Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	23767
Gene name	Fibronectin leucine rich transmembrane protein 3
Gene symbol	FLRT3
Synonyms (NCBI Gene)	HH21
Chromosome	20
Chromosome location	20p12.1
Summary	This gene encodes a member of the fibronectin leucine rich transmembrane protein (FLRT) family. FLRTs may function in cell adhesion and/or receptor signalling. Their protein structures resemble small leucine-rich proteoglycans found in the extracellular m

miRTarBase ID	miRNA	Experiments
MIRT1996037	hsa-miR-323b-3p	CLIP-seq
MIRT1996038	hsa-miR-450b-5p	CLIP-seq
MIRT1996039	hsa-miR-4708-3p	CLIP-seq
MIRT1996040	hsa-miR-3065-5p	CLIP-seq
MIRT1996041	hsa-miR-3647-3p	CLIP-seq

63 Show/Hide all (63)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003345	Process	Proepicardium cell migration involved in pericardium morphogenesis	IEA
GO:0003345	Process	Proepicardium cell migration involved in pericardium morphogenesis	ISS
GO:0005104	Function	Fibroblast growth factor receptor binding	IEA
GO:0005515	Function	Protein binding	IPI	26235030, 26960425
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IDA	14706654, 26235030
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	NAS	10644439
GO:0005886	Component	Plasma membrane	TAS
GO:0005911	Component	Cell-cell junction	IEA
GO:0005925	Component	Focal adhesion	IEA
GO:0005925	Component	Focal adhesion	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007411	Process	Axon guidance	IEA
GO:0007411	Process	Axon guidance	IEA
GO:0007416	Process	Synapse assembly	IEA
GO:0007416	Process	Synapse assembly	ISS
GO:0007507	Process	Heart development	IEA
GO:0007507	Process	Heart development	ISS
GO:0008543	Process	Fibroblast growth factor receptor signaling pathway	IEA
GO:0008543	Process	Fibroblast growth factor receptor signaling pathway	ISS
GO:0016020	Component	Membrane	IEA
GO:0030054	Component	Cell junction	IDA
GO:0030054	Component	Cell junction	IEA
GO:0030424	Component	Axon	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	NAS	10644439
GO:0031012	Component	Extracellular matrix	NAS	10644439
GO:0031175	Process	Neuron projection development	IEA
GO:0031175	Process	Neuron projection development	ISS
GO:0032584	Component	Growth cone membrane	IEA
GO:0042734	Component	Presynaptic membrane	IEA
GO:0042803	Function	Protein homodimerization activity	IDA	26235030
GO:0042995	Component	Cell projection	IEA
GO:0043679	Component	Axon terminus	IEA
GO:0043679	Component	Axon terminus	ISS
GO:0044295	Component	Axonal growth cone	IEA
GO:0044295	Component	Axonal growth cone	ISS
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0045499	Function	Chemorepellent activity	IEA
GO:0048598	Process	Embryonic morphogenesis	IEA
GO:0048598	Process	Embryonic morphogenesis	ISS
GO:0048678	Process	Response to axon injury	IEA
GO:0048678	Process	Response to axon injury	ISS
GO:0050919	Process	Negative chemotaxis	IEA
GO:0051965	Process	Positive regulation of synapse assembly	IEA
GO:0060322	Process	Head development	IEA
GO:0060322	Process	Head development	ISS
GO:0070161	Component	Anchoring junction	IEA
GO:0097060	Component	Synaptic membrane	IEA
GO:0097060	Component	Synaptic membrane	ISS
GO:0098742	Process	Cell-cell adhesion via plasma-membrane adhesion molecules	IDA	26235030
GO:0098742	Process	Cell-cell adhesion via plasma-membrane adhesion molecules	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099560	Process	Synaptic membrane adhesion	IEA
GO:1990138	Process	Neuron projection extension	IEA
GO:1990138	Process	Neuron projection extension	IMP	14706654
GO:1990138	Process	Neuron projection extension	ISS

MIM	HGNC	e!Ensembl
604808	3762	ENSG00000125848

Q9NZU0

Protein name

Leucine-rich repeat transmembrane protein FLRT3 (Fibronectin-like domain-containing leucine-rich transmembrane protein 3)

Protein function

Functions in cell-cell adhesion, cell migration and axon guidance, exerting an attractive or repulsive role depending on its interaction partners. Plays a role in the spatial organization of brain neurons. Plays a role in vascular development in

PDB

5CMN , 5CMP , 6JBU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13855	LRR_8	247 → 306	Leucine rich repeat	Repeat
PF13855	LRR_8	175 → 237	Leucine rich repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Expressed in kidney, brain, pancreas, skeletal muscle, lung, liver, placenta, and heart. {ECO:0000269|PubMed:10644439}.

Sequence

MISAAWSIFLIGTKIGLFLQVAPLSVMAKSCPSVCRCDAGFIYCNDRFLTSIPTGIPEDA
TTLYLQNNQINNAGIPSDLKNLLKVERIYLYHNSLDEFPTNLPKYVKELHLQENNIRTIT
YDSLSKIPYLEELHLDDNSVSAVSIEEGAFRDSNYLRLLFLSRNHLSTIPWGLPRTIEEL
RLDDNRISTISSPSLQGLTSLKRLVLDGNLLNNHGLGDKVFFNLVNLTELSLVRNSLTAA
PVNLPGTNLRKLYLQDNHINRVPPNAFSYLRQLYRLDMSNNNLSNLPQGIFDDLDNITQL
ILRNNPWYCGCKMKWVRDWLQSLPVKVNVRGLMCQAPEKVRGMAIKDLNAELFDCKDSGI
VSTIQITTAIPNTVYPAQGQWPAPVTKQPDIKNPKLTKDHQTTGSPSRKTITITVKSVTS
DTIHISWKLALPMTALRLSWLKLGHSPAFGSITETIVTGERSEYLVTALEPDSPYKVCMV
PMETSNLYLFDETPVCIETETAPLRMYNPTTTLNREQEKEPYKNPNLPLAAIIGGAVALV
TIALLALVCWYVHRNGSLFSRNCAYSKGRRRKDDYAEAGTKKDNSILEIRETSFQMLPIS
NEPISKEEFVIHTIFPPNGMNLYKNNHSESSSNRSYRDSGIPDSDHSHS

Sequence length

649

Interactions

View interactions

Reactome Pathway
Downstream signaling of activated FGFR1

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hypogonadotropic hypogonadism 21 with or without anosmia	Pathogenic	rs398124654	RCV000043605	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (15)
Disorder of sexual differentiation	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FLRT3-related disorder	Likely benign; Conflicting classifications of pathogenicity	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
High myopia	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOGONADOTROPIC HYPOGONADISM	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOGONADOTROPIC HYPOGONADISM 21 WITH ANOSMIA, SUSCEPTIBILITY TO	risk factor	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOPITUITARISM	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC GROWTH HORMONE DEFICIENCY	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KALLMANN SYNDROME	—	Disgenet, GenCC, Orphanet Disgenet, GenCC, Orphanet Disgenet, GenCC, Orphanet	23643382, 23643382	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOOD DISORDER	—	GWAS catalog	25897833	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANHYPOPITUITARISM	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PITUITARY DWARFISM	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PITUITARY SHORT STATURE	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE MYOPIA	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHEEHAN SYNDROME	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (40)
Anterior hypopituitarism	Hypopituitarism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	22939004, 30110355		★★★★★ ★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet disease	Pubtator	39191728	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	39191728	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	35560224	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37689589	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	35676660	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cartilage-hair hypoplasia	Cartilage-Hair Hypoplasia	BEFREE	23643382		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	35560224	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital absence of kidneys syndrome	Renal agenesis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypogonadotropic hypogonadism	Congenital Hypogonadotropic Hypogonadism	BEFREE	23643382		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of breast	Breast hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Gynecomastia	Gynecomastia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	Pubtator	37108593	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOGONADOTROPIC HYPOGONADISM 21 WITH OR WITHOUT ANOSMIA	Hypogonadotropic Hypogonadism With Or Without Anosmia	GENOMICS_ENGLAND_DG	21700882		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
HYPOGONADOTROPIC HYPOGONADISM 21 WITH OR WITHOUT ANOSMIA	Hypogonadotropic Hypogonadism With Or Without Anosmia	UNIPROT_DG	23643382		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
HYPOGONADOTROPIC HYPOGONADISM 21 WITH OR WITHOUT ANOSMIA	Hypogonadotropic Hypogonadism With Or Without Anosmia	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
HYPOGONADOTROPIC HYPOGONADISM 21 WITH OR WITHOUT ANOSMIA	Hypogonadotropic Hypogonadism With Or Without Anosmia	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ichthyoses	Ichthyosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Hypogonadotropic Hypogonadism	Hypogonadotropic hypogonadism	Pubtator	36700485	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Kallmann Syndrome	Kallmann Syndrome	ORPHANET_DG	23643382		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kallmann syndrome	Kallmann Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kallmann Syndrome	Kallmann syndrome	Pubtator	37108593	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mirror movements disorder	Mirror Movements	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Miscarriage	Miscarriage	CTD_human_DG	18539642		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	40037332	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Paraplegia	Paraplegia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Penis agenesis	Penis Agenesis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary physiologic amenorrhea	Physiologic Amenorrhea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Skeletal dysplasia	Skeletal Dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
HS6ST1	8	["Hypogonadotropic hypogonadism","Hypopituitarism","Growth hormone deficiency","Kallmann syndrome","Panhypopituitarism","Pituitary dwarfism","Pituitary short stature","Sheehan syndrome"]	0	[]	12	["Disgenet (Hypogonadotropic hypogonadism)","GenCC (Hypogonadotropic hypogonadism)","CTD (Hypogonadotropic hypogonadism)","ClinVar (Hypogonadotropic hypogonadism)","Disgenet (Hypopituitarism)","Disgenet (Growth hormone deficiency)","Disgenet (Kallmann syndrome)","Orphanet (Kallmann syndrome)","Disgenet (Panhypopituitarism)","Disgenet (Pituitary dwarfism)","Disgenet (Pituitary short stature)","Disgenet (Sheehan syndrome)"]
FEZF1	8	["Hypogonadotropic hypogonadism","Hypopituitarism","Growth hormone deficiency","Kallmann syndrome","Panhypopituitarism","Pituitary dwarfism","Pituitary short stature","Sheehan syndrome"]	0	[]	12	["Disgenet (Hypogonadotropic hypogonadism)","CTD (Hypogonadotropic hypogonadism)","ClinVar (Hypogonadotropic hypogonadism)","HPO (Hypogonadotropic hypogonadism)","Disgenet (Hypopituitarism)","Disgenet (Growth hormone deficiency)","Disgenet (Kallmann syndrome)","Orphanet (Kallmann syndrome)","Disgenet (Panhypopituitarism)","Disgenet (Pituitary dwarfism)","Disgenet (Pituitary short stature)","Disgenet (Sheehan syndrome)"]
FGF17	8	["Hypogonadotropic hypogonadism","Hypopituitarism","Growth hormone deficiency","Kallmann syndrome","Panhypopituitarism","Pituitary dwarfism","Pituitary short stature","Sheehan syndrome"]	1	["Downstream signaling of activated FGFR1"]	12	["Disgenet (Hypogonadotropic hypogonadism)","CTD (Hypogonadotropic hypogonadism)","ClinVar (Hypogonadotropic hypogonadism)","HPO (Hypogonadotropic hypogonadism)","Disgenet (Hypopituitarism)","Disgenet (Growth hormone deficiency)","Disgenet (Kallmann syndrome)","Orphanet (Kallmann syndrome)","Disgenet (Panhypopituitarism)","Disgenet (Pituitary dwarfism)","Disgenet (Pituitary short stature)","Disgenet (Sheehan syndrome)"]
NDNF	8	["Hypogonadotropic hypogonadism","Hypopituitarism","Growth hormone deficiency","Kallmann syndrome","Panhypopituitarism","Pituitary dwarfism","Pituitary short stature","Sheehan syndrome"]	0	[]	11	["Disgenet (Hypogonadotropic hypogonadism)","ClinVar (Hypogonadotropic hypogonadism)","HPO (Hypogonadotropic hypogonadism)","Disgenet (Hypopituitarism)","Disgenet (Growth hormone deficiency)","Disgenet (Kallmann syndrome)","Orphanet (Kallmann syndrome)","Disgenet (Panhypopituitarism)","Disgenet (Pituitary dwarfism)","Disgenet (Pituitary short stature)","Disgenet (Sheehan syndrome)"]
KISS1	8	["Hypogonadotropic hypogonadism","Hypopituitarism","Growth hormone deficiency","Kallmann syndrome","Panhypopituitarism","Pituitary dwarfism","Pituitary short stature","Sheehan syndrome"]	0	[]	12	["Disgenet (Hypogonadotropic hypogonadism)","GenCC (Hypogonadotropic hypogonadism)","CTD (Hypogonadotropic hypogonadism)","ClinVar (Hypogonadotropic hypogonadism)","HPO (Hypogonadotropic hypogonadism)","Disgenet (Hypopituitarism)","Disgenet (Growth hormone deficiency)","Disgenet (Kallmann syndrome)","Disgenet (Panhypopituitarism)","Disgenet (Pituitary dwarfism)","Disgenet (Pituitary short stature)","Disgenet (Sheehan syndrome)"]

FLRT3 (fibronectin leucine rich transmembrane protein 3)

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