Aliases for LRRTM1 Gene

Aliases for LRRTM1 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 1 2 3 5
  • Leucine-Rich Repeat Transmembrane Neuronal Protein 1 3 4
  • Leucine-Rich Repeat Transmembrane Neuronal 1 Protein 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 and Reading Disorder. 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 Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J080303 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.6 552 1.6 USF1 EZH2 TCF7L2 POLR2A SUZ12 CTCF SIN3A SMARCA4 RNF2 GATA2 LRRTM1 RF00951-071
GH02J080305 Promoter 0.4 EPDnew 500.7 -0.3 -347 0.1 EZH2 LRRTM1 HSALNG0016301
GH02J080153 Enhancer 0.3 Ensembl 18.9 +151.5 151451 0.2 EZH2 LRRTM1 ENSG00000223427 lnc-LRRTM1-7 HSALNG0016297 CTNNA2
GH02J080135 Enhancer 0.3 Ensembl 4.7 +168.2 168151 1.2 ZNF316 HSALNG0016297 LRRTM1 ENSG00000223427 lnc-LRRTM1-7 CTNNA2
GH02J080301 Enhancer 0.3 FANTOM5 2 +3.3 3343 0.4 EZH2 LRRTM1 RF00951-071
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRTM1

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

Genomic Locations for LRRTM1 Gene

Genomic Locations for LRRTM1 Gene
chr2:80,288,280-80,304,752
(GRCh38/hg38)
Size:
16,473 bases
Orientation:
Minus strand
chr2:80,515,483-80,531,874
(GRCh37/hg19)
Size:
16,392 bases
Orientation:
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:
    Q86UE6-LRRT1_HUMAN
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 1
    Protein Accession:
    Q86UE6
    Secondary Accessions:
    • A8K397
    • D6W5K1
    • Q96DN1

    Protein attributes for LRRTM1 Gene

    Size:
    522 amino acids
    Molecular mass:
    58641 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • 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 Asn56, Asn63, Asn130, and Asn380
  • 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 intracellular proteins
  • Predicted membrane proteins

Protein Domains for LRRTM1 Gene

Blocks:
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LRRTM1 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat transmembrane neuronal protein 1 (LRRT1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86UE6

UniProtKB/Swiss-Prot:

LRRT1_HUMAN :
  • Belongs to the LRRTM family.
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.

Phenotypes From GWAS Catalog for LRRTM1 Gene

Gene Ontology (GO) - Molecular Function for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
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

CRISPR Products

miRNA for LRRTM1 Gene

miRTarBase miRNAs that target LRRTM1

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

COMPARTMENTS
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
plasma membrane 5
endoplasmic reticulum 5
extracellular 4
cytoskeleton 1
mitochondrion 1
nucleus 1
peroxisome 0
lysosome 0

Gene Ontology (GO) - Cellular Components for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005783 endoplasmic reticulum IDA 17667961
GO:0005886 plasma membrane IEA --
GO:0009986 NOT cell surface IDA 17667961
GO:0016020 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:0007626 locomotory behavior IEA --
GO:0008150 biological_process ND --
GO:0035418 protein localization to synapse IEA --
GO:0035640 exploration behavior IEA --
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

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

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

ExUns: 1a · 1b ^ 2a · 2b
SP1:
SP2:

Relevant External Links for LRRTM1 Gene

GeneLoc Exon Structure for
LRRTM1

Expression for LRRTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRTM1

SOURCE GeneReport for Unigene cluster for LRRTM1 Gene:

Hs.591580

mRNA Expression by UniProt/SwissProt for LRRTM1 Gene:

Q86UE6-LRRT1_HUMAN
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
chimpanzee
(Pan troglodytes)
Mammalia LRRTM1 31 30
  • 99.81 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRRTM1 31 30
  • 95.98 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRRTM1 30
  • 95.52 (n)
mouse
(Mus musculus)
Mammalia Lrrtm1 17 31 30
  • 92.19 (n)
rat
(Rattus norvegicus)
Mammalia LRRTM1 30
  • 91.76 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRTM1 31
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRRTM1 31
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRTM1 31 30
  • 79.21 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRRTM1 31
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrtm1 30
  • 74.97 (n)
zebrafish
(Danio rerio)
Actinopterygii lrrtm1 31 30
  • 66.41 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta haf 31
  • 9 (a)
OneToMany
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

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

Paralogs for LRRTM1 Gene

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

  • LRRT1_HUMAN
  • C9JEE2_HUMAN
  • C9JF97_HUMAN
  • C9JPM9_HUMAN
genes like me logo Genes that share paralogs with LRRTM1: view

Variants for LRRTM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRTM1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
778820 Benign: not provided 80,302,808(-) C/T MISSENSE_VARIANT,INTRON_VARIANT
rs6733871 - p.Asn330Ser

Additional dbSNP identifiers (rs#s) for LRRTM1 Gene

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
LRRTM1

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

Disorders for LRRTM1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
schizophrenia
  • sczd
reading disorder
  • dyslexia
autism spectrum disorder
  • asd
autism
  • autistic disorder
dyslexia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LRRTM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 54
  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 41 54
  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 54
  4. 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 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for LRRTM1 Gene

Sources for LRRTM1 Gene