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Aliases for NLGN4X Gene

Aliases for NLGN4X Gene

  • Neuroligin 4, X-Linked 2 3 5
  • NLGN4 3 4
  • 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 Cell adhesion molecules (CAMs). GO annotations related to this gene include protein homodimerization activity and receptor activity. An important paralog of this gene is CES2.

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 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 NLGN4X on UCSC Golden Path with GeneCards custom track

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

Proteomics data for NLGN4X Gene at MOPED

Post-translational modifications for NLGN4X Gene

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

Other Protein References for NLGN4X Gene

Antibody Products

  • R&D Systems Antibodies for NLGN4X (Neuroligin 4X/NLGN4X)

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:0042043 neurexin family protein binding IEA,IPI 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

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:0030425 dendrite IDA 19726642
GO:0045202 synapse IEA,ISS 18227507
genes like me logo Genes that share ontologies with NLGN4X: view

Pathways & Interactions for NLGN4X Gene

SuperPathways for NLGN4X Gene

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

Pathways by source for NLGN4X Gene

1 KEGG pathway for NLGN4X Gene

Gene Ontology (GO) - Biological Process for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007158 neuron cell-cell adhesion TAS 18923512
GO:0030534 adult behavior IMP 12669065
GO:0035265 organ growth ISS 18227507
GO:0050808 synapse organization IEA,NAS 11368788
GO:0090394 negative regulation of excitatory postsynaptic potential IDA 19726642
genes like me logo Genes that share ontologies with NLGN4X: view

No data available for SIGNOR curated interactions for NLGN4X Gene

Drugs & Compounds for NLGN4X Gene

No Compound Related Data Available

Transcripts for NLGN4X Gene

mRNA/cDNA for NLGN4X Gene

(10) 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:

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 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

SOURCE GeneReport for Unigene cluster for NLGN4X Gene Hs.21107

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

Protein tissue co-expression partners for NLGN4X Gene

- Elite partner

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 35
  • 99.47 (n)
  • 100 (a)
  • 98 (a)
(Bos Taurus)
Mammalia -- 36
  • 99 (a)
(Monodelphis domestica)
Mammalia NLGN4 36
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 95 (a)
(Gallus gallus)
Aves NLGN4 36
  • 94 (a)
(Anolis carolinensis)
Reptilia NLGN4 36
  • 93 (a)
(Danio rerio)
Actinopterygii nlgn4a 35
  • 74.03 (n)
  • 84.44 (a)
nlgn4a 36
  • 81 (a)
nlgn4b 36
  • 78 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU02679 35
  • 44.37 (n)
  • 31.2 (a)
Species with no ortholog for NLGN4X:
  • 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
VAR_036576 A colorectal cancer sample
rs747673629 -- 5,897,630(+) AACTG(C/G)TTCCC intron-variant
rs747684568 -- 5,957,708(+) AGAAA(C/T)CAACG intron-variant
rs747693241 -- 5,906,134(+) GACTG(C/T)TTTCT intron-variant
rs747693352 -- 6,098,362(+) TTAGG(A/C)AGAAA intron-variant

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

Variant ID Type Subtype PubMed ID
esv988822 CNV Gain 20482838
nsv522938 CNV Gain 19592680
nsv528749 CNV Gain 19592680
nsv526949 CNV Gain 19592680
nsv507943 CNV Insertion 20534489
nsv510523 CNV Loss 20534489
esv2662877 CNV Deletion 23128226
esv1398053 CNV Deletion 17803354
nsv520621 CNV Gain 19592680
nsv513718 OTHER Inversion 21212237
esv8448 OTHER Inversion 19470904
nsv513719 OTHER Inversion 21212237
esv33664 CNV Gain+Loss 17666407

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)

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. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10574462) Nagase T. … Ohara O. (DNA Res. 1999) 2 3 4 67
  2. 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 23
  3. Autism and nonsyndromic mental retardation associated with a de novo mutation in the NLGN4X gene promoter causing an increased expression level. (PMID: 19545860) Daoud H. … Briault S. (Biol. Psychiatry 2009) 3 23
  4. 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 23
  5. No evidence for involvement of genetic variants in the X-linked neuroligin genes NLGN3 and NLGN4X in probands with autism spectrum disorder on high functioning level. (PMID: 18189281) Wermter A.K. … Remschmidt H. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008) 3 23

Products for NLGN4X Gene

Sources for NLGN4X Gene