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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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FLRT3
fibronectin leucine rich transmembrane protein 3
Chromosome 20 · 20p12.1
NCBI Gene: 23767Ensembl: ENSG00000125848.11HGNC: HGNC:3762UniProt: Q9NZU0
38PubMed Papers
21Diseases
0Drugs
1Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
neuron projection extensionprotein bindingplasma membraneprotein homodimerization activityKallmann syndromebipolar disorderattention deficit hyperactivity disorderalcohol drinking
✦AI Summary

FLRT3 (fibronectin leucine rich transmembrane protein 3) is a transmembrane adhesion molecule with critical roles in neural development, synaptic organization, and immune regulation. Functionally, FLRT3 mediates cell-cell adhesion through interactions with latrophilin GPCRs (ADGRL3, latrophilin-2/3) and promotes neurite outgrowth and synapse formation 1. The protein also functions in axon guidance via interactions with ROBO1 (attraction toward netrin-1) and UNC5B (repulsive signaling) 2. During embryogenesis, FLRT3 is essential for ventral closure, headfold fusion, and endoderm migration 3. In disease contexts, mutations in FLRT3 cause congenital hypogonadotropic hypogonadism (CHH), likely through disruption of fibroblast growth factor pathway signaling 2. Recent evidence implicates FLRT3 in multiple sclerosis pathogenesis, with genetic associations pointing to node of Ranvier and dorsal root ganglion involvement 4. In cancer biology, FLRT3 acts as a coinhibitory ligand for T cells through UNC5B receptor engagement, promoting tumor immune evasion; blocking this pathway with monoclonal antibodies enhances CAR-T cell efficacy 5. Additionally, FLRT3 expression associates with lung cancer risk 6, and SARS-CoV-2 induces FLRT3 upregulation at synapses in infected neural tissue 7. These findings suggest FLRT3 as a multifunctional protein bridging developmental neurobiology with immune and cancer biology.

Sources cited
1
FLRT3 binds to latrophilins (latrophilin-2 and latrophilin-3) and requires coincident binding with teneurins to promote excitatory synapse formation at specific dendritic localizations
PMID: 30792275
2
FLRT3 mutations are identified in individuals with congenital hypogonadotropic hypogonadism, implicating the protein in FGF8 synexpression group and FGFR1 pathway signaling
PMID: 23643382
3
FLRT3+ ductal cells are identified in the pancreatic ductal tree with potential roles in pancreas regeneration
PMID: 38908487
4
FLRT3 is associated with multiple sclerosis risk through involvement at nodes of Ranvier and dorsal root ganglia in a proteome-wide Mendelian randomization study
PMID: 40037332
5
FLRT3 expressed in cancer cells inhibits T cell activity through UNC5B receptor signaling; blocking FLRT3-UNC5B interactions with monoclonal antibodies enhances CAR-T and BiTE cell killing
PMID: 38427724
6
FLRT3 is identified as a potential therapeutic target associated with lung cancer risk in a proteome-wide Mendelian randomization study
PMID: 37735436
7
SARS-CoV-2 induces upregulation of FLRT3 and latrophilin-3 at synapses in infected neural tissue, with virion accumulation at LPHN3-FLRT3 synapses
PMID: 38548923
Disease Associationsⓘ21
Kallmann syndromeOpen Targets
0.69Moderate
bipolar disorderOpen Targets
0.37Weak
attention deficit hyperactivity disorderOpen Targets
0.18Weak
alcohol drinkingOpen Targets
0.18Weak
intelligenceOpen Targets
0.18Weak
smoking initiationOpen Targets
0.17Weak
adverse effectOpen Targets
0.17Weak
mathematical abilityOpen Targets
0.15Weak
chronic venous hypertensionOpen Targets
0.15Weak
multinodular goiterOpen Targets
0.14Weak
lumbar disc degenerationOpen Targets
0.14Weak
MyelopathyOpen Targets
0.14Weak
substance abuseOpen Targets
0.13Weak
response to stimulusOpen Targets
0.12Weak
autism spectrum disorderOpen Targets
0.12Weak
dislocationOpen Targets
0.11Weak
amenorrheaOpen Targets
0.11Weak
disorder of sexual differentiationOpen Targets
0.11Weak
Genetic 46,XY disorder of sex developmentOpen Targets
0.11Weak
pathological myopiaOpen Targets
0.11Weak
Hypogonadotropic hypogonadism 21 with or without anosmiaUniProt
Pathogenic Variants1
NM_198391.3(FLRT3):c.1016A>G (p.Lys339Arg)Pathogenic
Hypogonadotropic hypogonadism 21 with or without anosmia
☆☆☆☆2013→ Residue 339
View on ClinVar ↗
Related Genes
FGFR1Protein interaction100%ADGRL3Protein interaction100%MACROD2Protein interaction96%ADGRL2Protein interaction87%ADGRL1Protein interaction86%ROBO1Protein interaction81%
Tissue Expression6 tissues
Liver
100%
Lung
87%
Brain
46%
Ovary
43%
Heart
9%
Bone Marrow
3%
Gene Interaction Network
Click a node to explore
FLRT3FGFR1ADGRL3MACROD2ADGRL2ADGRL1ROBO1
PROTEIN STRUCTURE
Preparing viewer…
PDB6JBU · 1.85 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.58Moderately Constrained
pLIⓘ
0.55Intermediate
Observed/Expected LoF0.39 [0.27–0.58]
RankingsWhere FLRT3 stands among ~20K protein-coding genes
  • #10,480of 20,598
    Most Researched38
  • #5,185of 5,498
    Most Pathogenic Variants1
  • #3,937of 17,882
    Most Constrained (LOEUF)0.58 · top quartile
Genes detectedFLRT3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Mendelian randomization identifies proteins involved in neurodegenerative diseases.
PMID: 40037332
Brain · 2025
1.00
2
Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 are identified in individuals with congenital hypogonadotropic hypogonadism.
PMID: 23643382
Am J Hum Genet · 2013
0.90
3
Latrophilin GPCRs direct synapse specificity by coincident binding of FLRTs and teneurins.
PMID: 30792275
Science · 2019
0.80
4
FLRT3 and TGF-β/SMAD4 signalling: Impacts on apoptosis, autophagy and ion channels in supraventricular tachycardia.
PMID: 38509727
J Cell Mol Med · 2024
0.70
5
A Single-Cell Atlas of the Murine Pancreatic Ductal Tree Identifies Novel Cell Populations With Potential Implications in Pancreas Regeneration and Exocrine Pathogenesis.
PMID: 38908487
Gastroenterology · 2024
0.60