LRFN5

gene
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Also known as FIGLER8SALM5

Summary

LRFN5 (leucine rich repeat and fibronectin type III domain containing 5, HGNC:20360) is a protein-coding gene on chromosome 14q21.1, encoding Leucine-rich repeat and fibronectin type-III domain-containing protein 5 (Q96NI6). Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner.

This gene encodes a protein that belongs to the leucine-rich repeat and fibronectin type III domain-containing family of proteins. A similar protein in mouse, a glycosylated transmembrane protein, is thought to function in presynaptic differentiation.

Source: NCBI Gene 145581 — RefSeq curated summary.

At a glance

  • GWAS associations: 17
  • Clinical variants (ClinVar): 103 total
  • MANE Select transcript: NM_152447

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20360
Approved symbolLRFN5
Nameleucine rich repeat and fibronectin type III domain containing 5
Location14q21.1
Locus typegene with protein product
StatusApproved
AliasesFIGLER8, SALM5
Ensembl geneENSG00000165379
Ensembl biotypeprotein_coding
OMIM612811
Entrez145581

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000298119, ENST00000553926, ENST00000554120, ENST00000554171, ENST00000555279, ENST00000935948, ENST00000935949, ENST00000935950, ENST00000955328, ENST00000955329

RefSeq mRNA: 4 — MANE Select: NM_152447 NM_001330106, NM_001346173, NM_001346175, NM_152447

CCDS: CCDS81800, CCDS9678

Canonical transcript exons

ENST00000298119 — 6 exons

ExonStartEnd
ENSE000010925944189125041891962
ENSE000010925954188660641888010
ENSE000012291154176685441767029
ENSE000018187234160687641608562
ENSE000036303884189891741898960
ENSE000036397744190415841904549

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 96.41.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8464 / max 129.1825, expressed in 473 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
1393950.6086139
1393880.5466291
1393930.5066120
1393890.4878132
1393940.214196
1393900.194689
1393920.109669
1393960.103059
1393910.075637

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277196.41gold quality
Brodmann (1909) area 23UBERON:001355496.00gold quality
Brodmann (1909) area 46UBERON:000648390.61gold quality
primary visual cortexUBERON:000243689.85gold quality
endothelial cellCL:000011588.46gold quality
superior frontal gyrusUBERON:000266187.50gold quality
occipital lobeUBERON:000202187.27gold quality
postcentral gyrusUBERON:000258186.24gold quality
parietal lobeUBERON:000187285.85gold quality
entorhinal cortexUBERON:000272885.52gold quality
buccal mucosa cellCL:000233685.47gold quality
prefrontal cortexUBERON:000045184.42gold quality
dorsolateral prefrontal cortexUBERON:000983484.03gold quality
frontal cortexUBERON:000187083.97gold quality
cortical plateUBERON:000534383.41gold quality
sural nerveUBERON:001548882.96gold quality
neocortexUBERON:000195082.93gold quality
Brodmann (1909) area 9UBERON:001354082.88gold quality
cerebral cortexUBERON:000095682.28gold quality
oviduct epitheliumUBERON:000480481.93gold quality
right frontal lobeUBERON:000281080.88gold quality
endocervixUBERON:000045880.42gold quality
substantia nigra pars compactaUBERON:000196579.25gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.73gold quality
anterior cingulate cortexUBERON:000983578.62gold quality
lateral nuclear group of thalamusUBERON:000273678.59gold quality
uterine cervixUBERON:000000278.33gold quality
temporal lobeUBERON:000187178.28gold quality
ectocervixUBERON:001224977.92gold quality
superior vestibular nucleusUBERON:000722777.72gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-HCAD-35yes100.28
E-HCAD-25yes89.28
E-MTAB-5061yes13.45
E-GEOD-81608yes6.72
E-GEOD-81547yes6.48
E-ENAD-27yes5.41
E-ANND-3yes4.81
E-MTAB-8060no41.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting LRFN5, 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-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-139-5P99.8069.501399
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-430699.7270.503630
HSA-MIR-494-3P99.7071.452795
HSA-MIR-472999.6972.184233
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-510-3P99.5470.062965
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-1212399.5271.792990
HSA-MIR-520E-5P99.2768.901513
HSA-MIR-569399.2466.671106
HSA-MIR-442699.1766.741949
HSA-MIR-478499.1567.411733
HSA-MIR-3688-5P99.1269.671091
HSA-MIR-62298.9966.481050
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-58398.7167.441791
HSA-MIR-3689A-5P98.3570.121049
HSA-MIR-3689B-5P98.3570.121049
HSA-MIR-3689E98.3570.121049
HSA-MIR-3689F98.3570.081052
HSA-MIR-4662B98.3366.371163
HSA-MIR-464798.3066.411139
HSA-MIR-2681-3P98.1865.28577
HSA-MIR-4768-3P98.1666.022330

Literature-anchored findings (GeneRIF, showing 9)

  • Expression of SALM family proteins SALM3 and SALM5 in nonneural and neural cells induces both excitatory and inhibitory presynaptic differentiation in contacting axons. (PMID:20410109)
  • SALM5/Lrfn5, has recently been implicated in severe progressive autism and familial schizophrenia, pointing to the clinical importance of SALMs.[review] (PMID:21736948)
  • Presynaptic differentiation induced by protein tyrosine phosphatase receptor type D (PTPdelta)-leucine rich repeat and fibronectin type III domain containing 5 (SALM5) requires the dimeric property of SALM5. (PMID:29348429)
  • In the 2:2 heterotetrameric SALM5/PTPdelta complex, a SALM5 dimer bridges two separate PTPdelta molecules. (PMID:29348579)
  • we found that chr14.232.a increases expression of LRFN5 in his fibroblasts. Reduced expression of LRFN5 in fibroblasts should be interpreted with caution as these cells might not be representative of expression in brain cells, which are involved in the neurodevelopmental phenotype. (PMID:31152157)
  • Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5. (PMID:31748543)
  • LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions. (PMID:35088940)
  • CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis. (PMID:36266731)
  • LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study. (PMID:37280213)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriolrfn5aENSDARG00000071230
mus_musculusLrfn5ENSMUSG00000035653
rattus_norvegicusLrfn5ENSRNOG00000005550

Paralogs (25): SLITRK3 (ENSG00000121871), LRFN3 (ENSG00000126243), LRFN1 (ENSG00000128011), SLIT2 (ENSG00000145147), LRFN2 (ENSG00000156564), LRRC38 (ENSG00000162494), SLITRK5 (ENSG00000165300), 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 5Q96NI6 (reviewed: Q96NI6)

All UniProt accessions (3): Q96NI6, G3V364, G3V4N1

UniProt curated annotations — full annotation on UniProt →

Function. Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons.

Subunit / interactions. Can form heteromeric complexes with LRFN1, LRFN2, LRFN3 and LFRN4. Able to form homomeric complexes across cell junctions, between adjacent cells. Does not interact with DLG1, DLG2, DLG3 and DLG4.

Subcellular location. Membrane.

Domain organisation. Lacks a cytoplasmic PDZ-binding motif, which has been implicated in function of related LRFN proteins.

Similarity. Belongs to the LRFN family.

RefSeq proteins (4): NP_001317035, NP_001333102, NP_001333104, NP_689660* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR032675LRR_dom_sfHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050467LRFNFamily

Pfam: PF13855, PF13927

UniProt features (54 total): strand 13, helix 8, repeat 7, glycosylation site 6, domain 4, compositionally biased region 4, region of interest 2, topological domain 2, sequence conflict 2, turn 2, signal peptide 1, chain 1, disulfide bond 1, transmembrane region 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
5XNQX-RAY DIFFRACTION2.8
5XWSX-RAY DIFFRACTION3.08
5XNPX-RAY DIFFRACTION3.73
5XWTX-RAY DIFFRACTION4.18

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96NI6-F174.660.49

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): 308–357

Glycosylation sites (6): 73, 330, 339, 382, 406, 452

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, BENPORATH_ES_WITH_H3K27ME3, WHITEHURST_PACLITAXEL_SENSITIVITY, GOBP_INFLAMMATORY_RESPONSE, GOBP_SYNAPSE_ASSEMBLY, GCANCTGNY_MYOD_Q6, GOBP_REGULATION_OF_MACROPHAGE_ACTIVATION, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, TGACCTY_ERR1_Q2, CHX10_01, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GOBP_CELL_CELL_ADHESION

GO Biological Process (4): negative regulation of macrophage activation (GO:0043031), negative regulation of inflammatory response (GO:0050728), synaptic membrane adhesion (GO:0099560), regulation of presynapse assembly (GO:1905606)

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

GO Cellular Component (5): cell surface (GO:0009986), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
synapse2
negative regulation of leukocyte activation1
macrophage activation1
regulation of macrophage activation1
inflammatory response1
negative regulation of defense response1
negative regulation of response to external stimulus1
regulation of inflammatory response1
synapse organization1
cell-cell adhesion1
regulation of synapse assembly1
presynapse assembly1
regulation of presynapse organization1
binding1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1

Protein interactions and networks

STRING

1412 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRFN5DLG4P78352726
LRFN5PTPRSQ13332694
LRFN5ANTXR2P58335601
LRFN5IL1RAPL1Q9NZN1582
LRFN5FBXO33Q7Z6M2555
LRFN5FN1P02751517
LRFN5TNFRSF14Q92956514
LRFN5CTNND2Q9UQB3506
LRFN5TJP2Q9UDY2488
LRFN5SYPP08247466
LRFN5RABEPKQ7Z6M1459
LRFN5TRAPPC6BQ86SZ2451
LRFN5LAD1O00515444
LRFN5SHANK3Q9BYB0431
LRFN5FNDC10F2Z333428

IntAct

9 interactions, top by confidence:

ABTypeScore
LRFN5PTPRDpsi-mi:“MI:0915”(physical association)0.540
PTPRFLRFN5psi-mi:“MI:0915”(physical association)0.540
PTPRSLRFN5psi-mi:“MI:0915”(physical association)0.540
PTPRSLRFN5psi-mi:“MI:0407”(direct interaction)0.540
LRFN5PTPRDpsi-mi:“MI:0407”(direct interaction)0.540
LRFN5PTPRFpsi-mi:“MI:0407”(direct interaction)0.540
BTNL9LRFN5psi-mi:“MI:0915”(physical association)0.400
TLK2IGKV1D-13psi-mi:“MI:0914”(association)0.350

BioGRID (2): LRFN5 (Affinity Capture-RNA), LRFN5 (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

6 interactions.

AEffectBMechanism
LRFN5up-regulatesSynaptic_plasticity
LRFN5“up-regulates activity”PTPRDbinding
LRFN5“up-regulates activity”PTPRFbinding
LRFN5“up-regulates activity”PTPRSbinding
LRFN5up-regulatesNeurite_outgrowth

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance81
Likely benign8
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

2936 predictions. Top by Δscore:

VariantEffectΔscore
14:41767027:GAA:Gdonor_gain1.0000
14:41767030:G:GGdonor_gain1.0000
14:41891249:GA:Gacceptor_gain1.0000
14:41610224:G:GAdonor_gain0.9900
14:41639479:T:Gdonor_gain0.9900
14:41766836:T:TAacceptor_gain0.9900
14:41766840:T:TAacceptor_gain0.9900
14:41766849:T:Aacceptor_gain0.9900
14:41766852:A:AGacceptor_gain0.9900
14:41766853:G:GGacceptor_gain0.9900
14:41766853:GA:Gacceptor_gain0.9900
14:41767028:AAGT:Adonor_loss0.9900
14:41767029:AGT:Adonor_loss0.9900
14:41767031:TA:Tdonor_loss0.9900
14:41767032:AAGTT:Adonor_loss0.9900
14:41891245:CTCAG:Cacceptor_loss0.9900
14:41891246:TCAGA:Tacceptor_loss0.9900
14:41891247:CAG:Cacceptor_loss0.9900
14:41891248:A:AGacceptor_gain0.9900
14:41891248:AG:Aacceptor_loss0.9900
14:41891248:AGAAT:Aacceptor_gain0.9900
14:41891249:G:GGacceptor_gain0.9900
14:41891249:GAAT:Gacceptor_gain0.9900
14:41891249:GAATG:Gacceptor_gain0.9900
14:41610223:T:TAdonor_gain0.9800
14:41680848:G:GTdonor_gain0.9800
14:41761557:T:TAacceptor_gain0.9800
14:41874059:A:Gacceptor_gain0.9800
14:41876178:A:AGdonor_gain0.9800
14:41889838:T:TAdonor_gain0.9800

AlphaMissense

4747 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:41886792:T:CL56P1.000
14:41886837:T:CF71S1.000
14:41886864:T:CL80P1.000
14:41886879:A:TN85I1.000
14:41886880:T:AN85K1.000
14:41886880:T:GN85K1.000
14:41887080:T:CL152P1.000
14:41887096:T:AN157K1.000
14:41887096:T:GN157K1.000
14:41887168:T:AN181K1.000
14:41887168:T:GN181K1.000
14:41887239:A:TN205I1.000
14:41887240:T:AN205K1.000
14:41887240:T:GN205K1.000
14:41887245:T:CL207S1.000
14:41887345:C:AN240K1.000
14:41887345:C:GN240K1.000
14:41887375:G:CW250C1.000
14:41887375:G:TW250C1.000
14:41887485:C:AP287H1.000
14:41887547:T:AC308S1.000
14:41887547:T:CC308R1.000
14:41887548:G:CC308S1.000
14:41887549:C:GC308W1.000
14:41887559:G:AG312R1.000
14:41887559:G:CG312R1.000
14:41887560:G:AG312E1.000
14:41887583:T:AW320R1.000
14:41887583:T:CW320R1.000
14:41887584:G:CW320S1.000

dbSNP variants (sampled 300 via entrez): RS1000032149 (14:41697974 G>A,T), RS1000041305 (14:41772953 C>A,G), RS1000042995 (14:41660142 C>G), RS1000058658 (14:41681824 A>T), RS1000065550 (14:41703982 A>G), RS1000075723 (14:41866111 A>G,T), RS1000089643 (14:41801934 C>G,T), RS1000092589 (14:41615460 T>G), RS1000109398 (14:41694548 C>A), RS1000120041 (14:41744442 G>A), RS1000132746 (14:41685658 G>A), RS1000134769 (14:41850048 C>G,T), RS1000137286 (14:41730148 T>A), RS1000139556 (14:41785107 G>T), RS1000159499 (14:41607864 G>A)

Disease associations

OMIM: gene MIM:612811 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

StudyTraitp-value
GCST001378_1Hemostatic factors and hematological phenotypes7.000000e-06
GCST001890_3QT interval (drug interaction)5.000000e-06
GCST002828_30Urate levels in obese individuals9.000000e-06
GCST002937_6Molybdenum levels2.000000e-06
GCST003997_40Myopia2.000000e-16
GCST005839_34Depression3.000000e-09
GCST006291_102Spherical equivalent or myopia (age of diagnosis)1.000000e-19
GCST006485_10Telomere length8.000000e-08
GCST006616_5Uterine fibroid number (single vs multiple)7.000000e-07
GCST007324_6Adventurousness8.000000e-10
GCST007325_165General risk tolerance (MTAG)2.000000e-11
GCST007576_183Chronotype6.000000e-09
GCST009600_25Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)2.000000e-08
GCST009863_22Insulin-related traits (multivariate analysis)5.000000e-08
GCST010002_149Refractive error1.000000e-39
GCST010988_535Adult body size2.000000e-09
GCST010988_536Adult body size4.000000e-10

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004503hematological measurement
EFO:0004637protein S measurement
EFO:0004682QT interval
EFO:0007922response to sulfonylurea
EFO:0004531urate measurement
EFO:0004847age at onset
EFO:0009410uterine fibroid measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0004467insulin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Idecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
arseniteincreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
dorsomorphinincreases expression, affects cotreatment1
Resveratroldecreases expression, affects cotreatment1
Sunitinibdecreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Vorinostataffects cotreatment, increases expression1
Acetaminophendecreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cytarabinedecreases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Plant Extractsaffects cotreatment, decreases expression1
Rotenonedecreases expression1
Silicon Dioxideincreases expression1
Valproic Aciddecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): refractive error