

Leucine rich repeat transmembrane neuronal 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRTM1 Gene

ExUns: 1a · 1b ^ 2a · 2b

Relevant External Links for LRRTM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LRRTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRTM1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x7.8), Brain - Putamen (basal ganglia) (x6.1), Brain - Caudate (basal ganglia) (x5.6), Brain - Hippocampus (x4.9), Brain - Cortex (x4.9), Brain - Anterior cingulate cortex (BA24) (x4.3), and Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for LRRTM1 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRTM1 Gene

Protein tissue co-expression partners for LRRTM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRTM1 Gene:


SOURCE GeneReport for Unigene cluster for LRRTM1 Gene:


mRNA Expression by UniProt/SwissProt for LRRTM1 Gene:

Tissue specificity: Predominantly expressed in forebrain regions including thalamus and cerebral cortex.

Evidence on tissue expression from TISSUES for LRRTM1 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with LRRTM1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRTM1 Gene

Orthologs for LRRTM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRTM1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LRRTM1 34 33
  • 99.81 (n)
(Canis familiaris)
Mammalia LRRTM1 34 33
  • 95.98 (n)
(Bos Taurus)
Mammalia LRRTM1 33
  • 95.52 (n)
(Mus musculus)
Mammalia Lrrtm1 16 34 33
  • 92.19 (n)
(Rattus norvegicus)
Mammalia LRRTM1 33
  • 91.76 (n)
(Monodelphis domestica)
Mammalia LRRTM1 34
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia LRRTM1 34
  • 85 (a)
(Gallus gallus)
Aves LRRTM1 34 33
  • 79.21 (n)
(Anolis carolinensis)
Reptilia LRRTM1 34
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrtm1 33
  • 74.97 (n)
(Danio rerio)
Actinopterygii lrrtm1 34 33
  • 66.41 (n)
fruit fly
(Drosophila melanogaster)
Insecta haf 34
  • 9 (a)
Species where no ortholog for LRRTM1 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)

Evolution for LRRTM1 Gene

Gene Tree for LRRTM1 (if available)
Gene Tree for LRRTM1 (if available)
Evolutionary constrained regions (ECRs) for LRRTM1: view image

Paralogs for LRRTM1 Gene

Paralogs for LRRTM1 Gene

(7) SIMAP similar genes for LRRTM1 Gene using alignment to 4 proteins:

  • C9JF97_HUMAN
genes like me logo Genes that share paralogs with LRRTM1: view

Variants for LRRTM1 Gene

Sequence variations from dbSNP and Humsavar for LRRTM1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1001985415 -- 80,301,505(-) G/A downstream_transcript_variant
rs1002902617 -- 80,306,329(-) A/T upstream_transcript_variant
rs1002974987 -- 80,305,962(-) G/C upstream_transcript_variant
rs1003719076 -- 80,305,571(-) T/A upstream_transcript_variant
rs1004090041 -- 80,302,044(-) G/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for LRRTM1 Gene

Variant ID Type Subtype PubMed ID
esv2759069 CNV loss 17122850

Variation tolerance for LRRTM1 Gene

Residual Variation Intolerance Score: 21.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.25; 92.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRTM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRTM1 Gene

Disorders for LRRTM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRRTM1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
  • sczd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LRRTM1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LRRTM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRTM1 Gene

Publications for LRRTM1 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. Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up. (PMID: 21041608) van Winkel R … Genetic Risk and Outcome of Psychosis (GROUP) Investigators (Archives of general psychiatry 2011) 3 44 58
  3. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. (PMID: 17667961) Francks C … Monaco AP (Molecular psychiatry 2007) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. 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

Products for LRRTM1 Gene

Sources for LRRTM1 Gene

Loading form....