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Aliases for LINGO1 Gene

Aliases for LINGO1 Gene

  • Leucine Rich Repeat And Ig Domain Containing 1 2 3 5
  • Leucine-Rich Repeat And Immunoglobulin Domain-Containing Protein 1 3 4
  • Leucine-Rich Repeat Neuronal Protein 1 3 4
  • Leucine Rich Repeat Neuronal 6A 2 3
  • LRRN6A 3 4
  • LERN1 3 4
  • Leucine-Rich Repeat And Immunoglobulin-Like Domain-Containing Nogo Receptor-Interacting Protein 1 3
  • Leucine-Rich Repeat Neuronal Protein 6A 4
  • UNQ201 3

External Ids for LINGO1 Gene

Previous HGNC Symbols for LINGO1 Gene

  • LRRN6A

Previous GeneCards Identifiers for LINGO1 Gene

  • GC15M075694
  • GC15M077905
  • GC15M054660

Summaries for LINGO1 Gene

GeneCards Summary for LINGO1 Gene

LINGO1 (Leucine Rich Repeat And Ig Domain Containing 1) is a Protein Coding gene. Diseases associated with LINGO1 include Essential Tremor. Among its related pathways are Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases and RET signaling. Gene Ontology (GO) annotations related to this gene include epidermal growth factor receptor binding. An important paralog of this gene is LINGO2.

UniProtKB/Swiss-Prot for LINGO1 Gene

  • Functional component of the Nogo receptor signaling complex (RTN4R/NGFR) in RhoA activation responsible for some inhibition of axonal regeneration by myelin-associated factors (PubMed:14966521, PubMed:15694321). Is also an important negative regulator of oligodentrocyte differentiation and axonal myelination (PubMed:15895088). Acts in conjunction with RTN4 and RTN4R in regulating neuronal precursor cell motility during cortical development (By similarity).

Gene Wiki entry for LINGO1 Gene

Additional gene information for LINGO1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LINGO1 Gene

Genomics for LINGO1 Gene

GeneHancer (GH) Regulatory Elements for LINGO1 Gene

Promoters and enhancers for LINGO1 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
GH15J077630 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.1 +188.2 188199 3.9 HDGF CLOCK MLX ARID4B SIN3A ZNF2 ZBTB7B IRF4 ZNF213 E2F8 LINGO1 ENSG00000259562 IREB2 ENSG00000259322 HMG20A TBC1D2B LINGO1-AS1 PEAK1 GC15P077635 PIR57145
GH15J077817 Enhancer 1.4 FANTOM5 Ensembl ENCODE 681.7 +1.7 1712 3.1 ATF1 RB1 ARNT SIN3A KLF14 YY1 ZNF335 ZNF121 GLIS2 ZFP91 LINGO1 ENSG00000259213 LOC645752 ACSBG1 HMG20A DNAJA4 GC15M077805
GH15J077821 Enhancer 0.9 FANTOM5 ENCODE 655.1 -0.7 -683 0.3 CTCF MXI1 KLF17 ZNF2 RAD21 CC2D1A ARID2 PATZ1 ZNF143 SMC3 LINGO1 ENSG00000259213 GC15P077854
GH15J077822 Enhancer 0.3 FANTOM5 657.8 -1.6 -1552 0.3 ZIC2 LINGO1 ACSBG1 GC15P077854
GH15J077606 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.5 +213.3 213306 1.7 HDGF BCOR MAX EBF1 CEBPG ZIC2 YY1 ZNF335 ZFHX2 ZNF316 LINGO1 LOC101929457 GC15P077635 LOC105370906 PIR57145
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LINGO1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LINGO1 gene promoter:
  • Gfi-1
  • C/EBPbeta
  • CUTL1
  • S8
  • RelA
  • SRF
  • AP-1
  • Egr-3
  • SRF (504 AA)
  • CP2

Genomic Locations for LINGO1 Gene

Genomic Locations for LINGO1 Gene
chr15:77,613,024-77,820,900
(GRCh38/hg38)
Size:
207,877 bases
Orientation:
Minus strand
chr15:77,905,369-78,113,242
(GRCh37/hg19)
Size:
207,874 bases
Orientation:
Minus strand

Genomic View for LINGO1 Gene

Genes around LINGO1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LINGO1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINGO1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINGO1 Gene

Proteins for LINGO1 Gene

  • Protein details for LINGO1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96FE5-LIGO1_HUMAN
    Recommended name:
    Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
    Protein Accession:
    Q96FE5
    Secondary Accessions:
    • D3DW80
    • Q6NUK3
    • Q6UXM3
    • Q6VVG0
    • Q6VVG1
    • Q6VVG2
    • Q8N3K5
    • Q96K52

    Protein attributes for LINGO1 Gene

    Size:
    620 amino acids
    Molecular mass:
    69876 Da
    Quaternary structure:
    • Homotetramer (PubMed:17005555). Forms a ternary complex with RTN4R/NGFR and RTN4R/TNFRSF19 (PubMed:14966521, PubMed:15694321, PubMed:17005555). Interacts with NGRF and MYT1L (By similarity). Interacts with RTN4R (PubMed:19052207).

    Three dimensional structures from OCA and Proteopedia for LINGO1 Gene

    Alternative splice isoforms for LINGO1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LINGO1 Gene

Post-translational modifications for LINGO1 Gene

  • N-glycosylated. Contains predominantly high-mannose glycans.
  • Glycosylation at posLast=542542, isoforms=2526, isoforms=2505, isoforms=2492, isoforms=2341, isoforms=2293, posLast=274274, posLast=264264, isoforms=2202, and isoforms=2144
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LINGO1 Gene

Domains & Families for LINGO1 Gene

Gene Families for LINGO1 Gene

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

Suggested Antigen Peptide Sequences for LINGO1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96FE5

UniProtKB/Swiss-Prot:

LIGO1_HUMAN :
  • The intracellular domain of LINGO1 interacts with MYT1L.
Domain:
  • The intracellular domain of LINGO1 interacts with MYT1L.
genes like me logo Genes that share domains with LINGO1: view

Function for LINGO1 Gene

Molecular function for LINGO1 Gene

UniProtKB/Swiss-Prot Function:
Functional component of the Nogo receptor signaling complex (RTN4R/NGFR) in RhoA activation responsible for some inhibition of axonal regeneration by myelin-associated factors (PubMed:14966521, PubMed:15694321). Is also an important negative regulator of oligodentrocyte differentiation and axonal myelination (PubMed:15895088). Acts in conjunction with RTN4 and RTN4R in regulating neuronal precursor cell motility during cortical development (By similarity).

Phenotypes From GWAS Catalog for LINGO1 Gene

Gene Ontology (GO) - Molecular Function for LINGO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005154 epidermal growth factor receptor binding IBA --
GO:0005515 protein binding IPI,IEA 17726113
genes like me logo Genes that share ontologies with LINGO1: view
genes like me logo Genes that share phenotypes with LINGO1: view

Animal Models for LINGO1 Gene

MGI Knock Outs for LINGO1:

Animal Model Products

  • Taconic Biosciences Mouse Models for LINGO1

miRNA for LINGO1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LINGO1 Gene

Localization for LINGO1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LINGO1 Gene

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 LINGO1 gene
Compartment Confidence
plasma membrane 5
extracellular 4
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LINGO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LINGO1: view

Pathways & Interactions for LINGO1 Gene

genes like me logo Genes that share pathways with LINGO1: view

Pathways by source for LINGO1 Gene

1 GeneGo (Thomson Reuters) pathway for LINGO1 Gene
1 Cell Signaling Technology pathway for LINGO1 Gene

SIGNOR curated interactions for LINGO1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for LINGO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IBA --
GO:0007409 axonogenesis IBA --
GO:0050771 negative regulation of axonogenesis TAS --
genes like me logo Genes that share ontologies with LINGO1: view

Drugs & Compounds for LINGO1 Gene

No Compound Related Data Available

Transcripts for LINGO1 Gene

mRNA/cDNA for LINGO1 Gene

Unigene Clusters for LINGO1 Gene

Leucine rich repeat and Ig domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LINGO1 Gene

No ASD Table

Relevant External Links for LINGO1 Gene

GeneLoc Exon Structure for
LINGO1
ECgene alternative splicing isoforms for
LINGO1

Expression for LINGO1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LINGO1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LINGO1 Gene

This gene is overexpressed in Brain - Cortex (x9.2), Brain - Frontal Cortex (BA9) (x7.3), Brain - Anterior cingulate cortex (BA24) (x7.0), Brain - Hippocampus (x5.7), and Brain - Amygdala (x5.0).

Protein differential expression in normal tissues from HIPED for LINGO1 Gene

This gene is overexpressed in Brain (25.7), Fetal Brain (14.9), Pancreas (11.7), and Frontal cortex (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LINGO1 Gene



Protein tissue co-expression partners for LINGO1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LINGO1 Gene:

LINGO1

SOURCE GeneReport for Unigene cluster for LINGO1 Gene:

Hs.656765

mRNA Expression by UniProt/SwissProt for LINGO1 Gene:

Q96FE5-LIGO1_HUMAN
Tissue specificity: Expressed exclusively in the central nervous system. Highest level in the in amygdala, hippocampus, thalamus and cerebral cortex. In the rest of the brain a basal expression seems to be always present. Up-regulated in substantia nigra neurons from Parkinson disease patients.

Evidence on tissue expression from TISSUES for LINGO1 Gene

  • Nervous system(4.9)
  • Eye(2.3)
genes like me logo Genes that share expression patterns with LINGO1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LINGO1 Gene

Orthologs for LINGO1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LINGO1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LINGO1 34 33
  • 99.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LINGO1 34 33
  • 95.16 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LINGO1 34 33
  • 94.84 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LINGO1 34
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lingo1 16 34 33
  • 92.07 (n)
rat
(Rattus norvegicus)
Mammalia Lingo1 33
  • 92.04 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LINGO1 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves LINGO1 34 33
  • 84.28 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LINGO1 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lingo1 33
  • 73.98 (n)
zebrafish
(Danio rerio)
Actinopterygii lingo1a 34 33
  • 74.23 (n)
OneToMany
lingo1b 34
  • 72 (a)
OneToMany
Dr.12903 33
Species where no ortholog for LINGO1 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)
  • fruit fly (Drosophila melanogaster)
  • 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 LINGO1 Gene

ENSEMBL:
Gene Tree for LINGO1 (if available)
TreeFam:
Gene Tree for LINGO1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LINGO1: view image

Paralogs for LINGO1 Gene

(9) SIMAP similar genes for LINGO1 Gene using alignment to 9 proteins:

  • LIGO1_HUMAN
  • H0YMX3_HUMAN
  • H0YNK7_HUMAN
  • H3BM59_HUMAN
  • H3BMN3_HUMAN
  • H3BMW2_HUMAN
  • H3BN48_HUMAN
  • H3BQ49_HUMAN
  • H3BS32_HUMAN
genes like me logo Genes that share paralogs with LINGO1: view

Variants for LINGO1 Gene

Sequence variations from dbSNP and Humsavar for LINGO1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000002354 -- 77,615,381(-) C/T coding_sequence_variant, missense_variant
rs1000010605 -- 77,693,832(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000032442 -- 77,752,815(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000041754 -- 77,693,538(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000052402 -- 77,655,844(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LINGO1 Gene

Variant ID Type Subtype PubMed ID
nsv958021 CNV deletion 24416366
nsv94941 CNV deletion 16902084
nsv833062 CNV loss 17160897
nsv833061 CNV loss 17160897
nsv833060 CNV gain 17160897
nsv827403 CNV loss 20364138
nsv827402 CNV loss 20364138
nsv819143 CNV loss 19587683
nsv570190 CNV gain+loss 21841781
nsv570173 CNV loss 21841781
nsv570172 CNV loss 21841781
nsv570171 CNV loss 21841781
nsv570159 CNV loss 21841781
nsv570150 CNV loss 21841781
nsv570142 CNV loss 21841781
nsv519383 CNV loss 19592680
nsv512407 CNV loss 21212237
nsv479401 CNV novel sequence insertion 20440878
nsv476397 CNV novel sequence insertion 20440878
nsv472256 CNV novel sequence insertion 20440878
nsv471255 CNV loss 18288195
nsv1625 CNV insertion 18451855
nsv1131205 CNV deletion 24896259
nsv1116463 OTHER inversion 24896259
nsv1116086 CNV deletion 24896259
nsv1071221 CNV deletion 25765185
nsv1070283 CNV deletion 25765185
nsv1070058 CNV deletion 25765185
nsv1040852 CNV gain 25217958
nsv1036749 CNV gain 25217958
esv996097 CNV deletion 20482838
esv9490 CNV loss 19470904
esv7618 CNV loss 19470904
esv7445 CNV loss 19470904
esv4114 CNV loss 18987735
esv3636976 CNV loss 21293372
esv3636975 CNV loss 21293372
esv3636974 CNV loss 21293372
esv3569742 CNV gain 25503493
esv3553 CNV loss 18987735
esv3552712 CNV deletion 23714750
esv3552710 CNV deletion 23714750
esv3438594 CNV insertion 20981092
esv3422804 CNV duplication 20981092
esv3397637 CNV duplication 20981092
esv3305803 CNV mobile element insertion 20981092
esv2749909 CNV deletion 23290073
esv2749908 CNV deletion 23290073
esv2749898 CNV deletion 23290073
esv2675154 CNV deletion 23128226
esv2667411 CNV deletion 23128226
esv2662208 CNV deletion 23128226
esv2569789 CNV deletion 19546169
esv25321 CNV loss 19812545
esv23904 CNV loss 19812545
esv23682 CNV loss 19812545
esv21599 CNV loss 19812545
esv2102930 CNV deletion 18987734
esv1355090 CNV deletion 17803354
esv1180892 CNV insertion 17803354
esv1008836 CNV loss 20482838
dgv4672n54 CNV gain 21841781
dgv4671n54 CNV loss 21841781
dgv4670n54 CNV gain+loss 21841781
dgv4669n54 CNV gain 21841781
dgv4668n54 CNV loss 21841781
dgv4667n54 CNV gain 21841781
dgv4666n54 CNV loss 21841781
dgv4665n54 CNV loss 21841781
dgv4664n54 CNV loss 21841781
dgv4663n54 CNV loss 21841781
dgv4662n54 CNV loss 21841781
dgv4661n54 CNV loss 21841781
dgv4660n54 CNV loss 21841781
dgv443n67 CNV loss 20364138
dgv442n67 CNV loss 20364138
dgv1247n106 CNV deletion 24896259
dgv1246n106 CNV deletion 24896259

Variation tolerance for LINGO1 Gene

Residual Variation Intolerance Score: 8.07% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LINGO1 Gene

Human Gene Mutation Database (HGMD)
LINGO1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINGO1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LINGO1 Gene

Disorders for LINGO1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LINGO1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
essential tremor
  • benign essential tremor
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LINGO1

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 LINGO1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LINGO1 Gene

Publications for LINGO1 Gene

  1. LRRN6A/LERN1 (leucine-rich repeat neuronal protein 1), a novel gene with enriched expression in limbic system and neocortex. (PMID: 14686891) Carim-Todd L … Sumoy L (The European journal of neuroscience 2003) 2 3 4 22 58
  2. LINGO1 rs9652490 is associated with essential tremor and Parkinson disease. (PMID: 19720553) Vilariño-Güell C … Farrer MJ (Parkinsonism & related disorders 2010) 3 44 58
  3. LINGO1 and LINGO2 variants are associated with essential tremor and Parkinson disease. (PMID: 20369371) Vilariño-Güell C … Farrer MJ (Neurogenetics 2010) 3 44 58
  4. LINGO1 polymorphisms are associated with essential tremor in Europeans. (PMID: 20310002) Thier S … Klebe S (Movement disorders : official journal of the Movement Disorder Society 2010) 3 44 58
  5. Analysis of LINGO1 (rs9652490) polymorphism in sporadic Parkinson's disease in a Polish population, and a meta-analysis. (PMID: 20117178) Białecka M … Drozdzik M (Neuroscience letters 2010) 3 44 58

Products for LINGO1 Gene

Sources for LINGO1 Gene

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