NETO1

gene
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Also known as BTCL1BCTL1

Summary

NETO1 (neuropilin and tolloid like 1, HGNC:13823) is a protein-coding gene on chromosome 18q22.3, encoding Neuropilin and tolloid-like protein 1 (Q8TDF5). Involved in the development and/or maintenance of neuronal circuitry.

This gene encodes a transmembrane protein containing two extracellular CUB domains followed by a low-density lipoprotein class A (LDLa) domain. This protein is thought to play a critical role in spatial learning and memory by regulating the function of synaptic N-methyl-D-aspartic acid receptor complexes in the hippocampus. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 81832 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 59 total — 1 pathogenic
  • MANE Select transcript: NM_138966

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13823
Approved symbolNETO1
Nameneuropilin and tolloid like 1
Location18q22.3
Locus typegene with protein product
StatusApproved
AliasesBTCL1, BCTL1
Ensembl geneENSG00000166342
Ensembl biotypeprotein_coding
OMIM607973
Entrez81832

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000327305, ENST00000397929, ENST00000577184, ENST00000579169, ENST00000579730, ENST00000582281, ENST00000583169, ENST00000876951, ENST00000916239, ENST00000916240, ENST00000916241

RefSeq mRNA: 8 — MANE Select: NM_138966 NM_001201465, NM_001354017, NM_001354018, NM_001354020, NM_001354021, NM_001354022, NM_138966, NM_138999

CCDS: CCDS12000, CCDS42444

Canonical transcript exons

ENST00000327305 — 11 exons

ExonStartEnd
ENSE000011799437279436372794404
ENSE000011799737286726472867987
ENSE000013056357275006272750620
ENSE000013058957278367872783906
ENSE000013262497279411772794244
ENSE000013274007274901472749088
ENSE000016340817275603472756147
ENSE000027220027274375672748164
ENSE000036173197285882672859074
ENSE000036302237286518872865241
ENSE000036696787286480872864945

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 88.98.

FANTOM5 (CAGE): breadth broad, TPM avg 3.8885 / max 139.1868, expressed in 369 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1724073.1389357
1724080.3992117
1724090.229492
1724050.058941
1724060.044329
1724040.01786

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
prefrontal cortexUBERON:000045188.98gold quality
Brodmann (1909) area 9UBERON:001354086.00gold quality
anterior cingulate cortexUBERON:000983585.21gold quality
dorsolateral prefrontal cortexUBERON:000983485.12gold quality
frontal cortexUBERON:000187083.41gold quality
neocortexUBERON:000195082.90gold quality
caudate nucleusUBERON:000187382.46gold quality
putamenUBERON:000187482.21gold quality
nucleus accumbensUBERON:000188282.21gold quality
right frontal lobeUBERON:000281081.73gold quality
cerebral cortexUBERON:000095681.22gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.75gold quality
amygdalaUBERON:000187677.81gold quality
Ammon’s hornUBERON:000195477.77gold quality
forebrainUBERON:000189076.01gold quality
primary visual cortexUBERON:000243674.92gold quality
buccal mucosa cellCL:000233674.72gold quality
temporal lobeUBERON:000187173.67gold quality
superior frontal gyrusUBERON:000266173.30gold quality
cortical plateUBERON:000534373.12gold quality
brainUBERON:000095571.36gold quality
Brodmann (1909) area 46UBERON:000648371.31gold quality
occipital lobeUBERON:000202171.16gold quality
hypothalamusUBERON:000189870.48gold quality
postcentral gyrusUBERON:000258170.09gold quality
parietal lobeUBERON:000187269.37gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099169.20gold quality
Brodmann (1909) area 23UBERON:001355469.10gold quality
entorhinal cortexUBERON:000272867.93gold quality
stromal cell of endometriumCL:000225567.35gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-11121yes657.20
E-GEOD-98556yes431.44
E-GEOD-137537yes20.18
E-ANND-3yes4.61

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GATA3

miRNA regulators (miRDB)

91 targeting NETO1, 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-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3924100.0072.092394
HSA-MIR-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-126-5P100.0072.713180
HSA-MIR-453499.9966.581907
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-569699.9872.364487
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-808299.9567.271170
HSA-MIR-651-3P99.9473.485177
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-314399.9371.963104
HSA-MIR-338-5P99.9272.342951
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-153-5P99.8973.866317
HSA-MIR-612499.8769.783551
HSA-MIR-369-3P99.8570.522264
HSA-MIR-469899.8471.414303

Literature-anchored findings (GeneRIF, showing 5)

  • Mouse neto1 plays a critical role in spatial learning and memory through the regulation of NMDAR subunit abundance at synapses. (PMID:19243221)
  • no evidence for the association of NETO1 with schizophrenia in the Japanese population (PMID:22205981)
  • Neto1 is concluded to be a component of amyloid precursor protein /NMDA receptor trafficking complexes (PMID:23621516)
  • Results suggested that the extracellular N-terminal region including the two CUB domains was largely responsible for the distinct regulatory effects of Neto1 and Neto2 on the desensitization properties of GluK1 homomeric receptors (PMID:26277340)
  • High neuropilin and tolloid-like 1 expression associated with metastasis and poor survival in epithelial ovarian cancer via regulation of actin cytoskeleton. (PMID:32638511)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioneto1ENSDARG00000068483
danio_rerioneto1lENSDARG00000071596
mus_musculusNeto1ENSMUSG00000050321
rattus_norvegicusNeto1ENSRNOG00000014006

Paralogs (35): NRXN3 (ENSG00000021645), TLL1 (ENSG00000038295), CP (ENSG00000047457), DCBLD2 (ENSG00000057019), HEPH (ENSG00000089472), TLL2 (ENSG00000095587), NRP1 (ENSG00000099250), PCOLCE (ENSG00000106333), CNTNAP3 (ENSG00000106714), CUBN (ENSG00000107611), CNTNAP1 (ENSG00000108797), NRXN2 (ENSG00000110076), MEP1A (ENSG00000112818), NRP2 (ENSG00000118257), CUZD1 (ENSG00000138161), MFGE8 (ENSG00000140545), MEP1B (ENSG00000141434), PDGFC (ENSG00000145431), CNTNAP4 (ENSG00000152910), CNTNAP3B (ENSG00000154529), CNTNAP5 (ENSG00000155052), CDCP2 (ENSG00000157211), PCOLCE2 (ENSG00000163710), EDIL3 (ENSG00000164176), BMP1 (ENSG00000168487), PDGFD (ENSG00000170962), NETO2 (ENSG00000171208), CNTNAP2 (ENSG00000174469), NRXN1 (ENSG00000179915), HEPHL1 (ENSG00000181333), F8 (ENSG00000185010), ASTL (ENSG00000188886), F5 (ENSG00000198734), MFRP (ENSG00000235718), CNTNAP3C (ENSG00000283378)

Protein

Protein identifiers

Neuropilin and tolloid-like protein 1Q8TDF5 (reviewed: Q8TDF5)

Alternative names: Brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1

All UniProt accessions (2): Q8TDF5, J3QRF5

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the development and/or maintenance of neuronal circuitry. Accessory subunit of the neuronal N-methyl-D-aspartate receptor (NMDAR) critical for maintaining the abundance of GRIN2A-containing NMDARs in the postsynaptic density. Regulates long-term NMDA receptor-dependent synaptic plasticity and cognition, at least in the context of spatial learning and memory.

Subunit / interactions. Interacts with PLZ domains of DLG2, DLG3 and DLG4 via its C-terminal TRV domain. Interacts with GRIN2A and GRIN2B via its CUB domains.

Subcellular location. Cell membrane. Postsynaptic density membrane Cell membrane Secreted.

Tissue specificity. Isoform 1 and isoform 2 are retina-specific. Isoform 3 is found in retina as well as at lower levels in adult and fetal brain.

Isoforms (3)

UniProt IDNamesCanonical?
Q8TDF5-33yes
Q8TDF5-11, Soluble, sNETO1
Q8TDF5-22

RefSeq proteins (8): NP_001188394, NP_001340946, NP_001340947, NP_001340949, NP_001340950, NP_001340951, NP_620416, NP_620552 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000859CUB_domDomain
IPR002172LDrepeatLR_classA_rptRepeat
IPR023415LDLR_class-A_CSConserved_site
IPR035914Sperma_CUB_dom_sfHomologous_superfamily
IPR036055LDL_receptor-like_sfHomologous_superfamily

Pfam: PF00057, PF00431

UniProt features (25 total): disulfide bond 7, splice variant 3, domain 3, glycosylation site 2, topological domain 2, sequence variant 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TDF5-F171.830.51

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 (1): 417

Disulfide bonds (7): 41–68, 96–118, 172–202, 229–251, 292–304, 299–317, 311–326

Glycosylation sites (2): 306, 340

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 228 (showing top): GOBP_MEMORY, GOBP_COGNITION, GOBP_AXO_DENDRITIC_TRANSPORT, GOBP_BEHAVIOR, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_REGULATION_OF_NEURONAL_SYNAPTIC_PLASTICITY, GOBP_ASSOCIATIVE_LEARNING, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_CELL_CELL_SIGNALING, STARK_HYPPOCAMPUS_22Q11_DELETION_UP, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, GOBP_REGULATION_OF_POSTSYNAPTIC_MEMBRANE_POTENTIAL, GOBP_LEARNING, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, IRF1_Q6

GO Biological Process (7): memory (GO:0007613), visual learning (GO:0008542), regulation of long-term neuronal synaptic plasticity (GO:0048169), neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0099645), anterograde axonal transport of neurotransmitter receptor complex (GO:0140231), positive regulation of excitatory postsynaptic potential (GO:2000463), receptor localization to synapse (GO:0097120)

GO Molecular Function (2): ionotropic glutamate receptor binding (GO:0035255), protein binding (GO:0005515)

GO Cellular Component (11): extracellular region (GO:0005576), postsynaptic density (GO:0014069), excitatory synapse (GO:0060076), Schaffer collateral - CA1 synapse (GO:0098685), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), axon cytoplasm (GO:1904115), plasma membrane (GO:0005886), membrane (GO:0016020), synapse (GO:0045202), postsynaptic membrane (GO:0045211)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
synapse3
receptor localization to synapse2
cellular anatomical structure2
learning or memory1
visual behavior1
associative learning1
regulation of neuronal synaptic plasticity1
protein-containing complex localization1
regulation of postsynaptic membrane neurotransmitter receptor levels1
protein localization to postsynaptic specialization membrane1
neurotransmitter receptor transport1
anterograde axonal protein transport1
positive regulation of signal transduction1
excitatory postsynaptic potential1
modulation of excitatory postsynaptic potential1
localization1
glutamate receptor binding1
binding1
asymmetric synapse1
postsynaptic specialization1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
axon1
neuron projection cytoplasm1
membrane1
cell periphery1
cell junction1
synaptic membrane1
postsynapse1

Protein interactions and networks

STRING

1144 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NETO1GRIK2Q13002872
NETO1GRIK1P39086773
NETO1KARS1Q15046724
NETO1SPADHA0A494C103623
NETO1GRIN2AQ12879621
NETO1C1SP09871602
NETO1SEMA3EO15041600
NETO1GRIK4Q16099593
NETO1GRIK5Q16478543
NETO1NTNG1Q9Y2I2526
NETO1NTNG2Q96CW9517
NETO1CAPNS2Q96L46515
NETO1FBXO15Q8NCQ5514
NETO1GRIK3Q13003507
NETO1CACNG2Q9Y698506

IntAct

3 interactions, top by confidence:

ABTypeScore
CHRNB2TMEM131Lpsi-mi:“MI:0914”(association)0.350
RSPH1NETO1psi-mi:“MI:0915”(physical association)0.000

BioGRID (11): NETO1 (Affinity Capture-RNA), NETO1 (Affinity Capture-Western), NETO1 (Affinity Capture-Western), NETO1 (Affinity Capture-Western), NETO1 (Affinity Capture-Western), NETO1 (Affinity Capture-MS), NETO1 (Proximity Label-MS), NETO1 (Two-hybrid), NETO1 (Reconstituted Complex), NETO1 (Affinity Capture-RNA), NETO1 (Affinity Capture-Luminescence)

ESM2 similar proteins: A1XQX1, A2A690, D0PRN2, F1LTE0, O73612, P0DI97, P13590, P15209, P52795, P52796, P52799, P52800, P58400, P97401, P98172, Q01973, Q03351, Q0PMD2, Q13330, Q16288, Q16620, Q17QD6, Q28142, Q28143, Q5RF67, Q62599, Q63373, Q63604, Q6NW40, Q6PFE7, Q8C4U3, Q8C985, Q8IYR6, Q8K4B0, Q8N474, Q8R4I7, Q8TDF5, Q8VHW2, Q8VHW5, Q91044

Diamond homologs: A8Q2D1, C6K2K4, C6KFA3, D5FM38, O43897, O57460, P48740, P79953, P97435, P98064, Q4A3R3, Q5E9P5, Q60997, Q62381, Q6F3F9, Q7Z408, Q86SQ4, Q86UP6, Q8BNJ6, Q8BQH6, Q8BU25, Q8BZE1, Q8CHN8, Q8CIZ5, Q8NC67, Q8R4I7, Q8TDF5, Q90WD8, Q923L3, Q95218, Q96PZ7, Q9EQT1, Q9JJS0, Q9NQ36, Q9QZT0, Q9UGM3, Q9W332, A8WCC4, B3EX01, B8VIV4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance47
Likely benign2
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2578813GRCh37/hg19 18q22.1-23(chr18:63476940-77960815)x1Pathogenic

SpliceAI

2639 predictions. Top by Δscore:

VariantEffectΔscore
18:72750623:A:Cacceptor_gain1.0000
18:72750628:T:Cacceptor_gain1.0000
18:72750628:T:TCacceptor_gain1.0000
18:72750637:G:Cacceptor_gain1.0000
18:72750637:G:GCacceptor_gain1.0000
18:72756028:CATTA:Cdonor_loss1.0000
18:72756029:ATTAC:Adonor_loss1.0000
18:72756030:TTA:Tdonor_loss1.0000
18:72756031:TA:Tdonor_loss1.0000
18:72756032:A:Tdonor_loss1.0000
18:72756033:C:Tdonor_loss1.0000
18:72756033:CCT:Cdonor_gain1.0000
18:72756148:C:CCacceptor_gain1.0000
18:72783676:A:ACdonor_gain1.0000
18:72783677:C:CCdonor_gain1.0000
18:72783677:CGTT:Cdonor_gain1.0000
18:72783680:T:Adonor_gain1.0000
18:72783803:G:Cdonor_gain1.0000
18:72783907:C:CGacceptor_loss1.0000
18:72783908:T:Gacceptor_loss1.0000
18:72794406:T:Cacceptor_gain1.0000
18:72858820:A:ACdonor_gain1.0000
18:72858821:C:CCdonor_gain1.0000
18:72859072:CGG:Cacceptor_gain1.0000
18:72859075:C:CCacceptor_gain1.0000
18:72864802:CCTTA:Cdonor_loss1.0000
18:72864803:CTTA:Cdonor_loss1.0000
18:72864804:TTA:Tdonor_loss1.0000
18:72864805:TACCT:Tdonor_loss1.0000
18:72864806:A:Tdonor_loss1.0000

AlphaMissense

3551 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:72756053:C:AW321C1.000
18:72756053:C:GW321C1.000
18:72794144:C:AW204C1.000
18:72794144:C:GW204C1.000
18:72794146:A:GW204R1.000
18:72794146:A:TW204R1.000
18:72858897:A:GL133P1.000
18:72858984:C:GR104P1.000
18:72859050:A:GL82P1.000
18:72756065:A:CC317W0.999
18:72756066:C:GC317S0.999
18:72756066:C:TC317Y0.999
18:72756067:A:GC317R0.999
18:72756067:A:TC317S0.999
18:72756083:G:CC311W0.999
18:72756084:C:GC311S0.999
18:72756084:C:TC311Y0.999
18:72756085:A:GC311R0.999
18:72756085:A:TC311S0.999
18:72756104:A:CC304W0.999
18:72756105:C:GC304S0.999
18:72756106:A:GC304R0.999
18:72756106:A:TC304S0.999
18:72756119:G:CC299W0.999
18:72756120:C:GC299S0.999
18:72756120:C:TC299Y0.999
18:72756121:A:GC299R0.999
18:72756121:A:TC299S0.999
18:72783736:C:AW270C0.999
18:72783736:C:GW270C0.999

dbSNP variants (sampled 300 via entrez): RS1000023769 (18:72854461 A>G), RS1000024583 (18:72792818 A>G), RS1000026280 (18:72819094 T>C), RS1000058084 (18:72754421 T>C), RS1000071969 (18:72744342 G>A,T), RS1000084470 (18:72834186 A>T), RS1000094399 (18:72860903 T>C), RS1000208150 (18:72804194 C>G), RS1000236341 (18:72815158 G>A), RS1000242588 (18:72851227 C>A,T), RS1000261444 (18:72777644 G>A), RS1000270843 (18:72838658 G>A), RS1000274762 (18:72759924 C>T), RS1000283683 (18:72844498 C>T), RS1000335642 (18:72844214 T>C)

Disease associations

OMIM: gene MIM:607973 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001511_4Economic and political preferences (time)6.000000e-07
GCST001856_49Thyroid hormone levels3.000000e-08
GCST002304_11Fractional exhaled nitric oxide (childhood)1.000000e-06
GCST002304_3Fractional exhaled nitric oxide (childhood)3.000000e-06
GCST005171_13QT interval7.000000e-07
GCST009391_1418Metabolite levels1.000000e-06
GCST009391_999Metabolite levels1.000000e-06
GCST010244_179Triglyceride levels2.000000e-08
GCST90026412_6Severe autoimmune type 2 diabetes6.000000e-06

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004827economic and social preference
EFO:0004730hormone measurement
EFO:0005536nitric oxide exhalation measurement
EFO:0004682QT interval
EFO:0010452adenosine diphosphate measurement
EFO:0010540thiamine measurement
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
Benzo(a)pyreneaffects methylation, increases methylation2
Estradiolaffects expression, affects cotreatment, increases expression2
Testosteroneaffects cotreatment, decreases expression, increases expression2
Aflatoxin B1decreases methylation2
methylmercuric chlorideincreases expression1
bisphenol Aaffects cotreatment, increases methylation1
terbufosincreases methylation1
trichostatin Aincreases expression1
arseniteincreases methylation1
sodium arsenitedecreases expression, increases abundance, affects cotreatment1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
benzo(e)pyreneaffects methylation1
aflatoxin B2increases methylation1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
dorsomorphinaffects cotreatment, increases expression1
Decitabineincreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Acetaminophendecreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Calcitrioldecreases expression, affects cotreatment1
Fonofosincreases methylation1
Formaldehydeincreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Methapyrileneincreases methylation1
Parathionincreases methylation1
Phenylmercuric Acetateaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.