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NLGN3 neuroligin 3 [ Homo sapiens (human) ]

Gene ID: 54413, updated on 12-Aug-2022

Summary

Official Symbol
NLGN3provided by HGNC
Official Full Name
neuroligin 3provided by HGNC
Primary source
HGNC:HGNC:14289
See related
Ensembl:ENSG00000196338 MIM:300336; AllianceGenome:HGNC:14289
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
HNL3
Summary
This gene encodes a member of 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. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]
Expression
Biased expression in brain (RPKM 14.8), adrenal (RPKM 2.6) and 4 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See NLGN3 in Genome Data Viewer
Location:
Xq13.1
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71144841..71175307)
110 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69578926..69605291)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (70364691..70391051)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene interleukin 2 receptor subunit gamma Neighboring gene mediator complex subunit 12 Neighboring gene uncharacterized LOC124905197 Neighboring gene Sharpr-MPRA regulatory region 11812 Neighboring gene uncharacterized LOC107985688

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
Asperger syndrome, X-linked, susceptibility to, 1
MedGen: C1845341 OMIM: 300494 GeneReviews: Not available
Compare labs
Autism, susceptibility to, X-linked 1
MedGen: C1845540 OMIM: 300425 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-07-25)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2012-07-25)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of neuroligin 3 (NLGN3) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1480

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables molecular adaptor activity EXP
Inferred from Experiment
more info
PubMed 
enables molecular adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables neurexin family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables neurexin family protein binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
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
PubMed 
enables signaling receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in adult behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in axon extension ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inhibitory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
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
PubMed 
involved_in modulation of chemical synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neuron cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neuron cell-cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of AMPA receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in postsynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in postsynaptic membrane assembly ISS
Inferred from Sequence or Structural Similarity
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
PubMed 
involved_in presynaptic membrane assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in receptor-mediated endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of respiratory gaseous exchange by nervous system process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in rhythmic synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in social behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in synapse organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in vocalization behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in endocytic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in excitatory synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of postsynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in integral component of postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
 
located_in spanning component of membrane TAS
Traceable Author Statement
more info
PubMed 
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
PubMed 
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
neuroligin-3
Names
gliotactin homolog

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_015874.1 RefSeqGene

    Range
    5011..31371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166660.2NP_001160132.1  neuroligin-3 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001160132.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AF217411, BC028738, BC051715, BP201014
    Consensus CDS
    CCDS55442.1
    UniProtKB/Swiss-Prot
    Q9NZ94
    UniProtKB/TrEMBL
    Q4G160, X5D7L6
    Related
    ENSP00000445298.1, ENST00000536169.6
    Conserved Domains (1) summary
    pfam00135
    Location:36584
    COesterase; Carboxylesterase family
  2. NM_001321276.2NP_001308205.1  neuroligin-3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes isoform 4, which lacks a predicted signal peptide compared to isoforms 1-3.
    Source sequence(s)
    AF217411, AK296217, BC051715, BX641059
    UniProtKB/Swiss-Prot
    Q9NZ94
    UniProtKB/TrEMBL
    B7Z3P8, Q6MZK0
    Related
    ENSP00000508700.1, ENST00000692338.1
    Conserved Domains (1) summary
    pfam00135
    Location:19487
    COesterase; Carboxylesterase family
  3. NM_018977.4NP_061850.2  neuroligin-3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_061850.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1. Isoform 2 has also been referred to as HNL3L, or the long form.
    Source sequence(s)
    AF217411, BC028738, BC051715, BP201014
    Consensus CDS
    CCDS14407.1
    UniProtKB/Swiss-Prot
    Q9NZ94
    UniProtKB/TrEMBL
    Q4G160, X5D2P6
    Related
    ENSP00000363163.3, ENST00000374051.7
    Conserved Domains (1) summary
    pfam00135
    Location:36604
    COesterase; Carboxylesterase family
  4. NM_181303.2NP_851820.1  neuroligin-3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_851820.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF217411, AF217412, BC051715, BP201014
    Consensus CDS
    CCDS55441.1
    UniProtKB/Swiss-Prot
    Q9NZ94, Q9P248
    UniProtKB/TrEMBL
    X5DNV3
    Related
    ENSP00000351591.4, ENST00000358741.4
    Conserved Domains (1) summary
    pfam00135
    Location:36624
    COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    71144841..71175307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029597.3XP_016885086.1  neuroligin-3 isoform X5

    Related
    ENSP00000510435.1, ENST00000692905.1
    Conserved Domains (1) summary
    pfam00135
    Location:36568
    COesterase; Carboxylesterase family
  2. XM_006724663.5XP_006724726.1  neuroligin-3 isoform X3

    See identical proteins and their annotated locations for XP_006724726.1

    Related
    ENSP00000509531.1, ENST00000687220.1
    Conserved Domains (2) summary
    COG0657
    Location:84191
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:19507
    COesterase; Carboxylesterase family
  3. XM_047442186.1XP_047298142.1  neuroligin-3 isoform X4

    Related
    ENSP00000508912.1, ENST00000690133.1
  4. XM_011530974.4XP_011529276.1  neuroligin-3 isoform X3

    See identical proteins and their annotated locations for XP_011529276.1

    Related
    ENSP00000509202.1, ENST00000688566.1
    Conserved Domains (2) summary
    COG0657
    Location:84191
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:19507
    COesterase; Carboxylesterase family
  5. XM_047442185.1XP_047298141.1  neuroligin-3 isoform X1

    UniProtKB/Swiss-Prot
    Q9P248
    UniProtKB/TrEMBL
    X5DNV3
    Related
    ENST00000476589.2
  6. XM_006724662.5XP_006724725.2  neuroligin-3 isoform X2

    Conserved Domains (1) summary
    cl21494
    Location:89561
    Abhydrolase; alpha/beta hydrolases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    69578926..69605291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)