Aliases for LRTM1 Gene

Aliases for LRTM1 Gene

  • Leucine Rich Repeats And Transmembrane Domains 1 2 3 5
  • Leucine-Rich Repeat And Transmembrane Domain-Containing Protein 1 3 4
  • HT017 2 3
  • LRTM1 5

External Ids for LRTM1 Gene

Summaries for LRTM1 Gene

GeneCards Summary for LRTM1 Gene

LRTM1 (Leucine Rich Repeats And Transmembrane Domains 1) is a Protein Coding gene. Diseases associated with LRTM1 include Congenital Fiber-Type Disproportion. An important paralog of this gene is LRRTM3.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRTM1 Gene

Genomics for LRTM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRTM1 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
GH03J054964 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 0.0 -35 5.8 ZIC2 EBF1 PRDM6 JUND BHLHE40 ZNF7 EP300 FOS CEBPB EZH2 LRTM1 piR-47675-079 WNT5A CACNA2D3
GH03J054928 Promoter 0.3 EPDnew 250.3 +39.0 39023 0.1 LRTM1 CACNA2D3-AS1 HSALNG0026283 CACNA2D3
GH03J054888 Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.9 +75.6 75617 6.6 ZNF600 JUND NFIC ZIC2 REST CEBPB DEK ZNF341 CTCF MAX LRTM1 HQ292166 CACNA2D3-AS1 HSALNG0026281 CACNA2D3
GH03J054988 Promoter/Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas 11.5 -21.4 -21435 2.3 NFIC PRDM6 SPI1 MAFK ZNF362 NFIB GLIS1 ZNF398 PRDM4 ZNF561 LRTM1 HSALNG0026284 FJ601684-315 WNT5A CACNA2D3
GH03J055167 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 10.2 -202.1 -202142 4.5 JUND BRCA1 CEBPB MAX EP300 RFX5 STAT3 TCF7L2 USF2 RAD21 LRTM1 WNT5A WNT5A-AS1 ENSG00000239991 HSALNG0026288 LINC02017 HSALNG0026286 HSALNG0026287
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRTM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRTM1

Top Transcription factor binding sites by QIAGEN in the LRTM1 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • MyoD
  • NF-Y
  • NF-YA
  • NF-YB
  • USF-1
  • USF1

Genomic Locations for LRTM1 Gene

Latest Assembly
chr3:54,918,231-54,967,102
(GRCh38/hg38)
Size:
48,872 bases
Orientation:
Minus strand

Previous Assembly
chr3:54,952,258-55,001,129
(GRCh37/hg19 by Entrez Gene)
Size:
48,872 bases
Orientation:
Minus strand

chr3:54,952,264-55,001,115
(GRCh37/hg19 by Ensembl)
Size:
48,852 bases
Orientation:
Minus strand

Genomic View for LRTM1 Gene

Genes around LRTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRTM1 Gene

Proteins for LRTM1 Gene

  • Protein details for LRTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBL6-LRTM1_HUMAN
    Recommended name:
    Leucine-rich repeat and transmembrane domain-containing protein 1
    Protein Accession:
    Q9HBL6
    Secondary Accessions:
    • Q8IUU2

    Protein attributes for LRTM1 Gene

    Size:
    345 amino acids
    Molecular mass:
    38171 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LRTM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRTM1 Gene

Post-translational modifications for LRTM1 Gene

  • Glycosylation at Asn104 and Asn147
  • Modification sites at PhosphoSitePlus

Other Protein References for LRTM1 Gene

No data available for DME Specific Peptides for LRTM1 Gene

Domains & Families for LRTM1 Gene

Gene Families for LRTM1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for LRTM1 Gene

InterPro:
Blocks:
  • Leucine-rich repeat signature
  • Cysteine-rich flanking region, C-terminal

Suggested Antigen Peptide Sequences for LRTM1 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat and transmembrane domain-containing protein 1 (LRTM1_HUMAN)
genes like me logo Genes that share domains with LRTM1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRTM1 Gene

Function for LRTM1 Gene

Phenotypes From GWAS Catalog for LRTM1 Gene

Gene Ontology (GO) - Molecular Function for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
GO:0008201 heparin binding IBA 21873635
GO:0048495 Roundabout binding IBA 21873635
genes like me logo Genes that share ontologies with LRTM1: view
genes like me logo Genes that share phenotypes with LRTM1: view

Animal Models for research

  • Taconic Biosciences Mouse Models for LRTM1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRTM1

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRTM1 Gene

Localization for LRTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRTM1 Gene

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 LRTM1 gene
Compartment Confidence
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRTM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRTM1 Gene

Pathways & Interactions for LRTM1 Gene

PathCards logo

SuperPathways for LRTM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007411 axon guidance IBA 21873635
GO:0050919 negative chemotaxis IBA 21873635
genes like me logo Genes that share ontologies with LRTM1: view

No data available for Pathways by source and SIGNOR curated interactions for LRTM1 Gene

Drugs & Compounds for LRTM1 Gene

No Compound Related Data Available

Transcripts for LRTM1 Gene

mRNA/cDNA for LRTM1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRTM1

Alternative Splicing Database (ASD) splice patterns (SP) for LRTM1 Gene

No ASD Table

Relevant External Links for LRTM1 Gene

GeneLoc Exon Structure for
LRTM1

Expression for LRTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRTM1 Gene

This gene is overexpressed in Spleen (x40.1).

Protein differential expression in normal tissues from HIPED for LRTM1 Gene

This gene is overexpressed in Plasma (55.9) and Heart (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRTM1 Gene



Protein tissue co-expression partners for LRTM1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRTM1

SOURCE GeneReport for Unigene cluster for LRTM1 Gene:

Hs.591668

Evidence on tissue expression from TISSUES for LRTM1 Gene

  • Nervous system(4.6)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with LRTM1: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRTM1 Gene

Orthologs for LRTM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRTM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRTM1 29 30
  • 96.81 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRTM1 29 30
  • 82.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRTM1 30
  • 80 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC102547963 29
  • 73.55 (n)
Mouse
(Mus musculus)
Mammalia Lrtm1 29 16 30
  • 72.48 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRTM1 30
  • 62 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRTM1 30
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRTM1 30
  • 51 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRTM1 30
  • 42 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii LOC101883439 29
  • 54.09 (n)
LRTM1 30
  • 42 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta kek4 30
  • 11 (a)
ManyToMany
kek2 30
  • 9 (a)
ManyToMany
kek1 30
  • 8 (a)
ManyToMany
kek5 30
  • 8 (a)
ManyToMany
kek6 30
  • 8 (a)
ManyToMany
kek3 30
  • 8 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 22 (a)
ManyToMany
CSA.1672 30
  • 19 (a)
ManyToMany
-- 30
  • 13 (a)
ManyToMany
Species where no ortholog for LRTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LRTM1 Gene

ENSEMBL:
Gene Tree for LRTM1 (if available)
TreeFam:
Gene Tree for LRTM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRTM1: view image
Alliance of Genome Resources:
Additional Orthologs for LRTM1

Paralogs for LRTM1 Gene

(1) SIMAP similar genes for LRTM1 Gene using alignment to 1 proteins:

  • LRTM1_HUMAN
genes like me logo Genes that share paralogs with LRTM1: view

Variants for LRTM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRTM1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs11541701 Benign: not provided 54,918,700(-) C/A
NM_020678.4(LRTM1):c.797G>T (p.Arg266Leu)
MISSENSE_VARIANT,INTRON
rs144793991 Benign: not provided 54,924,736(-) G/A
NM_020678.4(LRTM1):c.487C>T (p.Arg163Ter)
NONSENSE,INTRON
rs370607786 Likely Benign: not provided 54,925,031(-) AT/A
NM_020678.4(LRTM1):c.191del (p.His64fs)
FRAMESHIFT_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
rs573640720 Likely Benign: not provided 54,918,482(-) GCT/G
NM_020678.4(LRTM1):c.1011_1012AG[1] (p.Glu338fs)
FRAMESHIFT_VARIANT,INTRON
rs61735200 Benign: not provided 54,918,704(-) C/G
NM_020678.4(LRTM1):c.793G>C (p.Glu265Gln)
MISSENSE_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRTM1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LRTM1 Gene

Variant ID Type Subtype PubMed ID
esv3561910 CNV deletion 23714750
nsv517851 CNV gain 19592680

Variation tolerance for LRTM1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRTM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRTM1
Leiden Open Variation Database (LOVD)
LRTM1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRTM1 Gene

Disorders for LRTM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRTM1 Gene - From: COP

Disorder Aliases PubMed IDs
congenital fiber-type disproportion
  • cftd
- elite association - COSMIC cancer census association via MalaCards
Search LRTM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRTM1

genes like me logo Genes that share disorders with LRTM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRTM1 Gene

Publications for LRTM1 Gene

  1. 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
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  3. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu RM … Chen JL (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3

Products for LRTM1 Gene

Sources for LRTM1 Gene