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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. GO annotations related to this gene include hydrolase activity and cell adhesion molecule binding. An important paralog of this gene is CES2.

UniProtKB/Swiss-Prot for NLGN4Y Gene

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

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

Genomics for NLGN4Y Gene

Regulatory Elements for NLGN4Y Gene

Enhancers for NLGN4Y Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around NLGN4Y on UCSC Golden Path with GeneCards custom track

Genomic Location for NLGN4Y Gene

14,522,608 bp from pter
14,845,650 bp from pter
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

Proteomics data for NLGN4Y Gene at MOPED

Post-translational modifications for NLGN4Y Gene

  • Glycosylation at Asn 102 and Asn 511
  • Modification sites at PhosphoSitePlus

Other Protein References for NLGN4Y Gene

No data available for DME Specific Peptides for NLGN4Y Gene

Domains & Families for NLGN4Y Gene

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

No data available for Gene Families for NLGN4Y Gene

Function for NLGN4Y Gene

Molecular function for NLGN4Y Gene

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

Gene Ontology (GO) - Molecular Function for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042043 neurexin family protein binding 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

miRNA for NLGN4Y Gene

miRTarBase miRNAs that target NLGN4Y

Inhibitory RNA Products

Flow Cytometry 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

Jensen Localization Image for NLGN4Y Gene COMPARTMENTS Subcellular localization image for NLGN4Y gene
Compartment Confidence
plasma membrane 4
endoplasmic reticulum 1
golgi apparatus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane IBA --
GO:0045202 synapse IBA --
genes like me logo Genes that share ontologies with NLGN4Y: view

Pathways & Interactions for NLGN4Y Gene

SuperPathways for NLGN4Y Gene

No Data Available

Interacting Proteins for NLGN4Y Gene

Gene Ontology (GO) - Biological Process for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007158 neuron cell-cell adhesion TAS 18923512
GO:0007416 synapse assembly IBA --
GO:0050804 modulation of synaptic transmission IBA --
GO:0071625 vocalization behavior IMP 18628683
GO:0097104 postsynaptic membrane assembly IBA --
genes like me logo Genes that share ontologies with NLGN4Y: view

No data available for Pathways by source and 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:

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 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

SOURCE GeneReport for Unigene cluster for NLGN4Y Gene Hs.439199

mRNA Expression by UniProt/SwissProt for NLGN4Y Gene

Tissue specificity: Expressed in fetal and adult brain, prostate and testis.
genes like me logo Genes that share expression patterns with NLGN4Y: view

Protein tissue co-expression partners for NLGN4Y Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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
(Bos Taurus)
Mammalia NLGN4Y 35
  • 84.07 (n)
  • 96.07 (a)
-- 36
  • 98 (a)
(Canis familiaris)
Mammalia NLGN4X 35
  • 87.83 (n)
  • 96.94 (a)
(Pan troglodytes)
Mammalia NLGN4Y 35
  • 98.49 (n)
  • 98.16 (a)
  • 98 (a)
(Monodelphis domestica)
Mammalia NLGN4 36
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 94 (a)
(Gallus gallus)
Aves NLGN4X 35
  • 80.51 (n)
  • 94.36 (a)
NLGN4 36
  • 92 (a)
(Anolis carolinensis)
Reptilia NLGN4 36
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn4x 35
  • 75.97 (n)
  • 89.79 (a)
(Danio rerio)
Actinopterygii nlgn4b 35
  • 70.74 (n)
  • 78.24 (a)
nlgn4a 36
  • 80 (a)
nlgn4b 36
  • 77 (a)
fruit fly
(Drosophila melanogaster)
Insecta neuroligin 35
  • 47.47 (n)
  • 38.86 (a)
(Caenorhabditis elegans)
Secernentea nlg-1 35
  • 46.42 (n)
  • 36.11 (a)
Species with no ortholog for NLGN4Y:
  • 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 Sequence Context AA Info Type
rs437785 -- 14,571,558(-) AACAG(A/C)ATGAA intron-variant
rs2115848 -- 14,692,972(+) ACTTA(A/G)GAAAG intron-variant
rs2213013 -- 14,607,695(-) agaca(C/T)atgca intron-variant
rs2451661 -- 14,572,314(-) AGGGA(C/T)GTGAA intron-variant
rs2451662 -- 14,572,061(-) caatc(C/G)taagc intron-variant

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

Variant ID Type Subtype PubMed ID
esv1500453 OTHER Inversion 17803354
nsv510572 CNV Loss 20534489

Variation tolerance for NLGN4Y Gene

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

Relevant External Links for NLGN4Y Gene

Human Gene Mutation Database (HGMD)

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

Disorders for NLGN4Y Gene

Relevant External Links for NLGN4Y

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for NLGN4Y Gene.

No data available for MalaCards , 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 Res. 1999) 2 3 4 67
  2. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J. … Sommer S.S. (Psychiatr. Genet. 2008) 3 23
  3. Analysis of four neuroligin genes as candidates for autism. (PMID: 16077734) Ylisaukko-oja T. … JAorvelAo I. (Eur. J. Hum. Genet. 2005) 3 23
  4. Behavioral phenotypes in males with XYY and possible role of increased NLGN4Y expression in autism features. (PMID: 25558953) Ross J.L. … Zinn A.R. (Genes Brain Behav. 2015) 3
  5. Association of Y chromosome haplotypes with autism. (PMID: 19605777) Serajee F.J. … Mahbubul Huq A.H. (J. Child Neurol. 2009) 3

Products for NLGN4Y Gene

Sources for NLGN4Y Gene