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Aliases for NLGN3 Gene

Aliases for NLGN3 Gene

  • Neuroligin 3 2 3 5
  • Gliotactin Homolog 3 4
  • Neuroligin-3 3
  • KIAA1480 4
  • HNL3 3
  • NL3 4

External Ids for NLGN3 Gene

Previous GeneCards Identifiers for NLGN3 Gene

  • GC0XP066538
  • GC0XP067842
  • GC0XP068597
  • GC0XP069231
  • GC0XP070147
  • GC0XP070281
  • GC0XP070364
  • GC0XP064183

Summaries for NLGN3 Gene

Entrez Gene Summary for NLGN3 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. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]

GeneCards Summary for NLGN3 Gene

NLGN3 (Neuroligin 3) is a Protein Coding gene. Diseases associated with NLGN3 include Asperger Syndrome, X-Linked 1 and Autism X-Linked 1. 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 NLGN4X.

UniProtKB/Swiss-Prot for NLGN3 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 may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity).

Gene Wiki entry for NLGN3 Gene

Additional gene information for NLGN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN3 Gene

Genomics for NLGN3 Gene

GeneHancer (GH) Regulatory Elements for NLGN3 Gene

Promoters and enhancers for NLGN3 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
GH0XJ071145 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 650.7 +1.3 1341 1.9 HDGF ATF1 FOXA2 ARNT ZNF493 TCF12 POLR2B GLIS2 E2F8 ZFP91 NLGN3 MED12 LOC392489 TAF1 NONO ZMYM3 LOC100420758 ARR3 P2RY4 OGT
GH0XJ071144 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 650.7 +0.0 24 0.1 MXI1 POLR2A ZBTB26 NLGN3 ENSG00000228427
GH0XJ071153 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.4 +8.6 8571 0.1 NLGN3 CXorf65 MED12 IL2RG SNX12 ENSG00000228427
GH0XJ071181 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 0.3 +38.0 38048 3.5 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B TAF1 NONO OGT MED12 LOC100420758 ENSG00000229601 P2RY4 ARR3 RPS26P11 RTL5
GH0XJ071170 Enhancer 1 Ensembl ENCODE dbSUPER 0.3 +26.5 26523 1.1 HDAC1 PKNOX1 DPF2 ZNF148 CTBP1 POLR2A VEZF1 IKZF1 NFE2 ZFX NLGN3 ENSG00000228427
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NLGN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NLGN3 gene promoter:
  • NF-kappaB1
  • E2F-5
  • E2F-4
  • E2F-3a
  • E2F-2
  • E2F-1
  • E2F
  • p300
  • HOXA5

Genomic Locations for NLGN3 Gene

Genomic Locations for NLGN3 Gene
chrX:71,144,823-71,175,307
(GRCh38/hg38)
Size:
30,485 bases
Orientation:
Plus strand
chrX:70,364,681-70,391,051
(GRCh37/hg19)
Size:
26,371 bases
Orientation:
Plus strand

Genomic View for NLGN3 Gene

Genes around NLGN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN3 Gene

Proteins for NLGN3 Gene

  • Protein details for NLGN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZ94-NLGN3_HUMAN
    Recommended name:
    Neuroligin-3
    Protein Accession:
    Q9NZ94
    Secondary Accessions:
    • B2RBK1
    • D2X2H6
    • D3DVV0
    • D3DVV1
    • Q86V51
    • Q8NCD0
    • Q9NZ95
    • Q9NZ96
    • Q9NZ97
    • Q9P248

    Protein attributes for NLGN3 Gene

    Size:
    848 amino acids
    Molecular mass:
    93895 Da
    Quaternary structure:
    • Interacts with NRXN1, NRXN2 and NRXN3. Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3) (By similarity). Homodimer, and heterodimer with NLGN1 and NLGN2 (By similarity).
    SequenceCaution:
    • Sequence=AAF71231.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA96004.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC11226.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NLGN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NLGN3 Gene

Post-translational modifications for NLGN3 Gene

  • Glycosylation at Asn545 and isoforms=2, 398
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NLGN3 Gene

Domains & Families for NLGN3 Gene

Gene Families for NLGN3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for NLGN3 Gene

Suggested Antigen Peptide Sequences for NLGN3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NZ94

UniProtKB/Swiss-Prot:

NLGN3_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 NLGN3: view

Function for NLGN3 Gene

Molecular function for NLGN3 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 may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity).

Gene Ontology (GO) - Molecular Function for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17292328
GO:0038023 signaling receptor activity ISS --
GO:0042043 neurexin family protein binding IEA,ISS 15152050
GO:0050839 cell adhesion molecule binding ISS 15152050
GO:0052689 carboxylic ester hydrolase activity IBA --
genes like me logo Genes that share ontologies with NLGN3: view
genes like me logo Genes that share phenotypes with NLGN3: view

Animal Models for NLGN3 Gene

MGI Knock Outs for NLGN3:

Animal Model Products

  • Taconic Biosciences Mouse Models for NLGN3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN3

Clone Products

  • Addgene plasmids for NLGN3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NLGN3 Gene

Localization for NLGN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN3 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse. Note=Detected at both glutamatergic and GABAergic synapses. {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 NLGN3 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 1
mitochondrion 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,IBA --
GO:0009986 cell surface IDA 15150161
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NLGN3: view

Pathways & Interactions for NLGN3 Gene

genes like me logo Genes that share pathways with NLGN3: view

Pathways by source for NLGN3 Gene

Gene Ontology (GO) - Biological Process for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002087 regulation of respiratory gaseous exchange by neurological system process ISS --
GO:0006898 receptor-mediated endocytosis ISS --
GO:0007155 cell adhesion IEA --
GO:0007158 neuron cell-cell adhesion IBA,ISS --
GO:0007416 synapse assembly ISS --
genes like me logo Genes that share ontologies with NLGN3: view

No data available for SIGNOR curated interactions for NLGN3 Gene

Drugs & Compounds for NLGN3 Gene

No Compound Related Data Available

Transcripts for NLGN3 Gene

mRNA/cDNA for NLGN3 Gene

Unigene Clusters for NLGN3 Gene

Neuroligin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN3

Clone Products

  • Addgene plasmids for NLGN3

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
SP1: - - - - -
SP2: - - -
SP3: - -
SP4: - - - -
SP5:

Relevant External Links for NLGN3 Gene

GeneLoc Exon Structure for
NLGN3
ECgene alternative splicing isoforms for
NLGN3

Expression for NLGN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NLGN3 Gene

mRNA differential expression in normal tissues according to GTEx for NLGN3 Gene

This gene is overexpressed in Brain - Amygdala (x4.2).

Protein differential expression in normal tissues from HIPED for NLGN3 Gene

This gene is overexpressed in Frontal cortex (37.8), Brain (9.2), and Spinal cord (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NLGN3 Gene



Protein tissue co-expression partners for NLGN3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NLGN3 Gene:

NLGN3

SOURCE GeneReport for Unigene cluster for NLGN3 Gene:

Hs.438877

mRNA Expression by UniProt/SwissProt for NLGN3 Gene:

Q9NZ94-NLGN3_HUMAN
Tissue specificity: Expressed in the blood vessel walls (at protein level). Detected in throughout the brain and in spinal cord. Detected in brain, and at lower levels in pancreas islet beta cells.

Evidence on tissue expression from TISSUES for NLGN3 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with NLGN3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NLGN3 Gene

Orthologs for NLGN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NLGN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NLGN3 34 33
  • 99.88 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NLGN3 34
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NLGN3 34 33
  • 94.27 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NLGN3 34 33
  • 94.06 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nlgn3 16 34 33
  • 93.29 (n)
rat
(Rattus norvegicus)
Mammalia Nlgn3 33
  • 92.85 (n)
chicken
(Gallus gallus)
Aves NLGN3 34 33
  • 82.19 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NLGN3 34
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn3 33
  • 74.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8772 33
zebrafish
(Danio rerio)
Actinopterygii nlgn3a 34 33
  • 74.59 (n)
OneToMany
nlgn3b 34
  • 71 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003115 33
  • 51.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34139 33
  • 50.92 (n)
CG5030 35
  • 41 (a)
neuroligin 35
  • 33 (a)
CG6018 35
  • 31 (a)
Gli 35
  • 31 (a)
CG3841 35
  • 29 (a)
alpha-Est1 35
  • 29 (a)
CG10175 35
  • 28 (a)
CG10339 35
  • 28 (a)
CG6414 35
  • 28 (a)
alpha-Est4 35
  • 28 (a)
CG9289 35
  • 28 (a)
CG8424 35
  • 27 (a)
Jhe 35
  • 27 (a)
alpha-Est7 35
  • 27 (a)
alpha-Est2 35
  • 27 (a)
CG7529 35
  • 26 (a)
worm
(Caenorhabditis elegans)
Secernentea F07C4.12 35
  • 30 (a)
K11G9.3 35
  • 29 (a)
T28C12.4b 35
  • 29 (a)
K11G9.2 35
  • 29 (a)
C52A10.1 35
  • 29 (a)
F13H6.3 35
  • 29 (a)
T28C12.4a 35
  • 29 (a)
F15A8.6 35
  • 28 (a)
K11G9.1 35
  • 28 (a)
B0238.7 35
  • 28 (a)
ges-1 35
  • 27 (a)
Y71H2AM.13 35
  • 27 (a)
F55D10.3 35
  • 26 (a)
Species where no ortholog for NLGN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 NLGN3 Gene

ENSEMBL:
Gene Tree for NLGN3 (if available)
TreeFam:
Gene Tree for NLGN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NLGN3: view image

Paralogs for NLGN3 Gene

Paralogs for NLGN3 Gene

(16) SIMAP similar genes for NLGN3 Gene using alignment to 3 proteins:

  • NLGN3_HUMAN
  • E7EVK0_HUMAN
  • Q4G160_HUMAN
genes like me logo Genes that share paralogs with NLGN3: view

Variants for NLGN3 Gene

Sequence variations from dbSNP and Humsavar for NLGN3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs121917893 risk-factor, Asperger syndrome X-linked 1, Autism, susceptibility to, X-linked 1 71,167,508(+) C/T coding_sequence_variant, missense_variant
rs144914894 benign, likely-benign, not specified, not provided 71,169,504(+) A/G coding_sequence_variant, intron_variant, missense_variant
rs746346104 uncertain-significance, not provided, not specified 71,169,903(+) C/T coding_sequence_variant, intron_variant, missense_variant
rs878853147 likely-pathogenic, Intellectual disability 71,169,399(+) C/T coding_sequence_variant, intron_variant, missense_variant
VAR_015668 Asperger syndrome, X-linked, 1 (ASPGX1) [MIM:300494] p.Arg451Cys

Structural Variations from Database of Genomic Variants (DGV) for NLGN3 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv27208 CNV gain 19812545
esv33082 CNV loss 17666407

Variation tolerance for NLGN3 Gene

Residual Variation Intolerance Score: 3.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.04; 21.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NLGN3 Gene

Human Gene Mutation Database (HGMD)
NLGN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NLGN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NLGN3 Gene

Disorders for NLGN3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for NLGN3 Gene - From: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
asperger syndrome, x-linked 1
  • asperger syndrome, x-linked, susceptibility to, 1
autism x-linked 1
  • autism, susceptibility to, x-linked 1
asperger syndrome
  • asperger disorder
autism
  • autistic disorder
pervasive developmental disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards
Search NLGN3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NLGN3_HUMAN
  • Autism, X-linked 1 (AUTSX1) [MIM:300425]: A complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation. {ECO:0000269 PubMed:12669065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Asperger syndrome, X-linked, 1 (ASPGX1) [MIM:300494]: A syndrome with features similar to autism. Affected individuals exhibit qualitative impairment in social interaction, as manifest by impairment in the use of non-verbal behaviors such as eye-to-eye gaze, facial expression, body postures, and gestures, failure to develop appropriate peer relationships, and lack of social sharing or reciprocity. Patients also exhibit restricted, repetitive and stereotyped patterns of behavior, interests, and activities, including abnormal preoccupation with certain activities and inflexible adherence to routines or rituals. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases. {ECO:0000269 PubMed:12669065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for NLGN3

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 NLGN3: view

No data available for Genatlas for NLGN3 Gene

Publications for NLGN3 Gene

  1. A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population. (PMID: 19645625) Pampanos A … Kitsiou-Tzeli S (Genetic testing and molecular biomarkers 2009) 3 22 44 58
  2. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J … Sommer SS (Psychiatric genetics 2008) 3 22 44 58
  3. NLGN3/NLGN4 gene mutations are not responsible for autism in the Quebec population. (PMID: 15389766) Gauthier J … Rouleau GA (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2005) 3 22 44 58
  4. Mutation screening of X-chromosomal neuroligin genes: no mutations in 196 autism probands. (PMID: 15274046) Vincent JB … Scherer SW (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2004) 3 22 44 58
  5. The structure and expression of the human neuroligin-3 gene. (PMID: 10767552) Philibert RA … Ginns EI (Gene 2000) 2 3 4 58

Products for NLGN3 Gene

Sources for NLGN3 Gene

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