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Nlgn3 Gene Detail
Summary
  • Symbol
    Nlgn3
  • Name
    neuroligin 3
  • Synonyms
    A230085M13Rik, HNL3, NL3, NLG3
  • Feature Type
    protein coding gene
  • IDs
    MGI:2444609
    NCBI Gene: 245537
  • Alliance
    gene page
  • Transcription Start Sites
    4 TSS
Location &
Maps
more
  • Sequence Map
    ChrX:100342785-100364956 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome X, 43.95 cM
  • Mapping Data
    1 experiment
Strain
Comparison
more
  • SNPs within 2kb
    232 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2444609
 protein coding gene ChrX:100342774-100369569 (+)
129S1/SvImJ MGP_129S1SvImJ_G0035958
 protein coding gene ChrX:97799400-97826197 (+)
A/J MGP_AJ_G0035943
 protein coding gene ChrX:97804199-97830887 (+)
AKR/J MGP_AKRJ_G0035859
 protein coding gene ChrX:100605372-100633337 (+)
BALB/cJ MGP_BALBcJ_G0035926
 protein coding gene ChrX:96543517-96570695 (+)
C3H/HeJ MGP_C3HHeJ_G0035635
 protein coding gene ChrX:98205721-98232590 (+)
C57BL/6NJ MGP_C57BL6NJ_G0036455
 protein coding gene ChrX:100706977-100733788 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0033285
 protein coding gene ChrX:95558327-95586168 (+)
CAST/EiJ MGP_CASTEiJ_G0034922
 protein coding gene ChrX:82509914-82536646 (+)
CBA/J MGP_CBAJ_G0035610
 protein coding gene ChrX:103820767-103847545 (+)
DBA/2J MGP_DBA2J_G0035764
 protein coding gene ChrX:97020917-97047702 (+)
FVB/NJ MGP_FVBNJ_G0035702
 protein coding gene ChrX:96403104-96429713 (+)
LP/J MGP_LPJ_G0035854
 protein coding gene ChrX:98761154-98788142 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0035737
 protein coding gene ChrX:108373328-108401460 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0036482
 protein coding gene ChrX:97493671-97520469 (+)
PWK/PhJ MGP_PWKPhJ_G0034621
 protein coding gene ChrX:80117162-80144014 (+)
SPRET/EiJ MGP_SPRETEiJ_G0034449
 protein coding gene ChrX:83415305-83443347 (+)
WSB/EiJ MGP_WSBEiJ_G0035061
 protein coding gene ChrX:96198608-96225381 (+)



Homology
more
  • Human Ortholog
    NLGN3, neuroligin 3
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    NLGN3, neuroligin 3
  • Synonyms
    HNL3
  • Links
    NCBI Gene ID: 54413
    neXtProt AC: NX_Q9NZ94
    UniProt: Q9NZ94

  • Chr Location
    Xq13.1; chrX:71144821-71175307 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Nlgn3 mouse models; 1 with human NLGN3 associations

Human Disease Mouse Models
      
IDs
 View 5 models
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    4 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    44 phenotypes from 8 alleles in 12 genetic backgrounds
    16 phenotypes from multigenic genotypes
    75 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Homozygous null mice show impaired context and cued conditioning, hyperactivity, altered social behavior, less vocalization, smaller brains, and impaired olfaction. Males carrying a knock-in allele show impaired social interaction, and enhanced spatial learning and inhibitory synaptic transmission.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    91
  • GO References
    11
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    764
  • Tissues
    37
  • cDNA Data
    30
  • Literature Summary
    12
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 245537 NCBI Gene Model | MGI Sequence Detail 22172 C57BL/6J ±  kb
    transcript NM_172932 RefSeq | MGI Sequence Detail 3899 C57BL/6  
    polypeptide Q8BYM5 UniProt | EBI | MGI Sequence Detail 825 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 31
      cDNA 30
      Primer pair 1

      Microarray probesets 1
    References
    more
    • Summaries
      All 118
      Developmental Gene Expression 12
      Diseases 4
      Gene Ontology 11
      Phenotypes 75
    • Earliest
      J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
    • Latest
      J:354619 Sun H, et al., Autism-associated neuroligin 3 deficiency in medial septum causes social deficits and sleep loss in mice. J Clin Invest. 2024 Jul 26;134(19)
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/12/2024
    MGI 6.24     		The Jackson Laboratory