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Aliases for NLGN4Y Gene

Aliases for NLGN4Y Gene

  • Neuroligin 4, Y-Linked 2 3 5
  • Neuroligin 4, Y Linked 2
  • Neuroligin Y 4
  • KIAA0951 4

External Ids for NLGN4Y Gene

Previous GeneCards Identifiers for NLGN4Y Gene

  • GC0YU990048
  • GC0YM9A0047
  • GC0XM005269
  • GC0YP015072
  • GC0YP015145
  • GC0YP016634
  • GC0YP011242

Summaries for NLGN4Y Gene

Entrez Gene Summary for NLGN4Y Gene

  • This gene encodes a type I membrane protein that belongs to the family of neuroligins, which are cell adhesion molecules present at the postsynaptic side of the synapse, and may be essential for the formation of functional synapses. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Mar 2011]

GeneCards Summary for NLGN4Y Gene

NLGN4Y (Neuroligin 4, Y-Linked) is a Protein Coding gene. Diseases associated with NLGN4Y include Autism. Among its related pathways are Transmission across Chemical Synapses and Protein-protein interactions at 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 NLGN4Y Gene

  • Putative neuronal cell surface protein involved in cell-cell-interactions.

Additional gene information for NLGN4Y Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN4Y Gene

Genomics for NLGN4Y Gene

GeneHancer (GH) Regulatory Elements for NLGN4Y Gene

Promoters and enhancers for NLGN4Y 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
GH0YI014621 Promoter 0.5 EPDnew 550.2 +99.4 99354 0.1 NLGN4Y PIR40161
GH0YI014522 Enhancer 0.4 ENCODE 550.8 +1.5 1488 4.1 CTCF POLR2A NLGN4Y PIR40161
GH0YI014828 Enhancer 0.3 ENCODE 0.1 +306.1 306138 0.2 JUN PIR51111 GC0YP014900 NLGN4Y
GH0YI014833 Enhancer 0.3 ENCODE 0.1 +312.1 312146 2.7 JUN PIR51111 GC0YP014900 NLGN4Y
GH0YI014644 Enhancer 0.2 ENCODE 0.1 +121.7 121748 0.2 GC0YP014640 NLGN4Y NLGN4Y-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NLGN4Y on UCSC Golden Path with GeneCards custom track

Genomic Locations for NLGN4Y Gene

Genomic Locations for NLGN4Y Gene
323,043 bases
Plus strand

Genomic View for NLGN4Y Gene

Genes around NLGN4Y on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN4Y Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN4Y Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN4Y Gene

Proteins for NLGN4Y Gene

  • Protein details for NLGN4Y Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuroligin-4, Y-linked
    Protein Accession:
    Secondary Accessions:
    • F5H6W0
    • Q14D08
    • Q7Z3T5
    • Q8N5B6
    • Q9Y2F8

    Protein attributes for NLGN4Y Gene

    816 amino acids
    Molecular mass:
    92021 Da
    Quaternary structure:
    • Homodimer. Interacts with NRXN1 in a calcium-dependent manner. Interacts through its C-terminus with DLG4/PSD-95 third PDZ domain (By similarity).
    • Sequence=BAA76795.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NLGN4Y Gene


neXtProt entry for NLGN4Y Gene

Post-translational modifications for NLGN4Y Gene

  • Glycosylation at isoforms=4102 and isoforms=2511

No data available for DME Specific Peptides for NLGN4Y Gene

Domains & Families for NLGN4Y Gene

Gene Families for NLGN4Y Gene

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

Protein Domains for NLGN4Y Gene

Suggested Antigen Peptide Sequences for NLGN4Y Gene

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 NLGN4Y: view

Function for NLGN4Y Gene

Molecular function for NLGN4Y Gene

UniProtKB/Swiss-Prot Function:
Putative neuronal cell surface protein involved in cell-cell-interactions.

Phenotypes From GWAS Catalog for NLGN4Y Gene

Gene Ontology (GO) - Molecular Function for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IBA --
GO:0005515 protein binding IPI 17292328
GO:0042043 neurexin family protein binding IEA,IBA --
GO:0050839 cell adhesion molecule binding TAS 18923512
GO:0052689 carboxylic ester hydrolase activity IBA --
genes like me logo Genes that share ontologies with NLGN4Y: view

Phenotypes for NLGN4Y Gene

genes like me logo Genes that share phenotypes with NLGN4Y: view

Animal Model Products

CRISPR Products

miRNA for NLGN4Y Gene

miRTarBase miRNAs that target NLGN4Y

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NLGN4Y Gene

Localization for NLGN4Y Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN4Y Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density.

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 NLGN4Y gene
Compartment Confidence
plasma membrane 5
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,IBA --
GO:0009986 cell surface IBA --
GO:0014069 postsynaptic density IEA --
genes like me logo Genes that share ontologies with NLGN4Y: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NLGN4Y Gene

Pathways & Interactions for NLGN4Y Gene

genes like me logo Genes that share pathways with NLGN4Y: view

Pathways by source for NLGN4Y Gene

Gene Ontology (GO) - Biological Process for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007158 neuron cell-cell adhesion TAS 18923512
GO:0007612 learning IMP 18628683
GO:0035176 social behavior IMP 18628683
GO:0048488 synaptic vesicle endocytosis IBA --
genes like me logo Genes that share ontologies with NLGN4Y: view

No data available for SIGNOR curated interactions for NLGN4Y Gene

Drugs & Compounds for NLGN4Y Gene

No Compound Related Data Available

Transcripts for NLGN4Y Gene

Unigene Clusters for NLGN4Y Gene

Neuroligin 4, Y-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN4Y Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8 ^ 9
SP3: - - - - - -
SP5: - -

Relevant External Links for NLGN4Y Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NLGN4Y Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NLGN4Y Gene

Protein differential expression in normal tissues from HIPED for NLGN4Y Gene

This gene is overexpressed in Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NLGN4Y Gene

Protein tissue co-expression partners for NLGN4Y Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NLGN4Y Gene:


SOURCE GeneReport for Unigene cluster for NLGN4Y Gene:


mRNA Expression by UniProt/SwissProt for NLGN4Y Gene:

Tissue specificity: Expressed in fetal and adult brain, prostate and testis.

Evidence on tissue expression from TISSUES for NLGN4Y Gene

  • Nervous system(4.3)
  • Pancreas(4)
genes like me logo Genes that share expression patterns with NLGN4Y: view

Primer Products

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 NLGN4Y Gene

Orthologs for NLGN4Y Gene

This gene was present in the common ancestor of animals.

Orthologs for NLGN4Y Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NLGN4Y 33
  • 98.49 (n)
  • 98 (a)
(Bos Taurus)
Mammalia -- 34
  • 98 (a)
  • 84.07 (n)
(Monodelphis domestica)
Mammalia NLGN4 34
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
(Canis familiaris)
Mammalia NLGN4X 33
  • 87.83 (n)
(Gallus gallus)
Aves NLGN4 34
  • 92 (a)
  • 80.51 (n)
(Anolis carolinensis)
Reptilia NLGN4 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn4x 33
  • 75.97 (n)
(Danio rerio)
Actinopterygii nlgn4a 34
  • 80 (a)
nlgn4b 33 34
  • 70.74 (n)
fruit fly
(Drosophila melanogaster)
Insecta neuroligin 33
  • 47.47 (n)
(Caenorhabditis elegans)
Secernentea nlg-1 33
  • 46.42 (n)
Species where no ortholog for NLGN4Y 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 NLGN4Y Gene

Gene Tree for NLGN4Y (if available)
Gene Tree for NLGN4Y (if available)

Paralogs for NLGN4Y Gene

Paralogs for NLGN4Y Gene

(6) SIMAP similar genes for NLGN4Y Gene using alignment to 3 proteins: Pseudogenes for NLGN4Y Gene

genes like me logo Genes that share paralogs with NLGN4Y: view

Variants for NLGN4Y Gene

Sequence variations from dbSNP and Humsavar for NLGN4Y Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs1057524272 uncertain-significance, not specified 14,830,121(+) C/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000032251 -- 14,756,472(+) C/G genic_downstream_transcript_variant, intron_variant
rs1000063290 -- 14,770,959(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000146919 -- 14,546,980(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000226611 -- 14,744,173(+) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NLGN4Y Gene

Variant ID Type Subtype PubMed ID
nsv510572 OTHER sequence alteration 20534489
nsv1132812 CNV duplication 24896259
esv1500453 OTHER inversion 17803354

Variation tolerance for NLGN4Y Gene

Gene Damage Index Score: 0.45; 9.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NLGN4Y Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NLGN4Y Gene

Disorders for NLGN4Y Gene

MalaCards: The human disease database

(1) MalaCards diseases for NLGN4Y Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NLGN4Y

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 NLGN4Y: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NLGN4Y Gene

Publications for NLGN4Y Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. Association of Y chromosome haplotypes with autism. (PMID: 19605777) Serajee FJ … Mahbubul Huq AH (Journal of child neurology 2009) 3 44 58
  3. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J … Sommer SS (Psychiatric genetics 2008) 3 22 58
  4. Analysis of four neuroligin genes as candidates for autism. (PMID: 16077734) Ylisaukko-oja T … Järvelä I (European journal of human genetics : EJHG 2005) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for NLGN4Y Gene

Sources for NLGN4Y Gene

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