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NLGN1 neuroligin 1 [ Homo sapiens (human) ]

Gene ID: 22871, updated on 11-Sep-2019

Summary

Official Symbol
NLGN1provided by HGNC
Official Full Name
neuroligin 1provided by HGNC
Primary source
HGNC:HGNC:14291
See related
Ensembl:ENSG00000169760 MIM:600568
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
NL1
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
Biased expression in brain (RPKM 1.7), testis (RPKM 0.4) and 11 other tissues See more
Orthologs

Genomic context

See NLGN1 in Genome Data Viewer
Location:
3q26.31
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (173395929..174294372)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (173115570..174004434)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 16 Neighboring gene uncharacterized LOC105374220 Neighboring gene uncharacterized LOC105374224 Neighboring gene transmembrane protein 229B-like Neighboring gene uncharacterized LOC105374225 Neighboring gene NLGN1 antisense RNA 1 Neighboring gene RN7SK pseudogene 234 Neighboring gene uncharacterized LOC105374226 Neighboring gene N-acetylated alpha-linked acidic dipeptidase like 2 Neighboring gene ribosomal protein L8 pseudogene 4

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2016-03-25)

ClinGen Genome Curation Page
Haploinsufficency

No evidence available (Last evaluated (2016-03-25)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Genome-wide association study of chronic periodontitis in a general German population.
NHGRI GWA Catalog
Genome-wide association study of major recurrent depression in the U.K. population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Interactions of neurexins and neuroligins at synapses, organism-specific biosystem (from REACTOME)
    Interactions of neurexins and neuroligins at synapses, organism-specific biosystemNeurexins (NRXNs) and neuroligins (NLGNs) are best characterized synaptic cell-adhesion molecules. They are part of excitatory glutamatergic and inhibitory GABAergic synapses in mammalian brain, medi...
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Protein-protein interactions at synapses, organism-specific biosystem (from REACTOME)
    Protein-protein interactions at synapses, organism-specific biosystemSynapses constitute highly specialized sites of asymmetric cell-cell adhesion and intercellular communication. Its formation involves the recruitment of presynaptic and postsynaptic molecules at newl...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1070, MGC45115

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding IDA
Inferred from Direct Assay
more info
PubMed 
amyloid-beta binding NAS
Non-traceable Author Statement
more info
PubMed 
cell adhesion molecule binding ISS
Inferred from Sequence or Structural Similarity
more info
 
neurexin family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neurexin family protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
neurexin family protein binding NAS
Non-traceable Author Statement
more info
PubMed 
protein dimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
scaffold protein binding IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signaling receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
AMPA glutamate receptor clustering ISS
Inferred from Sequence or Structural Similarity
more info
 
NMDA glutamate receptor clustering ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeletal matrix organization at active zone ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of protein localization ISS
Inferred from Sequence or Structural Similarity
more info
 
excitatory synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
 
modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
modulation of chemical synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of dendritic spine morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
 
neurexin clustering involved in presynaptic membrane assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron cell-cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron cell-cell adhesion NAS
Non-traceable Author Statement
more info
PubMed 
neuron cell-cell adhesion TAS
Traceable Author Statement
more info
PubMed 
neuron projection arborization ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection development IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
neuronal signal transduction TAS
Traceable Author Statement
more info
PubMed 
positive regulation of circadian sleep/wake cycle, wakefulness ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendritic spine development IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of dendritic spine development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of excitatory postsynaptic potential IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of filopodium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of intracellular signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of presynaptic active zone assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein localization to synapse IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ruffle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of synapse assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of synaptic transmission, GABAergic ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of synaptic vesicle clustering IEA
Inferred from Electronic Annotation
more info
 
positive regulation of synaptic vesicle endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of synaptic vesicle exocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density protein 95 clustering ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic membrane assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic specialization assembly IEA
Inferred from Electronic Annotation
more info
 
presynapse assembly TAS
Traceable Author Statement
more info
PubMed 
presynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynaptic membrane assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
protein heterotetramerization IEA
Inferred from Electronic Annotation
more info
 
protein homooligomerization ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
protein targeting ISS
Inferred from Sequence or Structural Similarity
more info
 
receptor localization to synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of AMPA receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of NMDA receptor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of NMDA receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of respiratory gaseous exchange by neurological system process IEA
Inferred from Electronic Annotation
more info
 
retrograde trans-synaptic signaling by trans-synaptic protein complex IEA
Inferred from Electronic Annotation
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle clustering ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptic vesicle targeting ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle transport IEA
Inferred from Electronic Annotation
more info
 
terminal button organization ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
NMDA selective glutamate receptor complex IEA
Inferred from Electronic Annotation
more info
 
asymmetric, glutamatergic, excitatory synapse TAS
Traceable Author Statement
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell surface ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic shaft IEA
Inferred from Electronic Annotation
more info
 
dendritic spine ISS
Inferred from Sequence or Structural Similarity
more info
 
excitatory synapse NAS
Non-traceable Author Statement
more info
PubMed 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
filopodium tip ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of postsynaptic membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of postsynaptic specialization membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynapse NAS
Non-traceable Author Statement
more info
PubMed 
colocalizes_with postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density TAS
Traceable Author Statement
more info
PubMed 
presynapse IEA
Inferred from Electronic Annotation
more info
 
spanning component of membrane TAS
Traceable Author Statement
more info
PubMed 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

NCBI Reference Sequences (RefSeq)

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_046919.2 RefSeqGene

    Range
    6846..903474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001365923.2NP_001352852.1  neuroligin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  2. NM_001365924.2NP_001352853.1  neuroligin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  3. NM_001365925.2NP_001352854.1  neuroligin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  4. NM_001365926.2NP_001352855.1  neuroligin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  5. NM_001365927.2NP_001352856.1  neuroligin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  6. NM_001365928.2NP_001352857.1  neuroligin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  7. NM_001365929.2NP_001352858.1  neuroligin-1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  8. NM_001365930.2NP_001352859.1  neuroligin-1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  9. NM_001365931.2NP_001352860.1  neuroligin-1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  10. NM_001365932.2NP_001352861.1  neuroligin-1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  11. NM_001365933.2NP_001352862.1  neuroligin-1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC092923, AC092967
    Related
    ENSP00000354541.4, ENST00000361589.8
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  12. NM_001365934.2NP_001352863.1  neuroligin-1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52597
    COesterase; Carboxylesterase family
  13. NM_001365935.2NP_001352864.1  neuroligin-1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52597
    COesterase; Carboxylesterase family
  14. NM_001365936.2NP_001352865.1  neuroligin-1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, AC092923, AC092967
    Conserved Domains (1) summary
    pfam00135
    Location:52597
    COesterase; Carboxylesterase family
  15. NM_014932.5NP_055747.1  neuroligin-1 isoform 3

    See identical proteins and their annotated locations for NP_055747.1

    Status: REVIEWED

    Source sequence(s)
    AC008120, AC018456, BC032555, DA310134
    Consensus CDS
    CCDS3222.1
    UniProtKB/Swiss-Prot
    Q8N2Q7
    Related
    ENSP00000392500.1, ENST00000457714.5
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    173395929..174294372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005893.1XP_016861382.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  2. XM_017005896.1XP_016861385.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  3. XM_017005888.1XP_016861377.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  4. XM_017005897.1XP_016861386.1  neuroligin-1 isoform X3

    Conserved Domains (2) summary
    COG0657
    Location:159284
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:50617
    COesterase; Carboxylesterase family
  5. XM_011512551.2XP_011510853.1  neuroligin-1 isoform X1

    See identical proteins and their annotated locations for XP_011510853.1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  6. XM_017005902.1XP_016861391.1  neuroligin-1 isoform X5

    Conserved Domains (1) summary
    pfam00135
    Location:52597
    COesterase; Carboxylesterase family
  7. XM_017005900.1XP_016861389.1  neuroligin-1 isoform X4

    UniProtKB/Swiss-Prot
    Q8N2Q7
    Conserved Domains (1) summary
    pfam00135
    Location:52606
    COesterase; Carboxylesterase family
  8. XM_017005895.2XP_016861384.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  9. XM_017005894.1XP_016861383.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:52626
    COesterase; Carboxylesterase family
  10. XM_005247237.3XP_005247294.1  neuroligin-1 isoform X6

    Conserved Domains (2) summary
    COG0657
    Location:14112
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:16454
    COesterase; Carboxylesterase family
  11. XM_011512553.2XP_011510855.1  neuroligin-1 isoform X7

    See identical proteins and their annotated locations for XP_011510855.1

    Conserved Domains (1) summary
    cl21494
    Location:2292
    Abhydrolase; alpha/beta hydrolases
  12. XM_011512554.2XP_011510856.1  neuroligin-1 isoform X7

    See identical proteins and their annotated locations for XP_011510856.1

    Conserved Domains (1) summary
    cl21494
    Location:2292
    Abhydrolase; alpha/beta hydrolases
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