FLRT1 Gene (Protein Coding)

Fibronectin Leucine Rich Transmembrane Protein 1

GC11P064036
GIFtS:
40
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 ... See more...

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 4
  • SPG68 2 3
  • MGC21624 2
  • FLRT1 5

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 Spastic Paraplegia, Optic Atrophy, And Neuropathy and Spastic Paraplegia 27, Autosomal Recessive. Among its related pathways are Signaling by GPCR and Negative regulation of FGFR1 signaling. Gene Ontology (GO) annotations related to this gene include protein binding, bridging and obsolete signal transducer activity, downstream of receptor. An important paralog of this gene is FLRT3.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for FLRT1 Gene

Genomics for FLRT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for FLRT1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FLRT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for FLRT1

Top Transcription factor binding sites by QIAGEN in the FLRT1 gene promoter:
  • Bach1
  • COUP
  • COUP-TF
  • COUP-TF1
  • Egr-1
  • FOXL1
  • FOXO4
  • HNF-4alpha1
  • HNF-4alpha2
  • S8

Genomic Locations for FLRT1 Gene

Latest Assembly
chr11:64,035,931-64,127,289
(GRCh38/hg38)
Size:
91,359 bases
Orientation:
Plus strand

Previous Assembly
chr11:63,803,403-63,886,643
(GRCh37/hg19 by Entrez Gene)
Size:
83,241 bases
Orientation:
Plus strand

chr11:63,870,660-63,886,645
(GRCh37/hg19 by Ensembl)
Size:
15,986 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for FLRT1 Gene

Proteins for FLRT1 Gene

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

    Protein Symbol:
    Q9NZU1-FLRT1_HUMAN
    Recommended name:
    Leucine-rich repeat transmembrane protein FLRT1
    Protein Accession:
    Q9NZU1
    Secondary Accessions:
    • Q8WVA2

    Protein attributes for FLRT1 Gene

    Size:
    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).
    SequenceCaution:
    • 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

Protein Expression for FLRT1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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 Asn221 and Asn277
  • Modification sites at PhosphoSitePlus

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

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

Protein Domains for FLRT1 Gene

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

Suggested Antigen Peptide Sequences for FLRT1 Gene

GenScript: Design optimal peptide antigens:
  • Fibronectin-like domain-containing leucine-rich transmembrane protein 1 (FLRT1_HUMAN)
genes like me logo Genes that share domains with FLRT1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for FLRT1 Gene

Function for FLRT1 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for FLRT1 Gene

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.
GENATLAS Biochemistry:
fibronectin,leucine rich transmembrane protein1,extracellular matrix protein,expressed in kidney and brain

Phenotypes From GWAS Catalog for FLRT1 Gene

Gene Ontology (GO) - Molecular Function for FLRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein 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

Human Phenotype Ontology for FLRT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FLRT1 Gene

MGI Knock Outs for FLRT1:

Animal Models for research

  • Taconic Biosciences Mouse Models for FLRT1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FLRT1

No data available for Enzyme Numbers (IUBMB) , 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, neuron 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

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 FLRT1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 1
peroxisome 1
nucleus 1
mitochondrion 0
cytosol 0
lysosome 0

Gene Ontology (GO) - Cellular Components for FLRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane ISS, NAS 10644439
GO:0005911 cell-cell junction ISS --
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:0007155 cell adhesion IEA --
GO:0008543 fibroblast growth factor receptor signaling pathway ISS, TAS --
GO:0016358 dendrite development ISS --
GO:1990138 neuron projection extension 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

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  1. Drug products for research
No Compound Related Data Available

Transcripts for FLRT1 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for FLRT1 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 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 FLRT1

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

No ASD Table

Relevant External Links for FLRT1 Gene

GeneLoc Exon Structure for
FLRT1

Expression for FLRT1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for FLRT1 Gene
mRNA expression by GTEx for FLRT1 GenemRNA expression by BioGPS for FLRT1 Gene

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for FLRT1

SOURCE GeneReport for Unigene cluster for FLRT1 Gene:

Hs.584876

mRNA Expression by UniProt/SwissProt for FLRT1 Gene:

Q9NZU1-FLRT1_HUMAN
Tissue specificity: Expressed in kidney and brain.

Evidence on tissue expression from TISSUES for FLRT1 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with FLRT1: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
 Mammalia FLRT1 30 31
  • 98.96 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia FLRT1 30 31
  • 92.76 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia FLRT1 30 31
  • 91.05 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Flrt1 30
  • 89.56 (n)
Mouse
(Mus musculus)
 Mammalia Flrt1 30 17 31
  • 89.27 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia FLRT1 31
  • 83 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 22 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves -- 31
  • 23 (a)
 ManyToMany
Lizard
(Anolis carolinensis)
 Reptilia FLRT1 31
  • 87 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia flrt1 30
  • 71.9 (n)
Zebrafish
(Danio rerio)
 Actinopterygii flrt1a 30 31
  • 60.91 (n)
 OneToMany
flrt1b 31
  • 57 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 35 (a)
 ManyToMany
-- 31
  • 33 (a)
 ManyToMany
Species where no ortholog for FLRT1 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)
  • 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for FLRT1 Gene

ENSEMBL:
Gene Tree for FLRT1 (if available)
TreeFam:
Gene Tree for FLRT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FLRT1: view image

Paralogs for FLRT1 Gene

Paralogs for FLRT1 Gene

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

  • FLRT1_HUMAN
genes like me logo Genes that share paralogs with FLRT1: view

Variants for FLRT1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for FLRT1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
835656 Uncertain Significance: Peripheral neuropathy 64,117,913(+) C/T
NM_014067.4(MACROD1):c.517+33326G>A 		MISSENSE_VARIANT,INTRON
840095 Uncertain Significance: Peripheral neuropathy 64,118,059(+) G/A
NM_014067.4(MACROD1):c.517+33180C>T 		MISSENSE_VARIANT,INTRON
842634 Uncertain Significance: Peripheral neuropathy 64,116,738(+) C/A
NM_014067.4(MACROD1):c.517+34501G>T 		MISSENSE_VARIANT,INTRON
845837 Uncertain Significance: Peripheral neuropathy 64,118,042(+) G/A
NM_014067.4(MACROD1):c.517+33197C>T 		MISSENSE_VARIANT,INTRON
857225 Uncertain Significance: Peripheral neuropathy 64,116,518(+) C/T
NM_014067.4(MACROD1):c.517+34721G>A 		MISSENSE_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FLRT1 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 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)
FLRT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FLRT1

SNP Genotyping and Copy Number Assays for research

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

Disorders for FLRT1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for FLRT1 Gene - From: ORP, COP, and GCD

- 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

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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
  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
  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 23
  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
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3

ExternalLinks

View latest publications for FLRT1 gene in Mastermind

Products for FLRT1 Gene

Sources for FLRT1 Gene