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Aliases for FLRT1 Gene

Aliases for FLRT1 Gene

  • Fibronectin Leucine Rich Transmembrane Protein 1 2 3 5
  • Fibronectin-Like Domain-Containing Leucine-Rich Transmembrane Protein 1 3 4
  • Leucine-Rich Repeat Transmembrane Protein FLRT1 3
  • SPG68 3

External Ids for FLRT1 Gene

Previous GeneCards Identifiers for FLRT1 Gene

  • GC11M066466
  • GC11M065550
  • GC11P064122
  • GC11P063646
  • GC11P063627
  • GC11P063871
  • GC11P060200

Summaries for FLRT1 Gene

Entrez Gene Summary for FLRT1 Gene

  • This gene encodes a member of the fibronectin leucine rich transmembrane protein (FLRT) family. The family members may function in cell adhesion and/or receptor signalling. Their protein structures resemble small leucine-rich proteoglycans found in the extracellular matrix. The encoded protein shares sequence similarity with two other family members, FLRT2 and FLRT3. This gene is expressed in kidney and brain. [provided by RefSeq, Jul 2008]

GeneCards Summary for FLRT1 Gene

FLRT1 (Fibronectin Leucine Rich Transmembrane Protein 1) is a Protein Coding gene. Diseases associated with FLRT1 include Autosomal Recessive Spastic Paraplegia Type 68. Among its related pathways are Signaling by FGFR2 and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include protein binding, bridging and signal transducer activity, downstream of receptor. An important paralog of this gene is FLRT3.

UniProtKB/Swiss-Prot for FLRT1 Gene

  • Plays a role in fibroblast growth factor-mediated signaling cascades that lead to the activation of MAP kinases. Promotes neurite outgrowth via FGFR1-mediated activation of downstream MAP kinases. Promotes an increase both in neurite number and in neurite length. May play a role in cell-cell adhesion and cell guidance via its interaction with ADGRL1/LPHN1 and ADGRL3.

Additional gene information for FLRT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FLRT1 Gene

Genomics for FLRT1 Gene

GeneHancer (GH) Regulatory Elements for FLRT1 Gene

Promoters and enhancers for FLRT1 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
GH11I064036 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 550.8 +0.6 585 1.1 CTCF MXI1 MAX ZIC2 FOXM1 GLIS2 PATZ1 PRDM10 EZH2 MAZ ENSG00000256824 FLRT1 VEGFB PIR44183 MACROD1
GH11I064034 Enhancer 0.7 dbSUPER 550.8 -1.1 -1077 1.7 CTCF SIN3A HIC1 ZNF335 ZFHX2 GLIS2 ZNF366 PATZ1 ZNF143 CHD2 FLRT1 ENSG00000256824 PIR58012 MACROD1
GH11I064103 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.2 +67.3 67275 0.1 FLRT1 PIR46997 ENSG00000256481 MACROD1 ENSG00000256824
GH11I064037 Enhancer 0.4 dbSUPER 550.8 +2.0 1970 0.5 SUZ12 EZH2 ENSG00000256824 FLRT1 MACROD1 PIR44183
GH11I064237 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 5.1 +209.3 209349 16.6 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC PPP1R14B FKBP2 LOC105369340 PLCB3 TRPT1 LOC102723878 VEGFB TRMT112 FERMT3 GPR137
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FLRT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FLRT1 gene promoter:

Genomic Locations for FLRT1 Gene

Genomic Locations for FLRT1 Gene
83,214 bases
Plus strand

Genomic View for FLRT1 Gene

Genes around FLRT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FLRT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FLRT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FLRT1 Gene

Proteins for FLRT1 Gene

  • Protein details for FLRT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Leucine-rich repeat transmembrane protein FLRT1
    Protein Accession:
    Secondary Accessions:
    • Q8WVA2

    Protein attributes for FLRT1 Gene

    646 amino acids
    Molecular mass:
    71358 Da
    Quaternary structure:
    • Interacts with FGFR1. Interacts (via extracellular domain) with ADGRL1/LPHN1 and ADGRL3 (via olfactomedin-like domain).
    • Sequence=AAF28459.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH18370.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAQ88675.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAF82620.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=EAW74194.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for FLRT1 Gene

Post-translational modifications for FLRT1 Gene

  • N-glycosylated.
  • Phosphorylated in response to FGFR1 signaling, but is not a direct substrate of FGFR1 or SRC. A mutant where the Tyr phosphorylation sites have been replaced by Phe displays constitutive FGFR1-dependent activation of downstream MAP kinases.
  • Proteolytic cleavage in the juxtamembrane region gives rise to a soluble ectodomain.
  • Glycosylation at posLast=221221 and posLast=277277

Other Protein References for FLRT1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FLRT1 Gene

Domains & Families for FLRT1 Gene

Gene Families for FLRT1 Gene

Suggested Antigen Peptide Sequences for FLRT1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FLRT1: view

No data available for UniProtKB/Swiss-Prot for FLRT1 Gene

Function for FLRT1 Gene

Molecular function for FLRT1 Gene

GENATLAS Biochemistry:
fibronectin,leucine rich transmembrane protein1,extracellular matrix protein,expressed in kidney and brain
UniProtKB/Swiss-Prot Function:
Plays a role in fibroblast growth factor-mediated signaling cascades that lead to the activation of MAP kinases. Promotes neurite outgrowth via FGFR1-mediated activation of downstream MAP kinases. Promotes an increase both in neurite number and in neurite length. May play a role in cell-cell adhesion and cell guidance via its interaction with ADGRL1/LPHN1 and ADGRL3.

Phenotypes From GWAS Catalog for FLRT1 Gene

Gene Ontology (GO) - Molecular Function for FLRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
GO:0005057 signal transducer activity, downstream of receptor NAS 10644439
GO:0005104 fibroblast growth factor receptor binding IEA --
GO:0030674 protein binding, bridging NAS 10644439
genes like me logo Genes that share ontologies with FLRT1: view
genes like me logo Genes that share phenotypes with FLRT1: view

Animal Models for FLRT1 Gene

MGI Knock Outs for FLRT1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for FLRT1 Gene

Localization for FLRT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FLRT1 Gene

Cell membrane; Single-pass membrane protein. Endoplasmic reticulum membrane. Cytoplasmic vesicle membrane. Cytoplasm, perinuclear region. Cell junction, focal adhesion. Secreted. Cell projection. Cell junction. Note=In addition to its location at the cell membrane, colocalizes with FGFR1 in punctate perinuclear cytoplasmic vesicles. Detected along neurites and at contacts between neurite termini and other cells. Proteolytic cleavage gives rise to a shedded ectodomain. {ECO:0000250 UniProtKB:Q6RKD8}.

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 FLRT1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 3
peroxisome 2
mitochondrion 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for FLRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix NAS 10644439
GO:0005615 extracellular space IEA --
GO:0005737 cytoplasm IBA --
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with FLRT1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for FLRT1 Gene

Pathways & Interactions for FLRT1 Gene

genes like me logo Genes that share pathways with FLRT1: view

Pathways by source for FLRT1 Gene

Gene Ontology (GO) - Biological Process for FLRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0007155 cell adhesion IEA --
GO:0007275 multicellular organism development IEA --
GO:0008543 fibroblast growth factor receptor signaling pathway IEA,TAS --
GO:0016358 dendrite development IEA,ISS --
genes like me logo Genes that share ontologies with FLRT1: view

No data available for SIGNOR curated interactions for FLRT1 Gene

Drugs & Compounds for FLRT1 Gene

No Compound Related Data Available

Transcripts for FLRT1 Gene

mRNA/cDNA for FLRT1 Gene

Unigene Clusters for FLRT1 Gene

Fibronectin leucine rich transmembrane protein 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FLRT1 Gene

No ASD Table

Relevant External Links for FLRT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FLRT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FLRT1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for FLRT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of FLRT1 Gene:


SOURCE GeneReport for Unigene cluster for FLRT1 Gene:


mRNA Expression by UniProt/SwissProt for FLRT1 Gene:

Tissue specificity: Expressed in kidney and brain.

Evidence on tissue expression from TISSUES for FLRT1 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with FLRT1: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for FLRT1 Gene

Orthologs for FLRT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for FLRT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FLRT1 33 34
  • 98.96 (n)
(Bos Taurus)
Mammalia FLRT1 33 34
  • 92.76 (n)
(Canis familiaris)
Mammalia FLRT1 33 34
  • 91.05 (n)
(Rattus norvegicus)
Mammalia Flrt1 33
  • 89.56 (n)
(Mus musculus)
Mammalia Flrt1 33 16 34
  • 89.27 (n)
(Ornithorhynchus anatinus)
Mammalia FLRT1 34
  • 83 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 22 (a)
(Gallus gallus)
Aves -- 34
  • 23 (a)
(Anolis carolinensis)
Reptilia FLRT1 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia flrt1 33
  • 71.9 (n)
(Danio rerio)
Actinopterygii flrt1a 33 34
  • 60.91 (n)
flrt1b 34
  • 57 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
-- 34
  • 33 (a)
Species where no ortholog for FLRT1 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 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 FLRT1 Gene

Gene Tree for FLRT1 (if available)
Gene Tree for FLRT1 (if available)

Paralogs for FLRT1 Gene

Paralogs for FLRT1 Gene

(2) SIMAP similar genes for FLRT1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with FLRT1: view

Variants for FLRT1 Gene

Sequence variations from dbSNP and Humsavar for FLRT1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs116999073 likely-benign, Peripheral neuropathy 64,116,674(+) A/G coding_sequence_variant, missense_variant
rs138676741 likely-benign, Peripheral neuropathy 64,117,451(+) C/T coding_sequence_variant, missense_variant
rs139711112 likely-benign, Peripheral neuropathy 64,117,050(+) C/T coding_sequence_variant, synonymous_variant
rs139768227 uncertain-significance, Peripheral neuropathy 64,116,305(+) C/G/T coding_sequence_variant, missense_variant
rs140274429 uncertain-significance, Peripheral neuropathy 64,117,996(+) G/A/C coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for FLRT1 Gene

Variant ID Type Subtype PubMed ID
dgv15n68 CNV loss 17160897
esv2744613 CNV deletion 23290073
esv3431264 CNV duplication 20981092
nsv1078325 CNV duplication 25765185
nsv1134139 CNV deletion 24896259
nsv1141196 CNV duplication 24896259
nsv356 CNV deletion 18451855
nsv469961 CNV loss 18288195
nsv473286 CNV novel sequence insertion 20440878
nsv951010 CNV deletion 24416366

Variation tolerance for FLRT1 Gene

Residual Variation Intolerance Score: 41.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.70; 32.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FLRT1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FLRT1 Gene

Disorders for FLRT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for FLRT1 Gene - From: Orphanet

Disorder Aliases PubMed IDs
autosomal recessive spastic paraplegia type 68
  • spg68
- elite association - COSMIC cancer census association via MalaCards
Search FLRT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FLRT1

genes like me logo Genes that share disorders with FLRT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FLRT1 Gene

Publications for FLRT1 Gene

  1. Identification of FLRT1, FLRT2, and FLRT3: a novel family of transmembrane leucine-rich repeat proteins. (PMID: 10644439) Lacy SE … Kunkel LM (Genomics 1999) 2 3 4 58
  2. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PMID: 24482476) Novarino G … Gleeson JG (Science (New York, N.Y.) 2014) 2 3 58
  3. Critical role of FLRT1 phosphorylation in the interdependent regulation of FLRT1 function and FGF receptor signalling. (PMID: 20421966) Wheldon LM … Heath JK (PloS one 2010) 3 22 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for FLRT1 Gene

Sources for FLRT1 Gene

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