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] See more...

Aliases for NLGN4Y Gene

Aliases for NLGN4Y Gene

  • Neuroligin 4 Y-Linked 2 3 5
  • Neuroligin-4, Y-Linked 3 4
  • KIAA0951 2 4
  • Neuroligin 4, Y Linked 2
  • Alternative HNL4Y 3
  • Neuroligin Y 4
  • NLGN4Y 5
  • HNL4Y 3

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. Among its related pathways are Protein-protein interactions at synapses and Cell adhesion molecules. 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 Summary for NLGN4Y Gene

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

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NLGN4Y Gene

Genomics for NLGN4Y Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NLGN4Y 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
GH0YJ014522 Enhancer 0.5 ENCODE 250.7 +1.5 1523 4.1 CTCF KMT2B GABPB1 KAT7 SPI1 TFDP1 PHF8 EGR1 HSALNG0141258 NLGN4Y
GH0YJ014343 Enhancer 0.6 FANTOM5 Ensembl ENCODE 0.1 -177.7 -177679 1.8 ENSG00000223517 piR-41838-041 MK280607-209 NLGN4Y VCY1B
GH0YJ014339 Enhancer 0.6 FANTOM5 ENCODE 0.1 -181.8 -181769 1.9 FOSL2 JUND SPI1 IRF2 ENSG00000223517 piR-41838-041 MK280607-209 NLGN4Y VCY1B
GH0YJ014350 Enhancer 0.3 Ensembl ENCODE 0.1 -171.2 -171199 1.6 piR-41838-041 ENSG00000223517 MK280607-209 NLGN4Y VCY1B
GH0YJ014410 Enhancer 0.2 ENCODE 0.1 -111.8 -111757 0.2 piR-31470-573 piR-47086-374 MK280607-209 NLGN4Y VCY1B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NLGN4Y on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NLGN4Y

Genomic Locations for NLGN4Y Gene

Latest Assembly
chrY:14,522,573-14,845,654
(GRCh38/hg38)
Size:
323,082 bases
Orientation:
Plus strand

Previous Assembly
chrY:16,634,496-16,957,534
(GRCh37/hg19 by Entrez Gene)
Size:
323,039 bases
Orientation:
Plus strand

chrY:16,634,518-16,957,530
(GRCh37/hg19 by Ensembl)
Size:
323,013 bases
Orientation:
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:
    Q8NFZ3-NLGNY_HUMAN
    Recommended name:
    Neuroligin-4, Y-linked
    Protein Accession:
    Q8NFZ3
    Secondary Accessions:
    • F5H6W0
    • Q14D08
    • Q7Z3T5
    • Q8N5B6
    • Q9Y2F8

    Protein attributes for NLGN4Y Gene

    Size:
    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).
    SequenceCaution:
    • Sequence=BAA76795.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NLGN4Y Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NLGN4Y Gene

Post-translational modifications for NLGN4Y Gene

  • Glycosylation at Asn102 and Asn511
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NLGN4Y Gene

Domains & Families for NLGN4Y Gene

Gene Families for NLGN4Y Gene

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

Protein Domains for NLGN4Y Gene

InterPro:
Blocks:
  • Neuroligin signature

Suggested Antigen Peptide Sequences for NLGN4Y Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ56436, highly similar to Neuroligin-4, Y linked (B4DHI3_HUMAN)
  • Neuroligin-4, Y-linked (NLGNY_HUMAN)
  • NLGN4Y protein (Q8N5B6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NFZ3

UniProtKB/Swiss-Prot:

NLGNY_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 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:0005515 protein binding IPI 17292328
GO:0038023 signaling receptor activity IBA 21873635
GO:0042043 neurexin family protein binding IEA,IBA 21873635
GO:0050839 cell adhesion molecule binding TAS 18923512
GO:0097110 scaffold protein binding IPI 17292328
genes like me logo Genes that share ontologies with NLGN4Y: view
genes like me logo Genes that share phenotypes with NLGN4Y: view

miRNA for NLGN4Y Gene

miRTarBase miRNAs that target NLGN4Y

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN4Y

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 density membrane.

Gene Ontology (GO) - Cellular Components for NLGN4Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,IBA 21873635
GO:0009986 cell surface IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NLGN4Y: view

No data available for Subcellular locations from COMPARTMENTS and 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

Interacting Proteins 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:0007268 chemical synaptic transmission IBA 21873635
GO:0007612 learning IMP 18628683
GO:0035176 social behavior IMP 18628683
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

mRNA/cDNA for NLGN4Y Gene

10 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN4Y

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
SP1:
SP2:
SP3: - - - - - -
SP4:
SP5: - -

Relevant External Links for NLGN4Y Gene

GeneLoc Exon Structure for
NLGN4Y

Expression for NLGN4Y Gene

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



Protein tissue co-expression partners for NLGN4Y Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NLGN4Y

SOURCE GeneReport for Unigene cluster for NLGN4Y Gene:

Hs.439199

mRNA Expression by UniProt/SwissProt for NLGN4Y Gene:

Q8NFZ3-NLGNY_HUMAN
Tissue specificity: Expressed in fetal and adult brain, prostate and testis.
genes like me logo Genes that share expression patterns with NLGN4Y: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from 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
Chimpanzee
(Pan troglodytes)
Mammalia NLGN4Y 29
  • 98.49 (n)
NLGN4X 30
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia -- 30
  • 98 (a)
OneToMany
NLGN4Y 29
  • 84.07 (n)
Oppossum
(Monodelphis domestica)
Mammalia NLGN4 30
  • 94 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 94 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia NLGN4X 29
  • 87.83 (n)
Chicken
(Gallus gallus)
Aves NLGN4 30
  • 92 (a)
OneToMany
NLGN4X 29
  • 80.51 (n)
Lizard
(Anolis carolinensis)
Reptilia NLGN4 30
  • 91 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nlgn4x 29
  • 75.97 (n)
Zebrafish
(Danio rerio)
Actinopterygii nlgn4a 30
  • 80 (a)
ManyToMany
nlgn4b 29 30
  • 70.74 (n)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta neuroligin 29
  • 47.47 (n)
Worm
(Caenorhabditis elegans)
Secernentea nlg-1 29
  • 46.42 (n)
Species where no ortholog for NLGN4Y was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for NLGN4Y (if available)
TreeFam:
Gene Tree for NLGN4Y (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NLGN4Y: view image
Alliance of Genome Resources:
Additional Orthologs for NLGN4Y

Paralogs for NLGN4Y Gene

Paralogs for NLGN4Y Gene

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

  • NLGNY_HUMAN
  • A6NMU8_HUMAN
  • H0Y7G6_HUMAN

Pseudogenes.org Pseudogenes for NLGN4Y Gene

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

Variants for NLGN4Y Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NLGN4Y Gene

SNP ID Clinical significance and condition Chr 0Y pos Variation AA Info Type
rs1057524272 Uncertain Significance: not provided 14,830,121(+) C/A
NM_014893.4(NLGN4Y):c.1203C>A (p.Asn401Lys)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs1556057385 Uncertain Significance: not provided 14,622,379(+) G/A
NM_014893.4(NLGN4Y):c.260G>A (p.Arg87Gln)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
rs35394227 Benign: not provided 14,824,201(+) C/T
NM_014893.4(NLGN4Y):c.639C>T (p.Thr213=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs767683335 Likely Benign: not provided 14,840,785(+) C/T
NM_014893.4(NLGN4Y):c.1974C>T (p.Pro658=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NLGN4Y Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

Additional Variant Information for NLGN4Y Gene

Human Gene Mutation Database (HGMD)
NLGN4Y
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NLGN4Y
Leiden Open Variation Database (LOVD)
NLGN4Y

SNP Genotyping and Copy Number Assays for research

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

Disorders for NLGN4Y Gene

Additional Disease Information for NLGN4Y

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

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 research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. Association of Y chromosome haplotypes with autism. (PMID: 19605777) Serajee FJ … Mahbubul Huq AH (Journal of child neurology 2009) 3 40
  3. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J … Sommer SS (Psychiatric genetics 2008) 3 22
  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
  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

Products for NLGN4Y Gene

Sources for NLGN4Y Gene