NLGN2 neuroligin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NLGN2provided by HGNC
Official Full Name: neuroligin 2provided by HGNC
Primary source: HGNC:HGNC:14290
See related: Ensembl:ENSG00000169992 MIM:606479; AllianceGenome:HGNC:14290
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
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. [provided by RefSeq, Jul 2008]
Expression: Broad expression in brain (RPKM 29.8), endometrium (RPKM 15.7) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7404653..7419860)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (7308683..7323908)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (7311164..7323179)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression and structural analysis of human neuroligin 2 and neuroligin 3 implicated in autism spectrum disorders.
Title: Expression and structural analysis of human neuroligin 2 and neuroligin 3 implicated in autism spectrum disorders.
Neuroligin-2 as a central organizer of inhibitory synapses in health and disease.
Title: Neuroligin-2 as a central organizer of inhibitory synapses in health and disease.
Neuroligin-2 dependent conformational activation of collybistin reconstituted in supported hybrid membranes.
Title: Neuroligin-2 dependent conformational activation of collybistin reconstituted in supported hybrid membranes.
nucleus accumbens neuroligin-2 has a role in depression and stress susceptibility
Title: Cell-type-specific role for nucleus accumbens neuroligin-2 in depression and stress susceptibility.
e found that NLGN3 function at inhibitory synapses in rat CA1 depends on the presence of NLGN2 and identified a domain in the extracellular region that accounted for this functional difference between NLGN2 and 3 specifically at inhibitory synapses.
Title: Distinct roles for extracellular and intracellular domains in neuroligin function at inhibitory synapses.
This is the first report of an NLGN2 nonsense variant in humans, adding to the accumulating evidence that links synaptic proteins with a spectrum of neurodevelopmental phenotypes.
Title: Neuroligin 2 nonsense variant associated with anxiety, autism, intellectual disability, hyperphagia, and obesity.
MDGAs regulate the formation of neuroligin-neurexin trans-synaptic bridges by sterically blocking access of neurexins to neuroligins.
Title: Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges.
Neuroligin-2 was down-regulated in aganglionic colonic segments from Hirschsprung's disease patients.
Title: The down-regulation of neuroligin-2 and the correlative clinical significance of serum GABA over-expression in Hirschsprung's disease.
Transcellular neuroligin-2 interactions enhance insulin secretion and are integral to pancreatic beta cell function
Title: Transcellular neuroligin-2 interactions enhance insulin secretion and are integral to pancreatic β cell function.
Data identified the R215H mutant as a loss-of-function mutant in inducing GABAergic synaptogenesis. Data also suggests that defects in GABAergic synapse formation in the brain may be an important contributing factor for the onset of schizophrenia.
Title: Identification and functional characterization of rare mutations of the neuroligin-2 gene (NLGN2) associated with schizophrenia.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of NLGN2	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH15991 (e-PCR)
- UniSTS:59425

A005P18 (e-PCR)
- UniSTS:60012

D17S1783 (e-PCR)
- UniSTS:154282

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables neurexin family protein binding	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cell-cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in cell-cell junction maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in gephyrin clustering involved in postsynaptic density assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in inhibitory synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in insulin metabolic process	IEA Inferred from Electronic Annotation more info
involved_in jump response	IEA Inferred from Electronic Annotation more info
involved_in locomotory exploration behavior	IEA Inferred from Electronic Annotation more info
involved_in modulation of chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
involved_in neuron cell-cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in neurotransmitter-gated ion channel clustering	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dendritic spine development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of inhibitory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of protein localization to synapse	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of synaptic transmission, GABAergic	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 positive regulation of synaptic vesicle clustering	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of t-SNARE clustering	IEA Inferred from Electronic Annotation more info
involved_in postsynaptic density protein 95 clustering	ISS Inferred from Sequence or Structural Similarity more info
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	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein localization to synapse	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of AMPA receptor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of presynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of respiratory gaseous exchange by nervous system process	ISS Inferred from Sequence or Structural Similarity more info
involved_in sensory perception of pain	IEA Inferred from Electronic Annotation more info
involved_in social behavior	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in synapse organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic transmission, GABAergic	IEA Inferred from Electronic Annotation more info
involved_in terminal button organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in thigmotaxis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic shaft	IEA Inferred from Electronic Annotation more info
located_in dopaminergic synapse	IEA Inferred from Electronic Annotation more info
located_in excitatory synapse	IEA Inferred from Electronic Annotation more info
located_in glycinergic synapse	IEA Inferred from Electronic Annotation more info
located_in inhibitory synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in postsynaptic specialization membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in ribbon synapse	IEA Inferred from Electronic Annotation more info
located_in symmetric, GABA-ergic, inhibitory synapse	TAS Traceable Author Statement more info	PubMed
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: neuroligin-2

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.

mRNA and Protein(s)

NM_020795.4 → NP_065846.1 neuroligin-2 precursor

See identical proteins and their annotated locations for NP_065846.1

Status: REVIEWED

Source sequence(s)

AA447769, AC113189, AF376802, AI613237, BM800364, DR763679, EL949788

Consensus CDS

CCDS11103.1

UniProtKB/Swiss-Prot

Q8NFZ4, Q9P2I1

Related

ENSP00000305288.2, ENST00000302926.7

Conserved Domains (2) summary

COG0657
Location:170 → 268

Aes; Acetyl esterase/lipase [Lipid transport and metabolism]

pfam00135
Location:41 → 601

COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

7404653..7419860

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047436464.1 → XP_047292420.1 neuroligin-2 isoform X1

UniProtKB/Swiss-Prot

Q8NFZ4, Q9P2I1
XM_047436463.1 → XP_047292419.1 neuroligin-2 isoform X1

UniProtKB/Swiss-Prot

Q8NFZ4, Q9P2I1
XM_047436465.1 → XP_047292421.1 neuroligin-2 isoform X2
XM_047436462.1 → XP_047292418.1 neuroligin-2 isoform X1

UniProtKB/Swiss-Prot

Q8NFZ4, Q9P2I1

Related

ENSP00000461168.1, ENST00000575301.5
XM_017024897.2 → XP_016880386.1 neuroligin-2 isoform X3

Conserved Domains (2) summary

COG0657
Location:1 → 89

Aes; Acetyl esterase/lipase [Lipid transport and metabolism]

pfam00135
Location:1 → 422

COesterase; Carboxylesterase family