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Aliases for NLGN1 Gene

Aliases for NLGN1 Gene

  • Neuroligin 1 2 3 5
  • Neuroligin-1 3
  • EC 3.1.1.1 61
  • KIAA1070 4
  • EC 3.1.1 61
  • 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 Corneal Granular Dystrophy and Corneal Dystrophy, Avellino Type. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. 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

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

Genomics for NLGN1 Gene

Regulatory Elements for NLGN1 Gene

Enhancers for NLGN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F173862 0.8 FANTOM5 3.1 +466.5 466477 0.2 PRDM1 NLGN1 NLGN1-AS1 LOC105374225
GH03F173479 0.3 FANTOM5 1.4 +83.5 83512 0.6 NLGN1 ENSG00000237645
GH03F173394 0.8 ENCODE 0.8 +0.4 372 3.9 PKNOX1 ZNF133 FEZF1 GLI4 ZNF2 ZNF121 GLIS2 KLF7 ZNF263 SP3 NLGN1 ENSG00000237645
GH03F173411 0.5 Ensembl 0.3 +15.2 15217 0.2 NLGN1 ENSG00000237645
GH03F173494 0.3 FANTOM5 0.1 +98.1 98073 0.0 NLGN1 ENSG00000237645
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around NLGN1 on UCSC Golden Path with GeneCards custom track

Promoters for NLGN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001486190 717 4400 ZNF133 FEZF1 GLI4 ZNF2 ZNF121 GLIS2 FOS KLF7 ZNF263 SP3

Genomic Location for NLGN1 Gene

Chromosome:
3
Start:
173,396,284 bp from pter
End:
174,286,644 bp from pter
Size:
890,361 bases
Orientation:
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:
    Q8N2Q7-NLGN1_HUMAN
    Recommended name:
    Neuroligin-1
    Protein Accession:
    Q8N2Q7
    Secondary Accessions:
    • Q9UPT2

    Protein attributes for NLGN1 Gene

    Size:
    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.
    SequenceCaution:
    • 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};

    Alternative splice isoforms for NLGN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NLGN1 Gene

Selected DME Specific Peptides for NLGN1 Gene

Post-translational modifications for NLGN1 Gene

  • Glycosylation at Asn 109, Asn 300, Asn 340, Asn 544, Ser 660, Thr 664, Ser 665, Thr 669, Ser 680, and Ser 683
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for NLGN1 (Neuroligin 1/NLGN1)

Domains & Families for NLGN1 Gene

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

Q8N2Q7

UniProtKB/Swiss-Prot:

NLGN1_HUMAN :
  • Belongs to the type-B carboxylesterase/lipase family.
Family:
  • Belongs to the type-B carboxylesterase/lipase family.
genes like me logo Genes that share domains with NLGN1: view

No data available for Gene Families for NLGN1 Gene

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

Gene Ontology (GO) - Molecular Function for NLGN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity ISS,IBA --
GO:0030165 PDZ domain binding IDA 17474715
GO:0042043 neurexin family protein binding IEA,ISS --
GO:0046983 protein dimerization activity ISS --
GO:0050839 cell adhesion molecule binding 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

Inhibitory RNA Products

Flow Cytometry 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

COMPARTMENTS
Jensen Localization Image for NLGN1 Gene COMPARTMENTS Subcellular localization image for NLGN1 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 3
extracellular 1

Gene Ontology (GO) - Cellular Components for NLGN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 NOT extracellular space IBA --
GO:0005794 Golgi apparatus ISS --
GO:0005886 plasma membrane IEA,ISS --
GO:0005887 integral component of plasma membrane IEA,ISS --
GO:0009897 external side of plasma membrane IEA --
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 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:

Inhibitory RNA Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for NLGN1 Gene

GeneLoc Exon Structure for
NLGN1
ECgene alternative splicing isoforms for
NLGN1

Expression for NLGN1 Gene

mRNA expression in normal human tissues 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:

NLGN1

SOURCE GeneReport for Unigene cluster for NLGN1 Gene:

Hs.478289

mRNA Expression by UniProt/SwissProt for NLGN1 Gene:

Q8N2Q7-NLGN1_HUMAN
Tissue specificity: Expressed in the blood vessel walls (at protein level). Detected in brain, and at lower levels in pancreas islet beta cells.
genes like me logo Genes that share expression patterns with NLGN1: view

Primer Products

No data available for mRNA differential expression in normal tissues 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
chimpanzee
(Pan troglodytes)
Mammalia NLGN1 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia NLGN1 34 35
  • 95.22 (n)
cow
(Bos Taurus)
Mammalia NLGN1 34 35
  • 95.06 (n)
oppossum
(Monodelphis domestica)
Mammalia NLGN1 35
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nlgn1 34 16 35
  • 91.21 (n)
rat
(Rattus norvegicus)
Mammalia Nlgn1 34
  • 91.13 (n)
chicken
(Gallus gallus)
Aves NLGN1 34 35
  • 87 (n)
lizard
(Anolis carolinensis)
Reptilia NLGN1 35
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn1 34
  • 80.06 (n)
zebrafish
(Danio rerio)
Actinopterygii nlgn1 34 35
  • 73.91 (n)
Dr.18973 34
fruit fly
(Drosophila melanogaster)
Insecta CG5030 36
  • 40 (a)
neuroligin 36
  • 34 (a)
alpha-Est5 36
  • 33 (a)
Gli 36
  • 31 (a)
CG10175 36
  • 30 (a)
CG6018 36
  • 30 (a)
CG6414 36
  • 30 (a)
clt 36
  • 30 (a)
Est-6 36
  • 30 (a)
Est-P 36
  • 30 (a)
CG10339 36
  • 29 (a)
CG3841 36
  • 29 (a)
alpha-Est2 36
  • 28 (a)
alpha-Est4 36
  • 28 (a)
alpha-Est8 36
  • 28 (a)
Jhe 36
  • 28 (a)
CG4382 36
  • 27 (a)
CG7529 36
  • 27 (a)
CG9287 36
  • 27 (a)
CG9289 36
  • 27 (a)
CG5397 36
  • 26 (a)
worm
(Caenorhabditis elegans)
Secernentea B0238.13 36
  • 31 (a)
F07C4.12 36
  • 30 (a)
R173.3 36
  • 30 (a)
C52A10.1 36
  • 29 (a)
K11G9.2 36
  • 29 (a)
T28C12.4a 36
  • 29 (a)
T28C12.4b 36
  • 29 (a)
F13H6.3 36
  • 28 (a)
K11G9.3 36
  • 28 (a)
Y71H2AM.13 36
  • 28 (a)
F13H6.4 36
  • 27 (a)
F15A8.6 36
  • 27 (a)
F55D10.3 36
  • 27 (a)
ges-1 36
  • 27 (a)
B0238.7 36
  • 26 (a)
K11G9.1 36
  • 26 (a)
T07H6.1a 36
  • 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

ENSEMBL:
Gene Tree for NLGN1 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs779083189 Likely benign 173,807,831(+) GTACT(C/T)GGTAA reference, synonymous-codon
rs1004964 -- 173,645,631(+) ATGGG(A/G)AAAAA intron-variant
rs1006180 -- 174,133,541(+) GGAAG(C/G)GGGTA intron-variant
rs10154973 -- 173,951,761(+) AGGCC(A/G)AGACC intron-variant
rs1017189 -- 174,192,301(+) TTTGA(A/G)AAATG 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)

Relevant External Links for NLGN1 Gene

Human Gene Mutation Database (HGMD)
NLGN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NLGN1

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

Disorders for NLGN1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NLGN1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
corneal granular dystrophy
  • granular corneal dystrophy
corneal dystrophy, avellino type
  • granular corneal dystrophy type ii
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

Relevant External Links for NLGN1

Genetic Association Database (GAD)
NLGN1
Human Genome Epidemiology (HuGE) Navigator
NLGN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NLGN1
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. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G. … White R.L. (Alcohol. Clin. Exp. Res. 2010) 3 46 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients. (PMID: 20398908) Saus E. … Estivill X. (J Psychiatr Res 2010) 3 46 64
  4. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PMID: 20677014) Shimada M. … Tokunaga K. (Hum. Genet. 2010) 3 46 64
  5. Genome-wide association study of major recurrent depression in the U.K. population. (PMID: 20516156) Lewis C.M. … McGuffin P. (Am J Psychiatry 2010) 3 46 64

Products for NLGN1 Gene

Sources for NLGN1 Gene

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