ELFN1

gene
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Summary

ELFN1 (extracellular leucine rich repeat and fibronectin type III domain containing 1, HGNC:33154) is a protein-coding gene on chromosome 7p22.3, encoding Protein ELFN1 (P0C7U0). Postsynaptic protein that regulates circuit dynamics in the central nervous system by modulating the temporal dynamics of interneuron recruitment.

Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synapse organization. Predicted to act upstream of or within several processes, including chemical synaptic transmission; synapse assembly; and visual perception. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in several cellular components, including axon terminus; glutamatergic synapse; and postsynaptic density membrane.

Source: NCBI Gene 392617 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 214 total — 5 pathogenic
  • Phenotypes (HPO): 120
  • MANE Select transcript: NM_001128636

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:33154
Approved symbolELFN1
Nameextracellular leucine rich repeat and fibronectin type III domain containing 1
Location7p22.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000225968
Ensembl biotypeprotein_coding
OMIM614964
Entrez392617

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 20 protein_coding, 1 retained_intron

ENST00000424383, ENST00000561626, ENST00000688716, ENST00000691883, ENST00000853552, ENST00000853553, ENST00000853554, ENST00000853555, ENST00000853556, ENST00000853557, ENST00000853558, ENST00000853559, ENST00000853560, ENST00000853561, ENST00000853562, ENST00000853563, ENST00000853564, ENST00000853565, ENST00000853566, ENST00000936129, ENST00000936130

RefSeq mRNA: 3 — MANE Select: NM_001128636 NM_001128636, NM_001394187, NM_001394188

CCDS: CCDS59046

Canonical transcript exons

ENST00000424383 — 4 exons

ExonStartEnd
ENSE0000162964717090911709252
ENSE0000393438717443041747946
ENSE0000393587716880581688150
ENSE0000393813416702771670354

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 91.84.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233691.84gold quality
kidney epitheliumUBERON:000481984.82silver quality
germinal epithelium of ovaryUBERON:000130484.30gold quality
heart right ventricleUBERON:000208082.79gold quality
middle temporal gyrusUBERON:000277180.17silver quality
Brodmann (1909) area 46UBERON:000648380.11silver quality
pigmented layer of retinaUBERON:000178279.23gold quality
parietal pleuraUBERON:000240078.80gold quality
right lobe of liverUBERON:000111478.59gold quality
liverUBERON:000210778.37gold quality
Brodmann (1909) area 23UBERON:001355477.72silver quality
visceral pleuraUBERON:000240176.63silver quality
apex of heartUBERON:000209875.98gold quality
endothelial cellCL:000011575.82silver quality
upper arm skinUBERON:000426375.46gold quality
spermCL:000001974.55gold quality
thymusUBERON:000237074.12silver quality
stromal cell of endometriumCL:000225574.09gold quality
lateral globus pallidusUBERON:000247674.05silver quality
substantia nigra pars compactaUBERON:000196573.98silver quality
tibiaUBERON:000097973.89gold quality
entorhinal cortexUBERON:000272873.50silver quality
substantia nigra pars reticulataUBERON:000196673.47gold quality
ventral tegmental areaUBERON:000269173.47gold quality
secondary oocyteCL:000065573.41silver quality
cardiac ventricleUBERON:000208272.93gold quality
superior frontal gyrusUBERON:000266172.70gold quality
heart left ventricleUBERON:000208472.64gold quality
primary visual cortexUBERON:000243672.59gold quality
occipital lobeUBERON:000202172.56gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no1.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting ELFN1, 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-6867-5P100.0082.213464
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-548AW99.9972.573559
HSA-LET-7C-3P99.9573.422862
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-545-3P99.9570.742783
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-368699.9070.532432
HSA-MIR-612499.8769.783551

Literature-anchored findings (GeneRIF, showing 4)

  • Damaging missense mutations of ELFN1, that are clustered in the carboxy-terminal region required for mGluR7 recruitment, are found in patients with epilepsy and attention deficit hyperactivity disorder. (PMID:25047565)
  • the binding specificity of ELFN1 and found it to be recruited selectively to all group III mGluRs (mGluR4, mGluR6, mGluR7, and mGluR8), but not other mGluR species. (PMID:29686062)
  • Biallelic mutations in ELFN1 gene associated with developmental and epileptic encephalopathy and joint laxity. (PMID:34509675)
  • ELFN1 is a new extracellular matrix (ECM)-associated protein. (PMID:38986898)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioelfn1bENSDARG00000074372
mus_musculusElfn1ENSMUSG00000048988
rattus_norvegicusElfn1ENSRNOG00000022767
drosophila_melanogasterConFBGN0005775
drosophila_melanogasterkek3FBGN0028370
caenorhabditis_eleganslron-9WBGENE00011971
caenorhabditis_elegansWBGENE00020649

Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LRIG3 (ENSG00000139263), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRRTM2 (ENSG00000146006), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LGI4 (ENSG00000153902), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRIT3 (ENSG00000183423), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), LRRC24 (ENSG00000254402), TRIL (ENSG00000255690)

Protein

Protein identifiers

Protein ELFN1P0C7U0 (reviewed: P0C7U0)

Alternative names: Extracellular leucine-rich repeat and fibronectin type-III domain-containing protein 1, Protein phosphatase 1 regulatory subunit 28

All UniProt accessions (1): P0C7U0

UniProt curated annotations — full annotation on UniProt →

Function. Postsynaptic protein that regulates circuit dynamics in the central nervous system by modulating the temporal dynamics of interneuron recruitment. Specifically present in excitatory synapses onto oriens-lacunosum molecular (OLM) interneurons and acts as a regulator of presynaptic release probability to direct the formation of highly facilitating pyramidal-OLM synapses. Inhibits phosphatase activity of protein phosphatase 1 (PP1) complexes.

Subunit / interactions. Interacts with PPP1CA.

Subcellular location. Membrane. Cell projection. Dendrite. Axon.

Disease relevance. Dursun-Ozgul neurodevelopmental syndrome (DONDS) [MIM:621344] An autosomal recessive neurodevelopmental disorder characterized by developmental delay, intellectual disability, behavioral abnormalities, epilepsy, and movement disorders. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (3): NP_001122108, NP_001381116, NP_001381117 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000483Cys-rich_flank_reg_CDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR050541LRR_TM_domain-containingFamily
IPR055106ELFN_Fn3Domain

Pfam: PF13855, PF22986

UniProt features (32 total): repeat 6, glycosylation site 6, compositionally biased region 5, region of interest 4, domain 2, topological domain 2, modified residue 2, sequence variant 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P0C7U0-F162.620.25

Functional residue map

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

Post-translational modifications (2): 461, 645

Glycosylation sites (6): 59, 85, 90, 122, 210, 376

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GOBP_SYNAPSE_ASSEMBLY, PEREZ_TP63_TARGETS, chr7p22, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_SYNAPTIC_SIGNALING, GOBP_SENSORY_PERCEPTION, GOBP_CELL_JUNCTION_ASSEMBLY, GOCC_NEURON_PROJECTION, GOCC_EXCITATORY_SYNAPSE, GOCC_NEURON_PROJECTION_TERMINUS, GOCC_POSTSYNAPSE, GOCC_SYNAPSE

GO Biological Process (7): chemical synaptic transmission (GO:0007268), synapse assembly (GO:0007416), visual perception (GO:0007601), establishment of protein localization (GO:0045184), synapse organization (GO:0050808), synaptic membrane adhesion (GO:0099560), synaptic signaling (GO:0099536)

GO Molecular Function (3): protein phosphatase inhibitor activity (GO:0004864), signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (10): plasma membrane (GO:0005886), dendrite (GO:0030425), axon terminus (GO:0043679), excitatory synapse (GO:0060076), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), membrane (GO:0016020), cell projection (GO:0042995), neuron projection terminus (GO:0044306), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
synapse3
cellular anatomical structure3
synapse organization2
neuron projection2
anterograde trans-synaptic signaling1
nervous system development1
cell junction assembly1
sensory perception of light stimulus1
establishment of localization1
cell junction organization1
cell-cell adhesion1
cell-cell signaling1
phosphoprotein phosphatase activity1
phosphatase inhibitor activity1
protein phosphatase regulator activity1
molecular transducer activity1
binding1
membrane1
cell periphery1
dendritic tree1
neuron projection terminus1
presynapse1
distal axon1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
cell junction1

Protein interactions and networks

STRING

1348 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ELFN1CACNA1FO60840663
ELFN1GRM6O15303653
ELFN1GRM7Q14831617
ELFN1TRPM1Q7Z4N2559
ELFN1IGSF9BQ9UPX0528
ELFN1EGFLAMQ63HQ2515
ELFN1GRM8O00222456
ELFN1KCNC3Q14003434
ELFN1DLX1P56177421
ELFN1DPYSQ14117418
ELFN1GRIN2BQ13224418
ELFN1GAD1Q99259409
ELFN1KCNC1P48547408
ELFN1FNDC1Q4ZHG4399
ELFN1DLX5P56178396

IntAct

8 interactions, top by confidence:

ABTypeScore
ELFN1PPP1CApsi-mi:“MI:0407”(direct interaction)0.440
MYCpsi-mi:“MI:0914”(association)0.350
ELFN2TBC1D4psi-mi:“MI:0914”(association)0.350
CLGNTMEM131Lpsi-mi:“MI:0914”(association)0.350
DLK1PLPP3psi-mi:“MI:0914”(association)0.350
SCN2BRIMOC1psi-mi:“MI:0914”(association)0.350
SIGLECL1IPO5psi-mi:“MI:0914”(association)0.350

BioGRID (17): ELFN1 (Affinity Capture-MS), ELFN1 (Affinity Capture-MS), ELFN1 (Affinity Capture-RNA), ELFN1 (Affinity Capture-MS), ELFN1 (Proximity Label-MS), ELFN1 (Cross-Linking-MS (XL-MS)), ELFN1 (Co-fractionation), ETFA (Co-fractionation), ETFB (Co-fractionation), OXSM (Co-fractionation), TPM4 (Co-fractionation), ELFN1 (Affinity Capture-MS), ELFN1 (Co-fractionation), ELFN1 (Co-fractionation), ELFN1 (Affinity Capture-RNA)

ESM2 similar proteins: A1XQX3, A1XQY0, A1XQY3, A2ALI5, A6QLD2, B5X216, D0PRN4, E9PUN2, O35181, O75151, O94933, O94991, P0C7U0, P15379, P23470, P49415, P56975, P58401, P80560, Q05909, Q3SXY7, Q3UH99, Q3V1G4, Q4W8E7, Q58EG3, Q5EGE1, Q5R3F8, Q5R5B8, Q63376, Q63475, Q68BL8, Q68FM6, Q6QD51, Q6ZSJ9, Q76KF0, Q80Z10, Q810B7, Q810B9, Q8AXP2, Q8C8T7

Diamond homologs: P0C7U0, Q5R3F8, Q68FM6, Q8C8T7, Q8BGX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic5
Likely pathogenic0
Uncertain significance167
Likely benign18
Benign13

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
4083482NM_001128636.4(ELFN1):c.149C>A (p.Pro50His)Pathogenic
4083483ELFN1, 92-KB DELPathogenic
4083484NM_001128636.4(ELFN1):c.1767del (p.Val591fs)Pathogenic
4083485NM_001128636.4(ELFN1):c.475_477del (p.Val159del)Pathogenic
4083486NM_001128636.4(ELFN1):c.128_137del (p.Ile43fs)Pathogenic

SpliceAI

726 predictions. Top by Δscore:

VariantEffectΔscore
7:1709253:G:GGdonor_gain1.0000
7:1709229:T:TAdonor_gain0.9900
7:1692950:C:Tdonor_gain0.9800
7:1744302:AGCAG:Aacceptor_gain0.9800
7:1744303:GCA:Gacceptor_gain0.9800
7:1744303:GCAGG:Gacceptor_gain0.9800
7:1744302:A:AGacceptor_gain0.9700
7:1744303:G:GAacceptor_gain0.9700
7:1744303:GC:Gacceptor_gain0.9700
7:1709230:C:CAdonor_gain0.9500
7:1744300:GCA:Gacceptor_loss0.9500
7:1744303:G:Cacceptor_loss0.9500
7:1709259:C:Tdonor_gain0.9400
7:1709190:G:GTdonor_gain0.9200
7:1744139:G:GTdonor_gain0.9200
7:1692928:G:Tdonor_gain0.9100
7:1709191:G:Tdonor_gain0.9100
7:1688146:TACAG:Tdonor_loss0.8900
7:1688147:ACAG:Adonor_loss0.8900
7:1688149:AGG:Adonor_loss0.8900
7:1688150:GG:Gdonor_loss0.8900
7:1688151:G:GAdonor_loss0.8900
7:1688152:T:Gdonor_loss0.8900
7:1689749:TGGC:Tdonor_gain0.8800
7:1689750:GGCG:Gdonor_gain0.8800
7:1709249:ACAAG:Adonor_loss0.8800
7:1709250:CAAG:Cdonor_loss0.8800
7:1709251:AAG:Adonor_loss0.8800
7:1709252:AGTAA:Adonor_loss0.8800
7:1709253:GTAAG:Gdonor_loss0.8800

AlphaMissense

5329 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:1744790:T:CL65P1.000
7:1744805:A:TN70I1.000
7:1744806:C:AN70K1.000
7:1744806:C:GN70K1.000
7:1744862:T:CL89P1.000
7:1744868:T:CL91P1.000
7:1744877:A:TN94I1.000
7:1744878:C:AN94K1.000
7:1744878:C:GN94K1.000
7:1744950:C:AN118K1.000
7:1744950:C:GN118K1.000
7:1745022:C:AN142K1.000
7:1745022:C:GN142K1.000
7:1745084:T:CL163P1.000
7:1745093:A:TN166I1.000
7:1745094:C:AN166K1.000
7:1745094:C:GN166K1.000
7:1744714:T:AW40R0.999
7:1744714:T:CW40R0.999
7:1744718:T:CL41P0.999
7:1744726:T:CC44R0.999
7:1744727:G:AC44Y0.999
7:1744728:C:GC44W0.999
7:1744796:T:AL67H0.999
7:1744796:T:CL67P0.999
7:1744804:A:GN70D0.999
7:1744811:T:CI72T0.999
7:1744853:T:AL86H0.999
7:1744853:T:CL86P0.999
7:1744862:T:AL89H0.999

dbSNP variants (sampled 300 via entrez): RS1000010891 (7:1693398 G>A,T), RS1000021918 (7:1667649 C>T), RS1000024525 (7:1700322 G>A), RS1000045716 (7:1744603 G>A), RS1000075173 (7:1691645 C>A,T), RS1000090724 (7:1744631 G>A), RS1000175904 (7:1732726 A>C), RS1000237401 (7:1732498 A>G), RS1000265957 (7:1695979 G>A), RS1000269596 (7:1741166 G>A,C), RS1000272977 (7:1676824 C>T), RS1000274282 (7:1680834 T>C), RS1000276417 (7:1727818 G>A), RS1000289620 (7:1732199 C>A,G,T), RS1000350433 (7:1705075 C>T)

Disease associations

OMIM: gene MIM:614964 | disease phenotypes: MIM:621344

GenCC curated gene-disease

Mondo (1): Dursun-Ozgul neurodevelopmental syndrome (MONDO:0979898)

Orphanet (0):

HPO phenotypes

120 total (30 of 120 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000154Wide mouth
HP:0000179Thick lower lip vermilion
HP:0000219Thin upper lip vermilion
HP:0000232Everted lower lip vermilion
HP:0000252Microcephaly
HP:0000276Long face
HP:0000278Retrognathia
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000297Facial hypotonia
HP:0000307Pointed chin
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000322Short philtrum
HP:0000325Triangular face
HP:0000341Narrow forehead
HP:0000343Long philtrum
HP:0000365Hearing impairment
HP:0000400Macrotia
HP:0000426Prominent nasal bridge
HP:0000486Strabismus
HP:0000490Deeply set eye
HP:0000520Proptosis
HP:0000582Upslanted palpebral fissure
HP:0000639Nystagmus
HP:0000664Synophrys
HP:0000729Autistic behavior
HP:0000733Motor stereotypy
HP:0000742Self-mutilation

GWAS associations

9 associations (top):

StudyTraitp-value
GCST006479_87Diverticular disease1.000000e-06
GCST006940_34Neurociticism8.000000e-09
GCST006943_43Feeling miserable6.000000e-12
GCST007094_162Diastolic blood pressure9.000000e-06
GCST007099_232Systolic blood pressure1.000000e-08
GCST007603_39Smoking initiation3.000000e-10
GCST008114_6Type 2 diabetes3.000000e-06
GCST008832_2Gastroesophageal reflux disease3.000000e-09
GCST011703_79Smoking initiation3.000000e-12

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0009959diverticular disease
EFO:0007660neuroticism measurement
EFO:0009598feeling miserable measurement
EFO:0006336diastolic blood pressure
EFO:0006335systolic blood pressure
EFO:0005670smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, affects methylation3
Valproic Acidincreases expression, increases methylation, affects expression3
(+)-JQ1 compounddecreases expression2
FR900359affects phosphorylation1
2-methyl-4-isothiazolin-3-oneincreases expression1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acidincreases abundance, affects methylation1
tobacco tardecreases reaction, increases expression1
benzo(e)pyreneincreases methylation1
diallyl disulfidedecreases reaction, increases expression1
allyl sulfideincreases expression, decreases reaction1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
abrineincreases expression1
Cannabinoidsaffects methylation, increases abundance1
Dexamethasonedecreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonatedecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Methapyrileneincreases methylation1
Methotrexatedecreases expression1
Niclosamideincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
Triclosandecreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Aflatoxin B1decreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_SL87HAP1 ELFN1 (-) 1Cancer cell lineMale
CVCL_SL88HAP1 ELFN1 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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