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Aliases for NLGN4X Gene

Aliases for NLGN4X Gene

  • Neuroligin 4 X-Linked 2 3 5
  • Neuroligin-4, X-Linked 3 4
  • NLGN4 3 4
  • Neuroligin X 4
  • Neuroligin 4 2
  • 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 X-Linked 2 and Asperger Syndrome, X-Linked 2. Among its related pathways are Transmission across Chemical Synapses and Protein-protein interactions at synapses. Gene Ontology (GO) annotations related to this gene include protein homodimerization 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

Additional gene information for NLGN4X Gene

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

Genomics for NLGN4X Gene

GeneHancer (GH) Regulatory Elements for NLGN4X Gene

Promoters and enhancers for NLGN4X 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
GH0XJ006225 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 600.7 +2.0 1977 5 POLR2A CTCF NLGN4X LOC105373156
GH0XJ006021 Enhancer 0.7 Ensembl ENCODE 13.5 +206.5 206544 2.1 CTCF RAD21 TRIM22 ZNF143 NLGN4X PIR41321 GC0XM006061 ENSG00000252291
GH0XJ006026 Enhancer 0.4 Ensembl ENCODE 15.8 +201.9 201881 2.8 NLGN4X PIR41321 GC0XM006061 ENSG00000252291
GH0XJ006184 Enhancer 0.6 Ensembl 9.5 +43.7 43666 0.8 SP1 RXRA DPF2 JUND YY1 IKZF1 IRF4 BATF HNF4A MAX NLGN4X GC0XM006143 LOC105373156
GH0XJ006095 Enhancer 0.5 Ensembl ENCODE 9.5 +133.2 133181 2.6 CTCF NLGN4X GC0XM006061 ENSG00000252291 GC0XM006143
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NLGN4X on UCSC Golden Path with GeneCards custom track

Genomic Locations for NLGN4X Gene

Genomic Locations for NLGN4X Gene
388,246 bases
Minus strand
388,227 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 posLast=102102 and isoforms=2511
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NLGN4X Gene

Domains & Families for NLGN4X Gene

Gene Families for NLGN4X Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

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

Function for NLGN4X Gene

Molecular function for NLGN4X Gene

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

Phenotypes From GWAS Catalog for NLGN4X Gene

Gene Ontology (GO) - Molecular Function for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11368788
GO:0031404 chloride ion binding IDA 18093521
GO:0038023 signaling receptor activity IBA 21873635
GO:0042043 neurexin family protein binding IPI,IBA 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

CRISPR Products

miRNA for NLGN4X Gene

miRTarBase miRNAs that target NLGN4X

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN4X

Clone Products

  • Applied Biological Materials (abm): Clones for NLGN4X - Now 50% OFF >
  • * NLGN4X as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NLGN4X tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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

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 NLGN4X gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for NLGN4X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IDA --
GO:0005887 integral component of plasma membrane IDA,IBA 11368788
GO:0009986 cell surface IDA,IBA 15150161
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with NLGN4X: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NLGN4X Gene

Pathways & Interactions for NLGN4X Gene

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

Pathways by source 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,IBA 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

Drugs & Compounds for NLGN4X Gene

No Compound Related Data Available

Transcripts for NLGN4X Gene

mRNA/cDNA for NLGN4X Gene

(4) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Unigene Clusters for NLGN4X Gene

Neuroligin 4, X-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NLGN4X

Clone Products

  • Applied Biological Materials (abm): Clones for NLGN4X - Now 50% OFF >
  • * NLGN4X as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NLGN4X tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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 CGAP 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 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.

Evidence on tissue expression from TISSUES for NLGN4X Gene

  • Nervous system(4.8)
  • Lung(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NLGN4X Gene

Germ Layers:
  • ectoderm
  • nervous
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with NLGN4X: view

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 34
  • 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 35 34
  • 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)
Evolutionary constrained regions (ECRs) for NLGN4X: view image

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 Variation AA Info Type
rs1226379186 uncertain-significance, Inborn genetic diseases 5,893,389(-) G/A coding_sequence_variant, stop_gained
rs1412018300 uncertain-significance, Inborn genetic diseases 5,903,624(-) C/T coding_sequence_variant, missense_variant
rs1555913640 pathogenic, Inborn genetic diseases 5,893,521(-) G/A coding_sequence_variant, missense_variant
rs398124365 uncertain-significance, not specified, not provided 6,151,419(-) C/T coding_sequence_variant, synonymous_variant
rs746531523 uncertain-significance, Inborn genetic diseases 5,892,944(-) G/A coding_sequence_variant, missense_variant

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)

Additional Variant Information for NLGN4X Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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: HGMD, OMIM, ClinVar, GTR, DISEASES, Novoseek, and GeneCards

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


  • 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.
  • 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.

Additional Disease Information for NLGN4X

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 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 (Psychiatric genetics 2009) 3 23 45 58
  2. A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population. (PMID: 19645625) Pampanos A … Kitsiou-Tzeli S (Genetic testing and molecular biomarkers 2009) 3 23 45 58
  3. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J … Sommer SS (Psychiatric genetics 2008) 3 23 45 58
  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 (American journal of human genetics 2004) 3 4 23 58
  5. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. (PMID: 12669065) Jamain S … Paris Autism Research International Sibpair Study (Nature genetics 2003) 3 4 23 58

Products for NLGN4X Gene

Sources for NLGN4X Gene

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