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NLGN4X neuroligin 4 X-linked [ Homo sapiens (human) ]

Gene ID: 57502, updated on 11-Apr-2024

Summary

Official Symbol
NLGN4Xprovided by HGNC
Official Full Name
neuroligin 4 X-linkedprovided by HGNC
Primary source
HGNC:HGNC:14287
See related
Ensembl:ENSG00000146938 MIM:300427; AllianceGenome:HGNC:14287
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HLNX; HNL4X; NLGN4; ASPGX2; AUTSX2
Summary
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]
Expression
Broad expression in brain (RPKM 6.8), ovary (RPKM 4.3) and 19 other tissues See more
Orthologs
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Genomic context

See NLGN4X in Genome Data Viewer
Location:
Xp22.32-p22.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (5890042..6228867, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (5442298..5781161, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (5808083..6146908, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:5398809-5399309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29380 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:5566951-5567836 Neighboring gene long intergenic non-protein coding RNA 3070 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:5945089-5945662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:6119195-6119695 Neighboring gene uncharacterized LOC105373156 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:6194636-6195374 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:6197302-6198185 Neighboring gene microRNA 4770 Neighboring gene RPS5 pseudogene 8

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autism, susceptibility to, X-linked 2
MedGen: C1845539 OMIM: 300495 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1260, MGC22376

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding TAS
Traceable Author Statement
more info
PubMed 
enables chloride ion binding IDA
Inferred from Direct Assay
more info
PubMed 
enables neurexin family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables neurexin family protein binding IDA
Inferred from Direct Assay
more info
PubMed 
enables neurexin family protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
enables scaffold protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in adult behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in brainstem development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in cell-cell junction organization NAS
Non-traceable Author Statement
more info
PubMed 
involved_in cerebellum development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in learning IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of excitatory postsynaptic potential IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neuron cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in neuron cell-cell adhesion TAS
Traceable Author Statement
more info
PubMed 
involved_in neuron differentiation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in organ growth ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in postsynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in presynapse assembly TAS
Traceable Author Statement
more info
PubMed 
involved_in presynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in presynaptic membrane assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in social behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synapse organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synapse organization NAS
Non-traceable Author Statement
more info
PubMed 
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in vocalization behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in vocalization behavior ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
located_in asymmetric, glutamatergic, excitatory synapse TAS
Traceable Author Statement
more info
PubMed 
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in dendrite IDA
Inferred from Direct Assay
more info
PubMed 
located_in excitatory synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
 
located_in symmetric, GABA-ergic, inhibitory synapse TAS
Traceable Author Statement
more info
PubMed 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008881.2 RefSeqGene

    Range
    5016..343841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282145.2NP_001269074.1  neuroligin-4, X-linked

    See identical proteins and their annotated locations for NP_001269074.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript. Variants 1, 2, 3, and 4 encode the same protein.
    Source sequence(s)
    AC078989, AC079173, AK055471, CN357526
    Consensus CDS
    CCDS14126.1
    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000370482.1, ENST00000381092.1
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  2. NM_001282146.2NP_001269075.1  neuroligin-4, X-linked

    See identical proteins and their annotated locations for NP_001269075.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 3. Variants 1, 2, 3, and 4 encode the same protein.
    Source sequence(s)
    AB033086, AC078989, AK291036, DA724500
    Consensus CDS
    CCDS14126.1
    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000370483.3, ENST00000381093.6
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  3. NM_020742.4NP_065793.1  neuroligin-4, X-linked

    See identical proteins and their annotated locations for NP_065793.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 3. Variants 1, 2, 3, and 4 encode the same protein.
    Source sequence(s)
    AB033086, AC078989, AC112654
    Consensus CDS
    CCDS14126.1
    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000275857.6, ENST00000275857.10
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  4. NM_181332.3NP_851849.1  neuroligin-4, X-linked

    See identical proteins and their annotated locations for NP_851849.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 3. Variants 1, 2, 3, and 4 encode the same protein.
    Source sequence(s)
    AB033086, AC078989, CN357526
    Consensus CDS
    CCDS14126.1
    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000370485.3, ENST00000381095.8
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    5890042..6228867 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274564.4XP_005274621.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_005274621.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family
  2. XM_011545548.3XP_011543850.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_011543850.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family
  3. XM_047442281.1XP_047298237.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  4. XM_005274565.3XP_005274622.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_005274622.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family
  5. XM_017029691.2XP_016885180.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  6. XM_011545547.3XP_011543849.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_011543849.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family
  7. XM_017029692.2XP_016885181.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  8. XM_005274566.5XP_005274623.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_005274623.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000439203.3, ENST00000538097.6
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family
  9. XM_017029693.2XP_016885182.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:46590
    COesterase; Carboxylesterase family
  10. XM_047442282.1XP_047298238.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  11. XM_006724504.3XP_006724567.1  neuroligin-4, X-linked isoform X1

    See identical proteins and their annotated locations for XP_006724567.1

    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (2) summary
    COG0657
    Location:179286
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:42610
    COesterase; Carboxylesterase family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    5442298..5781161 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327444.1XP_054183419.1  neuroligin-4, X-linked isoform X1

  2. XM_054327449.1XP_054183424.1  neuroligin-4, X-linked isoform X1

  3. XM_054327453.1XP_054183428.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  4. XM_054327451.1XP_054183426.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  5. XM_054327450.1XP_054183425.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  6. XM_054327446.1XP_054183421.1  neuroligin-4, X-linked isoform X1

  7. XM_054327445.1XP_054183420.1  neuroligin-4, X-linked isoform X1

  8. XM_054327448.1XP_054183423.1  neuroligin-4, X-linked isoform X1

  9. XM_054327452.1XP_054183427.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  10. XM_054327454.1XP_054183429.1  neuroligin-4, X-linked isoform X2

    UniProtKB/Swiss-Prot
    Q6UX10, Q8N0W4, Q9ULG0
  11. XM_054327447.1XP_054183422.1  neuroligin-4, X-linked isoform X1