LRFN2

gene
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Also known as FIGLER2

Summary

LRFN2 (leucine rich repeat and fibronectin type III domain containing 2, HGNC:21226) is a protein-coding gene on chromosome 6p21.2-p21.1, encoding Leucine-rich repeat and fibronectin type-III domain-containing protein 2 (Q9ULH4). Promotes neurite outgrowth in hippocampal neurons.

Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Predicted to be located in plasma membrane. Predicted to be active in several cellular components, including Schaffer collateral - CA1 synapse; cell surface; and postsynaptic density membrane.

Source: NCBI Gene 57497 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 115 total
  • MANE Select transcript: NM_020737

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21226
Approved symbolLRFN2
Nameleucine rich repeat and fibronectin type III domain containing 2
Location6p21.2-p21.1
Locus typegene with protein product
StatusApproved
AliasesFIGLER2
Ensembl geneENSG00000156564
Ensembl biotypeprotein_coding
OMIM612808
Entrez57497

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000338305, ENST00000700335

RefSeq mRNA: 1 — MANE Select: NM_020737 NM_020737

CCDS: CCDS34443

Canonical transcript exons

ENST00000338305 — 3 exons

ExonStartEnd
ENSE000013745584043171440433131
ENSE000014596954039159140392912
ENSE000014596984058694140587364

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 79.44.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9888 / max 66.9200, expressed in 129 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
735100.7419115
735110.086945
735080.047013
735070.044814
735090.038229
735120.030221

Top tissues by expression

227 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534379.44gold quality
prefrontal cortexUBERON:000045175.82gold quality
right frontal lobeUBERON:000281073.92gold quality
Brodmann (1909) area 9UBERON:001354073.75gold quality
dorsolateral prefrontal cortexUBERON:000983471.60gold quality
islet of LangerhansUBERON:000000671.53gold quality
frontal cortexUBERON:000187071.37gold quality
anterior cingulate cortexUBERON:000983571.34gold quality
neocortexUBERON:000195070.69gold quality
cerebral cortexUBERON:000095667.28gold quality
amygdalaUBERON:000187665.28gold quality
right hemisphere of cerebellumUBERON:001489065.13gold quality
cerebellar cortexUBERON:000212964.81gold quality
cerebellar hemisphereUBERON:000224564.78gold quality
hypothalamusUBERON:000189864.19gold quality
cerebellumUBERON:000203763.29gold quality
Ammon’s hornUBERON:000195459.83gold quality
temporal lobeUBERON:000187159.73gold quality
forebrainUBERON:000189059.51gold quality
brainUBERON:000095559.45gold quality
superior frontal gyrusUBERON:000266157.98gold quality
primary visual cortexUBERON:000243657.12gold quality
ganglionic eminenceUBERON:000402357.01gold quality
postcentral gyrusUBERON:000258155.85silver quality
substantia nigraUBERON:000203854.03gold quality
heart right ventricleUBERON:000208054.03gold quality
parietal lobeUBERON:000187253.36silver quality
occipital lobeUBERON:000202153.25gold quality
entorhinal cortexUBERON:000272852.97silver quality
nasal cavity epitheliumUBERON:000538452.55gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting LRFN2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6748-5P100.0065.811057
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-221-3P99.8671.561329
HSA-MIR-222-3P99.8671.351337
HSA-MIR-449599.8272.083080
HSA-MIR-431999.7669.832586
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-670-5P99.6769.941565
HSA-MIR-317599.6566.302031
HSA-MIR-24-3P99.5969.971934
HSA-MIR-426199.5970.303415
HSA-MIR-443799.5265.291266
HSA-MIR-444199.4966.563216
HSA-MIR-125A-5P99.3670.591640
HSA-MIR-125B-5P99.3670.361662
HSA-MIR-532-3P99.3465.761195
HSA-MIR-499A-3P99.1869.201392
HSA-MIR-499B-3P99.1869.271391
HSA-MIR-6799-5P99.1465.722093
HSA-MIR-491-5P99.1365.981468
HSA-MIR-807099.0769.301303
HSA-MIR-427099.0266.261987
HSA-MIR-6760-5P98.8766.731515
HSA-MIR-5006-5P98.7966.921246
HSA-MIR-6769B-5P98.7364.911092

Literature-anchored findings (GeneRIF, showing 7)

  • enrichment of SALM1 on the cell surface affects dendritic arborization, and intracellular motifs regulate its dendritic versus axonal localization. (PMID:22174418)
  • Microdeletion encompassing LRFN2 gene segregates with working memory deficits and learning disabilities in three family members. (PMID:26486473)
  • study demonstrated that the polymorphisms rs2494938 at 6p21.1 and rs2285947 at 7p15.3 may serve as independent prognostic biomarkers for ESCC, implying the potential biological role of their related genes (LRFN2 and DNAH11) in the process of ESCC development (PMID:31053115)
  • No significant association of variant rs2494938 of LRFN2 was observed with ovarian canceror breast cancer in a cohort of women in India. (PMID:31605628)
  • LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir. (PMID:32880595)
  • LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/beta-Catenin and NF-kappaB signaling pathway. (PMID:35879265)
  • Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8[+] T cell infiltration and functional transition. (PMID:37802603)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriolrfn2bENSDARG00000077489
danio_rerioLRFN2ENSDARG00000106248
mus_musculusLrfn2ENSMUSG00000040490
rattus_norvegicusLrfn2ENSRNOG00000011803

Paralogs (25): SLITRK3 (ENSG00000121871), LRFN3 (ENSG00000126243), LRFN1 (ENSG00000128011), SLIT2 (ENSG00000145147), LRRC38 (ENSG00000162494), SLITRK5 (ENSG00000165300), LRFN5 (ENSG00000165379), LRTM2 (ENSG00000166159), LINGO1 (ENSG00000169783), LRRN2 (ENSG00000170382), LRRN3 (ENSG00000173114), LRFN4 (ENSG00000173621), LINGO2 (ENSG00000174482), LRRN1 (ENSG00000175928), SLITRK1 (ENSG00000178235), GP5 (ENSG00000178732), SLITRK4 (ENSG00000179542), LRRC55 (ENSG00000183908), SLIT3 (ENSG00000184347), SLITRK6 (ENSG00000184564), SLITRK2 (ENSG00000185985), LRRC70 (ENSG00000186105), SLIT1 (ENSG00000187122), TLR9 (ENSG00000239732), TPBGL (ENSG00000261594)

Protein

Protein identifiers

Leucine-rich repeat and fibronectin type-III domain-containing protein 2Q9ULH4 (reviewed: Q9ULH4)

Alternative names: Synaptic adhesion-like molecule 1

All UniProt accessions (2): Q9ULH4, A0A8V8TQ63

UniProt curated annotations — full annotation on UniProt →

Function. Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery.

Subunit / interactions. Forms heteromeric complexes with LRFN1, LRFN3, LRFN4 and LRFN5. Can form homomeric complexes, but not across cell junctions. Directly interacts with 2 NMDA receptor subunits GRIN1 and GRIN2A. Interacts with DLG1, DLG2, DLG3 and DLG4.

Subcellular location. Membrane. Synapse. Postsynaptic cell membrane.

Post-translational modifications. Glycosylated.

Domain organisation. The PDZ-binding motif is required for cell surface expression, neurite outgrowth promotion. This motif is also involved in DLG1-, DLG3- and DLG4-binding.

Similarity. Belongs to the LRFN family.

RefSeq proteins (1): NP_065788* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000483Cys-rich_flank_reg_CDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR003961FN3_domDomain
IPR007110Ig-like_domDomain
IPR013098Ig_I-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR032675LRR_dom_sfHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050467LRFNFamily

Pfam: PF00041, PF07679, PF13855

UniProt features (32 total): repeat 7, domain 4, region of interest 4, compositionally biased region 4, glycosylation site 4, topological domain 2, signal peptide 1, chain 1, short sequence motif 1, disulfide bond 1, transmembrane region 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9ULH4-F170.360.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 310–359

Glycosylation sites (4): 29, 332, 341, 384

Mutagenesis-validated functional residues (1):

PositionPhenotype
787–789loss of dlg1-, dlg3- and dlg4-binding.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-8849932Synaptic adhesion-like molecules
R-HSA-112316Neuronal System
R-HSA-6794362Protein-protein interactions at synapses

MSigDB gene sets: 77 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOCC_CELL_SURFACE, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_JUNCTION_ORGANIZATION, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_SYNAPTIC_SIGNALING, GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOCC_POSTSYNAPSE, CTGAGCC_MIR24, GOCC_SYNAPSE, GOCC_POSTSYNAPTIC_MEMBRANE, GOCC_PLASMA_MEMBRANE_REGION, GOCC_PRESYNAPSE, GOCC_SYNAPTIC_MEMBRANE

GO Biological Process (2): modulation of chemical synaptic transmission (GO:0050804), regulation of postsynapse organization (GO:0099175)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (9): plasma membrane (GO:0005886), cell surface (GO:0009986), Schaffer collateral - CA1 synapse (GO:0098685), presynapse (GO:0098793), postsynaptic density membrane (GO:0098839), membrane (GO:0016020), synapse (GO:0045202), postsynaptic membrane (GO:0045211), postsynapse (GO:0098794)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Protein-protein interactions at synapses1
Neuronal System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
synapse3
chemical synaptic transmission1
regulation of trans-synaptic signaling1
regulation of synapse organization1
postsynapse organization1
binding1
membrane1
cell periphery1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
cell junction1
synaptic membrane1
postsynapse1

Protein interactions and networks

STRING

1762 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRFN2DLG4P78352881
LRFN2DLG3Q92796876
LRFN2DLG1Q12959860
LRFN2GRIN1P35437720
LRFN2FN1P02751605
LRFN2UNC5CLQ8IV45570
LRFN2GRIN2AQ12879542
LRFN2PRTGQ2VWP7540
LRFN2C6orf132Q5T0Z8506
LRFN2PTPRFP10586485
LRFN2PTPRSQ13332422
LRFN2IGSF11Q5DX21406
LRFN2DAAM2Q86T65405
LRFN2TUFT1Q9NNX1403
LRFN2MOCS1Q9NZB8399
LRFN2GRIN3AQ8TCU5399

IntAct

7 interactions, top by confidence:

ABTypeScore
LRFN2PTPRDpsi-mi:“MI:0407”(direct interaction)0.440
LRFN2PTPRFpsi-mi:“MI:0407”(direct interaction)0.440
PTPRSLRFN2psi-mi:“MI:0407”(direct interaction)0.440
VEZTS100A11psi-mi:“MI:0914”(association)0.350
PNPT1PDE12psi-mi:“MI:0914”(association)0.350
LRFN2LRFN4psi-mi:“MI:0914”(association)0.350

BioGRID (9): LRFN2 (Affinity Capture-RNA), LRFN4 (Affinity Capture-MS), LRFN2 (Affinity Capture-MS), LRFN2 (Affinity Capture-MS), ACAD11 (Affinity Capture-MS), LRFN2 (Two-hybrid), LRFN2 (Cross-Linking-MS (XL-MS)), LRFN2 (Affinity Capture-RNA), LRFN2 (Affinity Capture-MS)

ESM2 similar proteins: A1XQX1, A1XQX3, A1XQY0, A8WGA3, C6K2K4, D0PRN2, D0PRN4, D4A1J9, E9PUN2, O13097, O42596, O73612, O73874, P0DI97, P52795, P52796, P58400, P58401, P98172, Q01974, Q0PMD2, Q17QD6, Q28142, Q28143, Q460M5, Q63373, Q63376, Q6NW40, Q6PCX7, Q6PFE7, Q7TQ33, Q80TG9, Q8BNJ6, Q8BXA0, Q8C985, Q8IYR6, Q8NC67, Q91590, Q96B86, Q96NI6

Diamond homologs: A0A1Y9G8H0, A0A452E9Y6, A1KZ92, A2A8L5, A2AJ76, A4IFW2, A4IGL7, A4IIW9, A5JUY8, A7MBJ4, A8WGA3, A8WQH2, B0BNK7, B3A0P3, D2HFT7, D3YXG0, D4A1J9, D4ABX8, G5EBF1, G5EG78, H2A0M7, O15146, O35158, O55005, O89026, P05164, P07202, P09933, P0C6S8, P0C7J6, P11247, P11678, P14650, P16621, P22079, P23468, P35419, P49290, P70193, P80025

SIGNOR signaling

2 interactions.

AEffectBMechanism
DLG4“up-regulates activity”LRFN2binding
LRFN2up-regulatesNeurite_outgrowth

Disease & clinical

Clinical variants and AI predictions

ClinVar

115 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance107
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1418 predictions. Top by Δscore:

VariantEffectΔscore
6:40392908:TCATC:Tacceptor_gain1.0000
6:40392909:CATCC:Cacceptor_gain1.0000
6:40392910:ATC:Aacceptor_gain1.0000
6:40392911:TC:Tacceptor_gain1.0000
6:40392912:CC:Cacceptor_gain1.0000
6:40392913:C:CAacceptor_loss1.0000
6:40392913:C:CCacceptor_gain1.0000
6:40433127:AGCGC:Aacceptor_gain1.0000
6:40433128:GCGC:Gacceptor_gain1.0000
6:40433129:CGC:Cacceptor_gain1.0000
6:40433129:CGCC:Cacceptor_gain1.0000
6:40433130:GC:Gacceptor_gain1.0000
6:40433131:CC:Cacceptor_gain1.0000
6:40433132:C:CCacceptor_gain1.0000
6:40433133:T:Gacceptor_loss1.0000
6:40392909:CATC:Cacceptor_gain0.9900
6:40433132:C:Tacceptor_gain0.9900
6:40455918:AGC:Adonor_gain0.9800
6:40586936:CTCA:Cdonor_loss0.9800
6:40586937:TCACC:Tdonor_loss0.9800
6:40586938:CAC:Cdonor_loss0.9800
6:40586939:A:Tdonor_loss0.9800
6:40586940:C:CGdonor_loss0.9800
6:40392910:ATCCT:Aacceptor_gain0.9700
6:40392911:TCCT:Tacceptor_gain0.9700
6:40392913:C:Tacceptor_gain0.9700
6:40392925:G:Cacceptor_gain0.9700
6:40407741:C:CTdonor_gain0.9700
6:40431713:C:CGdonor_loss0.9700
6:40392912:CCT:Cacceptor_gain0.9600

AlphaMissense

5129 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:40431794:C:AW440C1.000
6:40431794:C:GW440C1.000
6:40431796:A:GW440R1.000
6:40431796:A:TW440R1.000
6:40432037:G:CC359W1.000
6:40432038:C:TC359Y1.000
6:40432039:A:GC359R1.000
6:40432083:A:GL344P1.000
6:40432148:C:AW322C1.000
6:40432148:C:GW322C1.000
6:40432150:A:GW322R1.000
6:40432150:A:TW322R1.000
6:40432185:C:GC310S1.000
6:40432186:A:GC310R1.000
6:40432186:A:TC310S1.000
6:40432388:G:CN242K1.000
6:40432388:G:TN242K1.000
6:40432493:A:CN207K1.000
6:40432493:A:TN207K1.000
6:40432565:G:CN183K1.000
6:40432565:G:TN183K1.000
6:40432637:G:CN159K1.000
6:40432637:G:TN159K1.000
6:40432638:T:AN159I1.000
6:40432653:A:GL154P1.000
6:40432712:G:CN134K1.000
6:40432712:G:TN134K1.000
6:40432728:A:GL129P1.000
6:40432784:A:CN110K1.000
6:40432784:A:TN110K1.000

dbSNP variants (sampled 300 via entrez): RS1000002099 (6:40424579 C>T), RS1000002458 (6:40399415 CTTTT>C), RS1000002717 (6:40497002 G>A), RS1000017873 (6:40578032 C>A,T), RS1000056896 (6:40419601 A>G), RS1000084304 (6:40461335 G>C), RS1000084971 (6:40522232 A>C), RS1000085564 (6:40548346 C>T), RS1000095468 (6:40399085 A>G), RS1000114807 (6:40577101 T>A,C), RS1000116597 (6:40548179 C>T), RS1000166124 (6:40441168 G>A), RS1000172821 (6:40554760 C>G,T), RS1000179249 (6:40585947 C>T), RS1000181756 (6:40518046 C>T)

Disease associations

OMIM: gene MIM:612808 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

24 associations (top):

StudyTraitp-value
GCST001718_2Multiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)2.000000e-06
GCST001718_3Multiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)5.000000e-09
GCST001718_4Multiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)1.000000e-12
GCST001762_524Obesity-related traits8.000000e-06
GCST001762_653Obesity-related traits3.000000e-06
GCST002283_3Amyotrophic lateral sclerosis (sporadic)9.000000e-09
GCST003431_2Incident coronary heart disease2.000000e-06
GCST004065_16Waist circumference6.000000e-06
GCST004065_17Waist circumference2.000000e-08
GCST004557_55Body mass index8.000000e-08
GCST004558_239Body mass index (joint analysis main effects and physical activity interaction)3.000000e-08
GCST004559_125Body mass index in physically active individuals2.000000e-06
GCST004559_167Body mass index in physically active individuals2.000000e-08
GCST004766_9Triglyceride change in response to fenofibrate in statin-treated type 2 diabetes2.000000e-08
GCST004904_74Body mass index7.000000e-10
GCST005830_54Hand grip strength1.000000e-08
GCST006979_278Heel bone mineral density2.000000e-09
GCST007324_17Adventurousness2.000000e-09
GCST007325_92General risk tolerance (MTAG)1.000000e-10
GCST008155_77Waist-hip ratio5.000000e-06
GCST008159_27Waist-to-hip ratio adjusted for BMI6.000000e-06
GCST009379_50Type 2 diabetes9.000000e-10
GCST010988_361Adult body size4.000000e-20
GCST011743_42HDL cholesterol levels in HIV infection3.000000e-06

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0004340body mass index
EFO:0008002physical activity measurement
EFO:0007681triglyceride change measurement
EFO:0006941grip strength measurement
EFO:0009270heel bone mineral density
EFO:0008579risk-taking behaviour
EFO:0004343waist-hip ratio
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
ethyl-p-hydroxybenzoatedecreases expression1
CGP 52608affects binding, increases reaction1
Benzo(a)pyrenedecreases methylation, increases methylation1
Calcitrioldecreases expression, affects cotreatment1
Estradioldecreases expression1
Testosteroneaffects cotreatment, decreases expression1
Tretinoindecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.