Format

Send to:

Choose Destination

NLGN1 neuroligin 1 [ Homo sapiens (human) ]

Gene ID: 22871, updated on 8-Jul-2021

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See NLGN1 in Genome Data Viewer
Location:
3q26.31
Exon count:
14
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (173395929..174294372)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (173113742..174012162)

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

Associated conditions

Description Tests
Autism, susceptibility to, 20
MedGen: C5394226 OMIM: 618830 GeneReviews: Not available
Compare labs
Genome-wide association study of chronic periodontitis in a general German population.
GeneReviews: Not available
Genome-wide association study of major recurrent depression in the U.K. population.
GeneReviews: Not available

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

Pathways from PubChem

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

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_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:53626
    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:53626
    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 Updated Annotation Release 109.20210514

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:53626
    COesterase; Carboxylesterase family
  2. XM_017005896.1XP_016861385.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:53626
    COesterase; Carboxylesterase family
  3. XM_017005888.1XP_016861377.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:53626
    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:53626
    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:53626
    COesterase; Carboxylesterase family
  9. XM_017005894.1XP_016861383.1  neuroligin-1 isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:53626
    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
Support Center