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Aliases for NLGN1 Gene

Aliases for NLGN1 Gene

  • Neuroligin 1 2 3 5
  • Neuroligin-1 3
  • EC 56
  • KIAA1070 4
  • EC 3.1.1 56
  • NL1 3

External Ids for NLGN1 Gene

Previous GeneCards Identifiers for NLGN1 Gene

  • GC03P170368
  • GC03P174328
  • GC03P174704
  • GC03P174437
  • GC03P174635
  • GC03P173114
  • GC03P170489

Summaries for NLGN1 Gene

Entrez Gene Summary for NLGN1 Gene

  • This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. [provided by RefSeq, Jul 2008]

GeneCards Summary for NLGN1 Gene

NLGN1 (Neuroligin 1) is a Protein Coding gene. Diseases associated with NLGN1 include Epilepsy, Familial Temporal Lobe, 3 and Seizure Disorder. Among its related pathways are Ectoderm Differentiation and Transmission across Chemical Synapses. Gene Ontology (GO) annotations related to this gene include hydrolase activity and protein dimerization activity. An important paralog of this gene is NLGN4X.

UniProtKB/Swiss-Prot for NLGN1 Gene

  • Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses. Required to maintain wakefulness quality and normal synchrony of cerebral cortex activity during wakefulness and sleep.

Gene Wiki entry for NLGN1 Gene

Additional gene information for NLGN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN1 Gene

Genomics for NLGN1 Gene

GeneHancer (GH) Regulatory Elements for NLGN1 Gene

Promoters and enhancers for NLGN1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I173394 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.4 372 3.9 PKNOX1 ZNF133 SIN3A FEZF1 GLI4 ZNF2 ZNF121 GLIS2 KLF7 SP3 NLGN1 ENSG00000237645
GH03I173402 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.4 +6.2 6159 0.1 NLGN1 ENSG00000237645
GH03I173862 Enhancer 0.2 FANTOM5 3.1 +466.5 466476 0.2 NLGN1 NLGN1-AS1 LOC105374225
GH03I173479 Enhancer 0.2 FANTOM5 1.4 +83.5 83511 0.6 NLGN1 ENSG00000237645
GH03I173411 Enhancer 0.5 Ensembl dbSUPER 0.4 +15.2 15217 0.2 CTCF NLGN1 ENSG00000237645
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NLGN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NLGN1 gene promoter:

Genomic Locations for NLGN1 Gene

Genomic Locations for NLGN1 Gene
890,361 bases
Plus strand

Genomic View for NLGN1 Gene

Genes around NLGN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN1 Gene

Proteins for NLGN1 Gene

  • Protein details for NLGN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q9UPT2

    Protein attributes for NLGN1 Gene

    840 amino acids
    Molecular mass:
    93835 Da
    Quaternary structure:
    • Interacts with NRXN1, NRXN2 and NRXN3. Interacts with NLGN3. Interacts with AIP1 and PDZRN3 (By similarity). Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3). Interacts with GOPC.
    • Sequence=BAA83022.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAC11039.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NLGN1 Gene

    Alternative splice isoforms for NLGN1 Gene


neXtProt entry for NLGN1 Gene

Selected DME Specific Peptides for NLGN1 Gene


Post-translational modifications for NLGN1 Gene

  • Glycosylation at Asn109, Asn300, isoforms=2340, Asn544, isoforms=2660, isoforms=2664, isoforms=2665, isoforms=2669, Ser680, and isoforms=2683
  • Modification sites at PhosphoSitePlus

Domains & Families for NLGN1 Gene

Gene Families for NLGN1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for NLGN1 Gene

Suggested Antigen Peptide Sequences for NLGN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the type-B carboxylesterase/lipase family.
  • Belongs to the type-B carboxylesterase/lipase family.
genes like me logo Genes that share domains with NLGN1: view

Function for NLGN1 Gene

Molecular function for NLGN1 Gene

UniProtKB/Swiss-Prot Function:
Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses. Required to maintain wakefulness quality and normal synchrony of cerebral cortex activity during wakefulness and sleep.

Enzyme Numbers (IUBMB) for NLGN1 Gene

Phenotypes From GWAS Catalog for NLGN1 Gene

Gene Ontology (GO) - Molecular Function for NLGN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 amyloid-beta binding NAS 21838267
GO:0004872 receptor activity ISS --
GO:0030165 PDZ domain binding IDA 17474715
GO:0042043 neurexin family protein binding NAS,IEA 14522992
GO:0046983 protein dimerization activity ISS --
genes like me logo Genes that share ontologies with NLGN1: view
genes like me logo Genes that share phenotypes with NLGN1: view

Animal Models for NLGN1 Gene

MGI Knock Outs for NLGN1:

Animal Model Products

  • Taconic Biosciences Mouse Models for NLGN1

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NLGN1 Gene

Localization for NLGN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN1 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Note=Enriched in synaptic plasma membranes and clustered in synaptic clefts and postsynaptic densities. Detected at dendritic spines. Colocalized with DLG4/PSD-95 and GRIN1/NMDAR1 (By similarity). {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NLGN1 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 3
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NLGN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus ISS --
GO:0005886 plasma membrane TAS,ISS --
GO:0005887 integral component of plasma membrane NAS,IEA 14522992
GO:0009897 external side of plasma membrane IEA --
GO:0009986 cell surface ISS 26440732
genes like me logo Genes that share ontologies with NLGN1: view

Pathways & Interactions for NLGN1 Gene

genes like me logo Genes that share pathways with NLGN1: view

Pathways by source for NLGN1 Gene

Gene Ontology (GO) - Biological Process for NLGN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002087 regulation of respiratory gaseous exchange by neurological system process IEA --
GO:0006605 protein targeting ISS --
GO:0007155 cell adhesion IEA --
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS --
GO:0007158 neuron cell-cell adhesion TAS,NAS 15797875
genes like me logo Genes that share ontologies with NLGN1: view

No data available for SIGNOR curated interactions for NLGN1 Gene

Drugs & Compounds for NLGN1 Gene

(1) Drugs for NLGN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with NLGN1: view

Transcripts for NLGN1 Gene

Unigene Clusters for NLGN1 Gene

Neuroligin 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN1 Gene

No ASD Table

Relevant External Links for NLGN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NLGN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NLGN1 Gene

Protein differential expression in normal tissues from HIPED for NLGN1 Gene

This gene is overexpressed in Brain (35.5), Fetal Brain (14.3), and Heart (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NLGN1 Gene

Protein tissue co-expression partners for NLGN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NLGN1 Gene:


SOURCE GeneReport for Unigene cluster for NLGN1 Gene:


mRNA Expression by UniProt/SwissProt for NLGN1 Gene:

Tissue specificity: Expressed in the blood vessel walls (at protein level). Detected in brain, and at lower levels in pancreas islet beta cells.

Evidence on tissue expression from TISSUES for NLGN1 Gene

  • Nervous system(4.7)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with NLGN1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NLGN1 Gene

Orthologs for NLGN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NLGN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NLGN1 33 34
  • 99.51 (n)
(Canis familiaris)
Mammalia NLGN1 33 34
  • 95.22 (n)
(Bos Taurus)
Mammalia NLGN1 33 34
  • 95.06 (n)
(Monodelphis domestica)
Mammalia NLGN1 34
  • 94 (a)
(Mus musculus)
Mammalia Nlgn1 33 16 34
  • 91.21 (n)
(Rattus norvegicus)
Mammalia Nlgn1 33
  • 91.13 (n)
(Gallus gallus)
Aves NLGN1 33 34
  • 87 (n)
(Anolis carolinensis)
Reptilia NLGN1 34
  • 97 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn1 33
  • 80.06 (n)
(Danio rerio)
Actinopterygii nlgn1 33 34
  • 73.91 (n)
Dr.18973 33
fruit fly
(Drosophila melanogaster)
Insecta CG5030 35
  • 40 (a)
neuroligin 35
  • 34 (a)
alpha-Est5 35
  • 33 (a)
Gli 35
  • 31 (a)
CG10175 35
  • 30 (a)
CG6018 35
  • 30 (a)
CG6414 35
  • 30 (a)
clt 35
  • 30 (a)
Est-6 35
  • 30 (a)
Est-P 35
  • 30 (a)
CG10339 35
  • 29 (a)
CG3841 35
  • 29 (a)
alpha-Est2 35
  • 28 (a)
alpha-Est4 35
  • 28 (a)
alpha-Est8 35
  • 28 (a)
Jhe 35
  • 28 (a)
CG4382 35
  • 27 (a)
CG7529 35
  • 27 (a)
CG9287 35
  • 27 (a)
CG9289 35
  • 27 (a)
CG5397 35
  • 26 (a)
(Caenorhabditis elegans)
Secernentea B0238.13 35
  • 31 (a)
F07C4.12 35
  • 30 (a)
R173.3 35
  • 30 (a)
C52A10.1 35
  • 29 (a)
K11G9.2 35
  • 29 (a)
T28C12.4a 35
  • 29 (a)
T28C12.4b 35
  • 29 (a)
F13H6.3 35
  • 28 (a)
K11G9.3 35
  • 28 (a)
Y71H2AM.13 35
  • 28 (a)
F13H6.4 35
  • 27 (a)
F15A8.6 35
  • 27 (a)
F55D10.3 35
  • 27 (a)
ges-1 35
  • 27 (a)
B0238.7 35
  • 26 (a)
K11G9.1 35
  • 26 (a)
T07H6.1a 35
  • 26 (a)
Species where no ortholog for NLGN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NLGN1 Gene

Gene Tree for NLGN1 (if available)
Gene Tree for NLGN1 (if available)

Paralogs for NLGN1 Gene

Paralogs for NLGN1 Gene

(10) SIMAP similar genes for NLGN1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with NLGN1: view

Variants for NLGN1 Gene

Sequence variations from dbSNP and Humsavar for NLGN1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs779083189 likely-benign, not specified 173,807,831(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant
rs1000000489 -- 174,019,654(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000000856 -- 173,610,543(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000002251 -- 173,671,312(+) C/A genic_upstream_transcript_variant, intron_variant
rs1000007924 -- 173,443,118(+) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NLGN1 Gene

Variant ID Type Subtype PubMed ID
dgv1429e212 CNV gain 25503493
dgv2842e59 CNV tandem duplication 20981092
dgv304n21 CNV gain 19592680
dgv305n21 CNV gain 19592680
dgv4984n100 CNV gain 25217958
dgv4985n100 CNV gain 25217958
dgv4986n100 CNV gain 25217958
dgv4987n100 CNV gain 25217958
dgv628n27 CNV gain 19166990
dgv629n27 CNV gain 19166990
dgv8732n54 CNV gain 21841781
dgv8733n54 CNV gain 21841781
dgv8734n54 CNV gain 21841781
dgv896e199 CNV deletion 23128226
dgv954e214 CNV loss 21293372
dgv955e214 CNV gain 21293372
dgv956e214 CNV loss 21293372
esv1173402 CNV insertion 17803354
esv1219198 CNV insertion 17803354
esv1345007 CNV insertion 17803354
esv2329791 CNV deletion 18987734
esv2421940 CNV deletion 20811451
esv25261 CNV loss 19812545
esv2658368 CNV deletion 23128226
esv2665338 CNV deletion 23128226
esv2670121 CNV deletion 23128226
esv2678094 CNV deletion 23128226
esv2678513 CNV deletion 23128226
esv2726215 CNV deletion 23290073
esv2726216 CNV deletion 23290073
esv2726217 CNV deletion 23290073
esv2726219 CNV deletion 23290073
esv2726220 CNV deletion 23290073
esv2726221 CNV deletion 23290073
esv2726222 CNV deletion 23290073
esv2759202 CNV gain+loss 17122850
esv2760761 CNV loss 21179565
esv2763325 CNV loss 21179565
esv2763721 CNV gain 21179565
esv33113 CNV gain 17666407
esv3334589 CNV duplication 20981092
esv3353284 CNV insertion 20981092
esv3381699 CNV duplication 20981092
esv3395198 CNV duplication 20981092
esv3433170 CNV duplication 20981092
esv3446159 CNV duplication 20981092
esv3562920 CNV deletion 23714750
esv3569119 CNV loss 25503493
esv3575640 CNV gain 25503493
esv3575641 CNV gain 25503493
esv3598692 CNV loss 21293372
esv3598693 CNV loss 21293372
esv3598694 CNV loss 21293372
esv3598695 CNV gain 21293372
esv3598696 CNV gain 21293372
esv3598697 CNV loss 21293372
esv3598699 CNV gain 21293372
esv3598703 CNV loss 21293372
esv3598709 CNV gain 21293372
esv3598712 CNV loss 21293372
esv3598713 CNV loss 21293372
esv3598715 CNV loss 21293372
esv3598719 CNV gain 21293372
esv3598720 CNV loss 21293372
esv3598721 CNV loss 21293372
esv3598723 CNV loss 21293372
esv3598724 CNV loss 21293372
esv3893816 CNV gain 25118596
esv989077 CNV insertion 20482838
nsv1000678 CNV loss 25217958
nsv1003504 CNV gain 25217958
nsv1003539 CNV loss 25217958
nsv1004769 CNV gain 25217958
nsv1005730 CNV gain 25217958
nsv10358 CNV loss 18304495
nsv10359 CNV gain 18304495
nsv1117039 CNV deletion 24896259
nsv1120463 CNV tandem duplication 24896259
nsv1123705 CNV deletion 24896259
nsv1143065 CNV tandem duplication 24896259
nsv1150077 CNV insertion 26484159
nsv1161004 CNV deletion 26073780
nsv236399 CNV deletion 16902084
nsv238018 CNV deletion 16902084
nsv4120 CNV insertion 18451855
nsv4122 CNV deletion 18451855
nsv4123 CNV insertion 18451855
nsv441850 CNV gain 18776908
nsv442884 CNV loss 18776908
nsv461018 CNV loss 19166990
nsv471071 CNV loss 18288195
nsv507137 OTHER sequence alteration 20534489
nsv514188 CNV loss 21397061
nsv520908 CNV loss 19592680
nsv592544 CNV loss 21841781
nsv7356 OTHER inversion 18451855
nsv818192 CNV gain 17921354
nsv829796 CNV gain 17160897
nsv980091 CNV deletion 23825009

Variation tolerance for NLGN1 Gene

Residual Variation Intolerance Score: 7.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.55; 29.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NLGN1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NLGN1 Gene

Disorders for NLGN1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for NLGN1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epilepsy, familial temporal lobe, 3
  • etl3
seizure disorder
  • epilepsy
  • autistic disorder
pervasive developmental disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards
Search NLGN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NLGN1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NLGN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NLGN1 Gene

Publications for NLGN1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PMID: 20677014) Shimada M … Tokunaga K (Human genetics 2010) 3 44 58
  3. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G … White RL (Alcoholism, clinical and experimental research 2010) 3 44 58
  4. Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients. (PMID: 20398908) Saus E … Estivill X (Journal of psychiatric research 2010) 3 44 58
  5. Genome-wide association study of major recurrent depression in the U.K. population. (PMID: 20516156) Lewis CM … McGuffin P (The American journal of psychiatry 2010) 3 44 58

Products for NLGN1 Gene

Sources for NLGN1 Gene

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