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Aliases for NLGN4X Gene

Aliases for NLGN4X Gene

  • Neuroligin 4, X-Linked 2 3 5
  • NLGN4 3 4
  • Neuroligin-4, X-Linked 3
  • Neuroligin 4 2
  • Neuroligin X 4
  • KIAA1260 4
  • ASPGX2 3
  • AUTSX2 3
  • HNL4X 3
  • HLNX 3
  • HNLX 4

External Ids for NLGN4X Gene

Previous HGNC Symbols for NLGN4X Gene

  • NLGN4

Previous GeneCards Identifiers for NLGN4X Gene

  • GC0XM005271
  • GC0XM005667
  • GC0XM005818
  • GC0XM003686
  • GC0XM005758

Summaries for NLGN4X Gene

Entrez Gene Summary for NLGN4X Gene

  • This gene encodes a member of the type-B carboxylesterase/lipase protein family. The encoded protein belongs to 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. The encoded protein interacts with discs large homolog 4 (DLG4). Mutations in this gene have been associated with autism and Asperger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

GeneCards Summary for NLGN4X Gene

NLGN4X (Neuroligin 4, X-Linked) is a Protein Coding gene. Diseases associated with NLGN4X include Autism Susceptibility, X-Linked 2 and Asperger Syndrome Susceptibility, X-Linked 2. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. GO annotations related to this gene include protein homodimerization activity and receptor activity. An important paralog of this gene is NLGN4Y.

UniProtKB/Swiss-Prot for NLGN4X Gene

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

Gene Wiki entry for NLGN4X Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN4X Gene

Genomics for NLGN4X Gene

Regulatory Elements for NLGN4X Gene

Enhancers for NLGN4X Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF006026 0.8 ENCODE 15.8 +202.1 202122 1.4 NLGN4X PIR41321 ENSG00000252291 GC0XM006061
GH0XF005242 0.5 ENCODE 4.6 +986.3 986273 1.0 NLGN4X LOC347381 MTCYBP12
GH0XF006219 0.4 FANTOM5 4.4 +9.0 8988 0.3 ZNF366 NLGN4X LOC105373156 GC0XM006143
GH0XF006692 0.6 ENCODE 4.2 -465.1 -465053 2.4 NLGN4X PIR56538 ENSG00000231217
GH0XF006225 0.4 ENCODE 0.8 +2.3 2278 2.4 CTCF SUZ12 EZH2 NLGN4X LOC105373156
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around NLGN4X on UCSC Golden Path with GeneCards custom track

Promoters for NLGN4X Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000475001 1881 4399 CTCF SUZ12 POLR2A EZH2

Genomic Location for NLGN4X Gene

5,840,637 bp from pter
6,228,882 bp from pter
388,246 bases
Minus strand

Genomic View for NLGN4X Gene

Genes around NLGN4X on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN4X Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN4X Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN4X Gene

Proteins for NLGN4X Gene

  • Protein details for NLGN4X Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuroligin-4, X-linked
    Protein Accession:
    Secondary Accessions:
    • Q6UX10
    • Q9ULG0

    Protein attributes for NLGN4X Gene

    816 amino acids
    Molecular mass:
    91915 Da
    Quaternary structure:
    • Homodimer. Interacts with NRXN1 in a calcium-dependent manner. Interacts through its C-terminus with DLG4/PSD-95 third PDZ domain.
    • Sequence=BAA86574.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NLGN4X Gene

    Alternative splice isoforms for NLGN4X Gene


neXtProt entry for NLGN4X Gene

Post-translational modifications for NLGN4X Gene

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

No data available for DME Specific Peptides for NLGN4X Gene

Domains & Families for NLGN4X Gene

Protein Domains for NLGN4X Gene

Suggested Antigen Peptide Sequences for NLGN4X Gene

GenScript: Design optimal peptide antigens:

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 NLGN4X: view

No data available for Gene Families for NLGN4X Gene

Function for NLGN4X Gene

Molecular function for NLGN4X Gene

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

Gene Ontology (GO) - Molecular Function for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IBA --
GO:0005515 protein binding IPI 11368788
GO:0031404 chloride ion binding IDA 18093521
GO:0042043 neurexin family protein binding IEA,IPI 18093521
GO:0042803 protein homodimerization activity IDA 18093521
genes like me logo Genes that share ontologies with NLGN4X: view
genes like me logo Genes that share phenotypes with NLGN4X: view

Human Phenotype Ontology for NLGN4X Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for NLGN4X Gene

miRTarBase miRNAs that target NLGN4X

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NLGN4X Gene

Localization for NLGN4X Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN4X Gene

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

Subcellular locations from

Jensen Localization Image for NLGN4X Gene COMPARTMENTS Subcellular localization image for NLGN4X gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 NOT extracellular space IBA --
GO:0005886 plasma membrane IDA 19726642
GO:0005887 integral component of plasma membrane IEA,IDA 11368788
GO:0009986 cell surface IDA 15150161
GO:0014069 postsynaptic density IEA --
genes like me logo Genes that share ontologies with NLGN4X: view

Pathways & Interactions for NLGN4X Gene

genes like me logo Genes that share pathways with NLGN4X: view

Pathways by source for NLGN4X Gene

Interacting Proteins for NLGN4X Gene

Gene Ontology (GO) - Biological Process for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003360 brainstem development ISS 18227507
GO:0007155 cell adhesion IEA --
GO:0007158 neuron cell-cell adhesion TAS 18923512
GO:0007612 learning IMP 12669065
GO:0021549 cerebellum development ISS 18227507
genes like me logo Genes that share ontologies with NLGN4X: view

No data available for SIGNOR curated interactions for NLGN4X Gene

Transcripts for NLGN4X Gene

mRNA/cDNA for NLGN4X Gene

(14) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NLGN4X Gene

Neuroligin 4, X-linked:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN4X Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10
SP2: - - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - -
SP7: - - -
SP8: -

Relevant External Links for NLGN4X Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NLGN4X Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NLGN4X Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NLGN4X Gene

This gene is overexpressed in Frontal cortex (37.1), Brain (13.5), Retina (11.7), and Testis (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NLGN4X Gene

Protein tissue co-expression partners for NLGN4X Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NLGN4X Gene:


SOURCE GeneReport for Unigene cluster for NLGN4X Gene:


mRNA Expression by UniProt/SwissProt for NLGN4X Gene:

Tissue specificity: Expressed at highest levels in heart. Expressed at lower levels in liver, skeletal muscle and pancreas and at very low levels in brain.
genes like me logo Genes that share expression patterns with NLGN4X: view

Primer Products

No data available for mRNA differential expression in normal tissues for NLGN4X Gene

Orthologs for NLGN4X Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NLGN4X Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NLGN4X 34 35
  • 99.47 (n)
(Bos Taurus)
Mammalia -- 35
  • 99 (a)
(Monodelphis domestica)
Mammalia NLGN4 35
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 95 (a)
(Gallus gallus)
Aves NLGN4 35
  • 94 (a)
(Anolis carolinensis)
Reptilia NLGN4 35
  • 93 (a)
(Danio rerio)
Actinopterygii nlgn4b 35
  • 78 (a)
nlgn4a 34 35
  • 74.03 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02679 34
  • 44.37 (n)
Species where no ortholog for NLGN4X 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NLGN4X Gene

Gene Tree for NLGN4X (if available)
Gene Tree for NLGN4X (if available)

Paralogs for NLGN4X Gene

Paralogs for NLGN4X Gene

(9) SIMAP similar genes for NLGN4X Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NLGN4X: view

Variants for NLGN4X Gene

Sequence variations from dbSNP and Humsavar for NLGN4X Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs749477993 A colorectal cancer sample 5,909,225(+) GTCAC(C/T)GGTAC reference, missense
rs149512448 Uncertain significance 5,903,373(+) CGCCG(C/T)GTCTC reference, synonymous-codon
rs182247389 Uncertain significance 6,029,389(+) CCATG(A/G)ATATA reference, synonymous-codon
rs201534650 Uncertain significance 6,151,352(+) GTCAA(C/T)GAGGG reference, missense
rs369373885 Uncertain significance 5,903,719(+) TCTTG(C/T)TCCGC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NLGN4X Gene

Variant ID Type Subtype PubMed ID
dgv2198e212 CNV loss 25503493
dgv2199e212 CNV loss 25503493
dgv2200e212 CNV loss 25503493
esv1398053 CNV deletion 17803354
esv2662877 CNV deletion 23128226
esv33664 CNV gain+loss 17666407
esv3448330 OTHER inversion 20981092
esv3558582 CNV deletion 23714750
esv3573474 CNV loss 25503493
esv3573482 CNV loss 25503493
esv3573483 CNV loss 25503493
esv3576723 CNV gain 25503493
esv3576724 CNV gain 25503493
esv3576725 CNV gain 25503493
esv8448 OTHER inversion 19470904
esv988822 CNV gain 20482838
nsv1068324 OTHER inversion 25765185
nsv1075307 CNV deletion 25765185
nsv1077217 CNV deletion 25765185
nsv1142042 OTHER inversion 24896259
nsv507943 OTHER sequence alteration 20534489
nsv510523 OTHER sequence alteration 20534489
nsv513718 OTHER inversion 21212237
nsv513719 OTHER inversion 21212237
nsv520621 CNV gain 19592680
nsv522938 CNV gain 19592680
nsv526949 CNV gain 19592680
nsv528749 CNV gain 19592680

Variation tolerance for NLGN4X Gene

Residual Variation Intolerance Score: 3.85% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.70; 57.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NLGN4X 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 NLGN4X Gene

Disorders for NLGN4X Gene

MalaCards: The human disease database

(10) MalaCards diseases for NLGN4X Gene - From: OMIM, ClinVar, GeneTests, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
autism susceptibility, x-linked 2
  • mental retardation, x-linked
asperger syndrome susceptibility, x-linked 2
  • asperger syndrome, x-linked, 2
non-syndromic x-linked intellectual disability
  • mrx
nlgn4-related x-linked mental retardation
autism spectrum disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards


  • Asperger syndrome, X-linked, 2 (ASPGX2) [MIM:300497]: 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:14963808}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Autism, X-linked 2 (AUTSX2) [MIM:300495]: 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. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for NLGN4X

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with NLGN4X: view

No data available for Genatlas for NLGN4X Gene

Publications for NLGN4X Gene

  1. Positive association of neuroligin-4 gene with nonspecific mental retardation in the Qinba Mountains Region of China. (PMID: 19125102) Qi H. … Zhang F. (Psychiatr. Genet. 2009) 3 22 46 64
  2. A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population. (PMID: 19645625) Pampanos A. … Kitsiou-Tzeli S. (Genet Test Mol Biomarkers 2009) 3 22 46 64
  3. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J. … Sommer S.S. (Psychiatr. Genet. 2008) 3 22 46 64
  4. X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family. (PMID: 14963808) Laumonnier F. … Briault S. (Am. J. Hum. Genet. 2004) 3 4 22 64
  5. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. (PMID: 12669065) Jamain S. … Van Maldergem L. (Nat. Genet. 2003) 3 4 22 64

Products for NLGN4X Gene

Sources for NLGN4X Gene

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