Evidence Detail for NLGN3

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Basic Information Top
Gene Symbol:NLGN3 ( HNL3,KIAA1480 )
Gene Full Name: neuroligin 3
Band: Xq13.1
Quick LinksEntrez ID:54413; OMIM: 300336; Uniprot ID:NLGN3_HUMAN; ENSEMBL ID: ENSG00000196338
Sequences Top
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Evidence Statistic Top

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Evidences Syndromic Gene GWAS Expression CNV Linkage Low Scale Association Other Studies Total
Score (No. of Studies) No 0 (0) 0 (0) 1 (2) 0 (0) 1 (1) 3 (6) 26 (7)
Syndromic Autism Gene Top
Low Scale Association Studies (by Ethnic Group) Top
Family Based Association Studies: 1
Case Control Based Association Studies: 0
Reference Population #SNPs/ #VNTRs ASD Cases Normal Controls Result
(% Women)
ADI-R ADOS Diagnosis Age
IQ #Subjects
(% Women)
No Evidence.
Genome-Wide Association Studies(By Ethnic Group) Top
Other Low Scale Gene Studies Top
Reference Orangnism Tissue ADI-R ADOS Diagnosis Evidence Level Result
Jamain, 2003_1 human -ASD genetics: mutation screen
  • Subjects: 2
  • Normal Controls: 350 (250 female, 100 male)
  • Methods: -
  • Evidence Details: R451C is found in a Swedish family and located in a predicted EF-hand domian.
Comoletti, 2004_1 - ---- protein function
  • Subjects: -
  • Normal Controls: -
  • Methods: Mass spectrometry
  • Evidence Details: Mass spectrometry comparison of the disulfide bonding pattern between the native and the mutated proteins indicates the absence of aberrant disulfide bonding, suggesting that the secondary structure of the mutated protein is conserved. The mutation separately affects protein expression and activity. The Cys mutation causes defective neuroligin trafficking, leading to retention of the protein in the endoplasmic reticulum.
Talebizadeh, 2004_1 human blood--ASD genetics: mutation screen
  • Subjects: 67 (64 autism and 3 Asperger Syndrome, 41 female, 26 male)
  • Normal Controls: -
  • Methods: PCR, sequence
  • Evidence Details: The reported mutations in the two neuroligin genes were not detected in our group of individuals with ASD (American males and females), suggesting that these specific gene mutations are not common or found in a low frequency in the autism population
Vincent, 2004_1 human ---AD genetics: mutation screen
  • Subjects: 196
  • Normal Controls: -
  • Methods: -
  • Evidence Details: Our own study, screening a larger sample of 196 autism probands, failed to identify any mutations that would affect the coding regions of these genes. Our findings suggest that mutations in these two genes are infrequent in autism.
Gauthier, 2005_1 human ---AD genetics: mutation screen
  • Subjects: 96
  • Normal Controls: -
  • Methods: mutation screen
  • Evidence Details: NLGN3/NLGN4 gene mutations are not responsible for autism in the Quebec population.
Blasi, 2006_1 human blood--ASD genetics: mutation screen
  • Subjects: 124
  • Normal Controls: -
  • Methods: mutation screen
  • Evidence Details: We identified a new non-synonymous variant in NLGN3 (Thr632Ala), which is likely to be a rare polymorphism.
Talebizadeh, 2006_1 human lymphoblastoid cell--AD function: alternative splice
  • Subjects: 10 female
  • Normal Controls: -
  • Methods: -
  • Evidence Details: A novel NLGN4 isoform lacking exon 4, which occurred de novo on the paternal allele, was identified in one of the autistic females. Monoallelic expression of NLGN4 was seen in this subject and in 11 of 14 informative autistic and non-autistic females using a single nucleotide polymorphism found at 3' UTR.
De Jaco, 2008_1 cell line HEK-293 cells--- protein function
  • Subjects: -
  • Normal Controls: -
  • Methods: transfection, western blotting, 2D electrophoresis
  • Evidence Details: The exposed Cys causes retention of the protein in the endoplasmic reticulum (ER) when expressed in HEK-293 cells.A 2D electrophoresis coupled with mass spectrometry based approach was used to analyze proteins co-immunoprecipitating with NL3 and show differential expression of factors interacting with wild type and mutant NL3.
Gong, 2008_1 human ---ASD X chromosome inactivation (XCI) screen
  • Subjects: 543 mothers and 163 affected girls
  • Normal Controls: 144 adult females and 40 young females
  • Methods: X chromosome inactivation (XCI) screen
  • Evidence Details: Interestingly, two mothers and one girl carrying known mutations in X-linked genes (NLGN3, ATRX, MECP2) showed highly skewed XCI, suggesting that ascertainment of XCI could reveal families with X-linked mutations.
Piton, 2010_1 human bloodASD genetics: mutation screen
  • Subjects: 142( 122 males and 20 females)
  • Normal Controls: -
  • Methods: direct sequencing
  • Evidence Details: Exonic variants identified during the the screening of the 170 X-linked synapic genes
Fujita, 2011_1 mouse neurons--- expression level
  • Subjects: -
  • Normal Controls: -
  • Methods: pull-down, western blot
  • Evidence Details: Both mutated CADM1 and NLGN3(R451C) induced upregulation of C/EBP-homologous protein(CHOP), an ER stress marker, suggesting that in addition to the trafficking impairment, this CHOP upregulation may also be involved in ASD pathogenesis
Etherton, 2011_1 mouse ---- mouse model
  • Subjects: -
  • Normal Controls: -
  • Methods: knock-in mouse
  • Evidence Details: Our results suggest that the cytoplasmic tail of neuroligin-3 has a central role in synaptic transmission by modulating the recruitment of AMPA receptors to postsynaptic sites at excitatory synapses."
Yasuda, 2011_1 human lymphoblastoid cellsASD mRNA expression level
  • Subjects: 35
  • Normal Controls: 35
  • Methods: RT-PCR
  • Evidence Details: The mRNA expression levels of NLGN3 normalized by b-actin or TBP were significantly decreased in the individuals with ASD compared to controls
Large Scale Expression Studies Top
CNV Studies Top
CNV Name Chr Band Gain/Loss Number of CNVs Evidence Type Reference
Case Control
AutCNV0003869 X 23q13.1 loss 1 - Denovo CNVs; Levy, 2011
AutCNV0004408 X Xq13.1 loss 1 - CNVs Only Present In Patients; Sanders, 2011
Linkage Studies Top

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Syndromic Genes

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AutismKB Statistics

  • Studies: 616
  • Genes: 3,075
  • SNPs/VNTRs: 3,386
  • CNVs: 4,617
  • Linkage Regions: 158
  • Last Update: 05/25/2012
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