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Aliases for NLGN2 Gene

Aliases for NLGN2 Gene

  • Neuroligin 2 2 3 5
  • Neuroligin-2 3
  • KIAA1366 4

External Ids for NLGN2 Gene

Previous GeneCards Identifiers for NLGN2 Gene

  • GC16M055752
  • GC17P008041
  • GC17P007254
  • GC17P007512
  • GC17P007252
  • GC17P007311
  • GC17P007205

Summaries for NLGN2 Gene

Entrez Gene Summary for NLGN2 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 NLGN2 Gene

NLGN2 (Neuroligin 2) is a Protein Coding gene. Diseases associated with NLGN2 include Autism. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. Gene Ontology (GO) annotations related to this gene include hydrolase activity and cell adhesion molecule binding. An important paralog of this gene is NLGN3.

UniProtKB/Swiss-Prot for NLGN2 Gene

  • Transmembrane scaffolding protein involved in cell-cell interactions via its interactions with neurexin family members. Mediates cell-cell interactions both in neurons and in other types of cells, such as Langerhans beta cells. Plays a role in synapse function and synaptic signal transmission, especially via gamma-aminobutyric acid receptors (GABA(A) receptors). Functions by recruiting and clustering synaptic proteins. Promotes clustering of postsynaptic GABRG2 and GPHN. Modulates signaling by inhibitory synapses, and thereby plays a role in controlling the ratio of signaling by excitatory and inhibitory synapses and information processing. Required for normal signal amplitude from inhibitory synapses, but is not essential for normal signal frequency. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. Mediates cell-cell interactions between Langerhans beta cells and modulates insulin secretion (By similarity).

Gene Wiki entry for NLGN2 Gene

Additional gene information for NLGN2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN2 Gene

Genomics for NLGN2 Gene

GeneHancer (GH) Regulatory Elements for NLGN2 Gene

Promoters and enhancers for NLGN2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J007401 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 659.2 -0.7 -748 4.8 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A ZNF2 ZBTB7B YY1 NLGN2 TMEM256 TMEM256-PLSCR3 ENSG00000262089 EIF4A1 SNORD10 SPEM2 CNTROB POLR2A CHRNB1
GH17J007408 Promoter 0.5 EPDnew 650.7 +3.3 3282 0.1 GC17M007407 NLGN2
GH17J007833 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 40.3 +434.9 434855 12.5 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 KDM6B CHD3 DVL2 PFAS CTC1 WRAP53 CNTROB POLR2A SNORD10 SNORA48
GH17J007233 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 40.3 -166.2 -166215 11.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 DVL2 GABARAP PHF23 CNTROB SNORD10 WRAP53 NEURL4 POLR2A KIAA0753 KCTD11
GH17J007010 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25.3 -387.2 -387160 13.7 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MIR497HG RNASEK BCL6B C17orf49 ENSG00000267047 MIR195 MIR497 DVL2 SNORD10 CNTROB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NLGN2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NLGN2 gene promoter:
  • Evi-1
  • PPAR-gamma2
  • p300
  • c-Myc
  • Max1
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • Bach2

Genomic Locations for NLGN2 Gene

Genomic Locations for NLGN2 Gene
chr17:7,404,874-7,419,864
(GRCh38/hg38)
Size:
14,991 bases
Orientation:
Plus strand
chr17:7,308,193-7,323,179
(GRCh37/hg19)
Size:
14,987 bases
Orientation:
Plus strand

Genomic View for NLGN2 Gene

Genes around NLGN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN2 Gene

Proteins for NLGN2 Gene

  • Protein details for NLGN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NFZ4-NLGN2_HUMAN
    Recommended name:
    Neuroligin-2
    Protein Accession:
    Q8NFZ4
    Secondary Accessions:
    • Q9P2I1

    Protein attributes for NLGN2 Gene

    Size:
    835 amino acids
    Molecular mass:
    90820 Da
    Quaternary structure:
    • Interacts with NRXN1, NRXN2 and NRXN3 (By similarity). Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3) (PubMed:9278515). Interacts with PATJ (By similarity). Interacts with GPHN (By similarity). Interacts with MDGA1 and MDGA2 (By similarity). Found in a complex with MAGI2 and IGSF9B, where it interacts with MAGI2 (via WW 1, WW 2 and PDZ 2 domains) (PubMed:23751499).

    Three dimensional structures from OCA and Proteopedia for NLGN2 Gene

neXtProt entry for NLGN2 Gene

Post-translational modifications for NLGN2 Gene

  • Glycosylation at isoforms=522, isoforms=136, and Asn98
  • Modification sites at PhosphoSitePlus

Other Protein References for NLGN2 Gene

No data available for DME Specific Peptides for NLGN2 Gene

Domains & Families for NLGN2 Gene

Gene Families for NLGN2 Gene

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

Protein Domains for NLGN2 Gene

Suggested Antigen Peptide Sequences for NLGN2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NFZ4

UniProtKB/Swiss-Prot:

NLGN2_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 NLGN2: view

Function for NLGN2 Gene

Molecular function for NLGN2 Gene

UniProtKB/Swiss-Prot Function:
Transmembrane scaffolding protein involved in cell-cell interactions via its interactions with neurexin family members. Mediates cell-cell interactions both in neurons and in other types of cells, such as Langerhans beta cells. Plays a role in synapse function and synaptic signal transmission, especially via gamma-aminobutyric acid receptors (GABA(A) receptors). Functions by recruiting and clustering synaptic proteins. Promotes clustering of postsynaptic GABRG2 and GPHN. Modulates signaling by inhibitory synapses, and thereby plays a role in controlling the ratio of signaling by excitatory and inhibitory synapses and information processing. Required for normal signal amplitude from inhibitory synapses, but is not essential for normal signal frequency. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. Mediates cell-cell interactions between Langerhans beta cells and modulates insulin secretion (By similarity).

Phenotypes From GWAS Catalog for NLGN2 Gene

Gene Ontology (GO) - Molecular Function for NLGN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042043 neurexin family protein binding IEA,NAS 10892652
GO:0042802 identical protein binding IEA --
GO:0050839 cell adhesion molecule binding ISS,IEA --
GO:0052689 carboxylic ester hydrolase activity IBA --
genes like me logo Genes that share ontologies with NLGN2: view
genes like me logo Genes that share phenotypes with NLGN2: view

Animal Models for NLGN2 Gene

MGI Knock Outs for NLGN2:

Animal Model Products

  • Taconic Biosciences Mouse Models for NLGN2

miRNA for NLGN2 Gene

miRTarBase miRNAs that target NLGN2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NLGN2 Gene

Localization for NLGN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN2 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane. Cell junction, synapse, presynaptic cell membrane. Note=Detected at postsynaptic membranes in brain. Detected at dendritic spines in cultured neurons. Colocalizes with GPHN and ARHGEF9 at neuronal cell membranes (By similarity). Localized at presynaptic membranes in retina. Colocalizes with GABRG2 at inhibitory synapses in the retina (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
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 NLGN2 gene
Compartment Confidence
plasma membrane 5
mitochondrion 3
extracellular 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NLGN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA,IEA --
GO:0009986 cell surface ISS --
GO:0016020 membrane NAS 10892652
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NLGN2: view

Pathways & Interactions for NLGN2 Gene

genes like me logo Genes that share pathways with NLGN2: view

Pathways by source for NLGN2 Gene

Gene Ontology (GO) - Biological Process for NLGN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002087 regulation of respiratory gaseous exchange by neurological system process ISS --
GO:0007155 cell adhesion IEA --
GO:0007158 neuron cell-cell adhesion IBA,ISS --
GO:0007416 synapse assembly NAS,ISS 10892652
GO:0019233 sensory perception of pain IEA --
genes like me logo Genes that share ontologies with NLGN2: view

No data available for SIGNOR curated interactions for NLGN2 Gene

Drugs & Compounds for NLGN2 Gene

(1) Additional Compounds for NLGN2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NLGN2: view

Transcripts for NLGN2 Gene

mRNA/cDNA for NLGN2 Gene

Unigene Clusters for NLGN2 Gene

Neuroligin 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN2 Gene

No ASD Table

Relevant External Links for NLGN2 Gene

GeneLoc Exon Structure for
NLGN2
ECgene alternative splicing isoforms for
NLGN2

Expression for NLGN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NLGN2 Gene

Protein differential expression in normal tissues from HIPED for NLGN2 Gene

This gene is overexpressed in Brain (29.3), Frontal cortex (19.1), and Fetal Brain (14.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NLGN2 Gene



Protein tissue co-expression partners for NLGN2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NLGN2 Gene:

NLGN2

SOURCE GeneReport for Unigene cluster for NLGN2 Gene:

Hs.26229

mRNA Expression by UniProt/SwissProt for NLGN2 Gene:

Q8NFZ4-NLGN2_HUMAN
Tissue specificity: Expressed in the blood vessel walls. Detected in colon, brain and pancreas islets of Langerhans (at protein level). Detected in brain, and at lower levels in pancreas islet beta cells.

Evidence on tissue expression from TISSUES for NLGN2 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with NLGN2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NLGN2 Gene

Orthologs for NLGN2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NLGN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NLGN2 34 33
  • 99.42 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NLGN2 34
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NLGN2 34 33
  • 92.97 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NLGN2 34 33
  • 92.46 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nlgn2 33
  • 91.78 (n)
mouse
(Mus musculus)
Mammalia Nlgn2 16 34 33
  • 91.22 (n)
lizard
(Anolis carolinensis)
Reptilia NLGN2 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn2 33
  • 71.19 (n)
zebrafish
(Danio rerio)
Actinopterygii nlgn2a 34
  • 74 (a)
OneToMany
nlgn2b 34 33
  • 71.46 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003568 33
  • 52.53 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34127 33
  • 50.46 (n)
Gli 35
  • 31 (a)
worm
(Caenorhabditis elegans)
Secernentea K11G9.3 35
  • 27 (a)
Species where no ortholog for NLGN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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 NLGN2 Gene

ENSEMBL:
Gene Tree for NLGN2 (if available)
TreeFam:
Gene Tree for NLGN2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NLGN2: view image

Paralogs for NLGN2 Gene

Paralogs for NLGN2 Gene

(14) SIMAP similar genes for NLGN2 Gene using alignment to 2 proteins:

  • NLGN2_HUMAN
  • I3L498_HUMAN
genes like me logo Genes that share paralogs with NLGN2: view

Variants for NLGN2 Gene

Sequence variations from dbSNP and Humsavar for NLGN2 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1085307473 uncertain-significance, not specified 7,408,628(+) G/A coding_sequence_variant, intron_variant, missense_variant
rs1000084076 -- 7,411,449(+) T/TT intron_variant
rs1000115121 -- 7,411,259(+) G/T intron_variant
rs1000826837 -- 7,405,982(+) G/A genic_upstream_transcript_variant, intron_variant
rs1001010828 -- 7,411,501(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NLGN2 Gene

Variant ID Type Subtype PubMed ID
esv2422288 CNV deletion 17116639
esv2662967 CNV deletion 23128226
nsv457659 CNV loss 19166990
nsv470575 CNV loss 18288195
nsv523672 CNV loss 19592680
nsv526176 CNV gain 19592680
nsv574322 CNV loss 21841781
nsv827874 CNV gain 20364138
nsv952118 CNV deletion 24416366

Variation tolerance for NLGN2 Gene

Residual Variation Intolerance Score: 6.77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.29; 41.03% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NLGN2 Gene

Human Gene Mutation Database (HGMD)
NLGN2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NLGN2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NLGN2 Gene

Disorders for NLGN2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NLGN2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
autism
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards
Search NLGN2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NLGN2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NLGN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NLGN2 Gene

Publications for NLGN2 Gene

  1. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58
  2. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. (PMID: 12669065) Jamain S … Paris Autism Research International Sibpair Study (Nature genetics 2003) 3 4 58
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 58
  4. The structure and expression of the human neuroligin-3 gene. (PMID: 10767552) Philibert RA … Ginns EI (Gene 2000) 2 3 58
  5. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58

Products for NLGN2 Gene

Sources for NLGN2 Gene

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