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FLRT1 fibronectin leucine rich transmembrane protein 1 [ Homo sapiens (human) ]

Gene ID: 23769, updated on 9-Sep-2025
Official Symbol
FLRT1provided by HGNC
Official Full Name
fibronectin leucine rich transmembrane protein 1provided by HGNC
Primary source
HGNC:HGNC:3760
See related
Ensembl:ENSG00000126500 MIM:604806; AllianceGenome:HGNC:3760
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPG68
Summary
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]
Expression
Broad expression in brain (RPKM 4.3), adrenal (RPKM 3.2) and 14 other tissues See more
Orthologs
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See FLRT1 in Genome Data Viewer
Location:
11q13.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64035931..64119171)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64025770..64109031)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (63803403..63886643)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63764275-63765212 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63766149-63767086 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:63767087-63768022 and GRCh37_chr11:63768035-63768542 Neighboring gene OTU deubiquitinase, ubiquitin aldehyde binding 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63775344-63775934 Neighboring gene mono-ADP ribosylhydrolase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63789022-63789720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63789721-63790419 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63791118-63791816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63795215-63796016 Neighboring gene uncharacterized LOC124902685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63803443-63804345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63804346-63805247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63815687-63816245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63816558-63817058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820013-63820556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820557-63821100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63821645-63822187 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63826482-63827200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63836633-63837360 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:63840775-63840963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63860723-63861393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63861723-63862230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63877842-63878622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63889359-63890290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63896949-63897542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63913439-63913940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63919856-63920851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63920852-63921846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63933104-63933604 Neighboring gene uncharacterized LOC105369339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3460 Neighboring gene MPRA-validated peak1294 silencer Neighboring gene uncharacterized LOC124902686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63948751-63949252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63949253-63949752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63951637-63952142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3461 Neighboring gene stress induced phosphoprotein 1

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Identification of FLRT1, FLRT2, and FLRT3: a novel family of transmembrane leucine-rich repeat proteins. Lacy SE, et al. Genomics, 1999 Dec 15. PMID 10644439
  2. Critical role of FLRT1 phosphorylation in the interdependent regulation of FLRT1 function and FGF receptor signalling. Wheldon LM, et al. PLoS One, 2010 Apr 22. PMID 20421966, Free PMC Article
  3. Yeast Two-Hybrid Screening for Proteins that Interact with the Extracellular Domain of Amyloid Precursor Protein. Yu Y, et al. Neurosci Bull, 2016 Apr. PMID 26960425, Free PMC Article
  4. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Novarino G, et al. Science, 2014 Jan 31. PMID 24482476, Free PMC Article
  5. The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis. Xu D, et al. Nature, 2020 Apr. PMID 32322062

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC21624

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables fibroblast growth factor receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables protein-macromolecule adaptor activity NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in dendrite development IEA
Inferred from Electronic Annotation
more info
  
involved_in dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in fibroblast growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in fibroblast growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron projection extension IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron projection extension ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular matrix NAS
Non-traceable Author Statement
more info
 PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with focal adhesion IEA
Inferred from Electronic Annotation
more info
  
located_in focal adhesion IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with focal adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in neuron projection IEA
Inferred from Electronic Annotation
more info
  
located_in neuron projection terminus IEA
Inferred from Electronic Annotation
more info
  
located_in neuron projection terminus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in neuronal cell body membrane IEA
Inferred from Electronic Annotation
more info
  
located_in neuronal cell body membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
Preferred Names
leucine-rich repeat transmembrane protein FLRT1
Names
fibronectin-like domain-containing leucine-rich transmembrane protein 1

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001384466.1 → NP_001371395.1  leucine-rich repeat transmembrane protein FLRT1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000721, AP006333
    Consensus CDS
    CCDS8057.1
    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1
    Conserved Domains (4) summary
    PRK15370
    Location:58 → 329
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    TIGR00864
    Location:300 → 406
    PCC; polycystin cation channel protein
    smart00060
    Location:441 → 505
    FN3; Fibronectin type 3 domain
    sd00033
    Location:108 → 128
    LRR_RI; leucine-rich repeat [structural motif]

  2. NM_001423967.1 → NP_001410896.1  leucine-rich repeat transmembrane protein FLRT1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has the same exon combination as variant 1 and uses a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1
    Source sequence(s)
    AP000721, AP006333
    Related
    ENSP00000520551.1, ENST00000715990.1

  3. NM_013280.5 → NP_037412.2  leucine-rich repeat transmembrane protein FLRT1 isoform 1

    See identical proteins and their annotated locations for NP_037412.2

    Status: REVIEWED

    Source sequence(s)
    AP000721, AP006333
    Consensus CDS
    CCDS8057.1
    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1
    Related
    ENSP00000507207.1, ENST00000682287.1
    Conserved Domains (4) summary
    PRK15370
    Location:58 → 329
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    TIGR00864
    Location:300 → 406
    PCC; polycystin cation channel protein
    smart00060
    Location:441 → 505
    FN3; Fibronectin type 3 domain
    sd00033
    Location:108 → 128
    LRR_RI; leucine-rich repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    64035931..64119171
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426696.1 → XP_047282652.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1
    Related
    ENSP00000579325.1, ENST00000909266.1

  2. XM_047426698.1 → XP_047282654.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1

  3. XM_047426699.1 → XP_047282655.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1

  4. XM_047426697.1 → XP_047282653.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1
    Related
    ENSP00000246841.3, ENST00000246841.3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64025770..64109031
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368272.1 → XP_054224247.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1

  2. XM_054368271.1 → XP_054224246.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

    UniProtKB/Swiss-Prot
    A0A6E1VY70, Q8WVA2, Q9NZU1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NZU1.4 GenPept UniProtKB/Swiss-Prot:Q9NZU1

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