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 Links	Entrez ID:54413; OMIM: 300336; Uniprot ID:NLGN3_HUMAN; ENSEMBL ID: ENSG00000196338

Sequences Top

nucleotide Sequence
Protein Sequence

>NLGN3|54413|nucleotide
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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

Reference	Population	#SNPs/ #VNTRs	#Families	Affecteds						Result
Reference	Population	#SNPs/ #VNTRs	#Families	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ (range)	Result
CAUCASIAN
Ylisaukko-oja, 2005_1	Finland	8 (detail)	100	122 (-)			ASD	- -	- -

Case Control Based Association Studies: 0

Reference	Population	#SNPs/ #VNTRs	ASD Cases						Normal Controls		Result
Reference	Population	#SNPs/ #VNTRs	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ	#Subjects (% Women)	Age (range)	Result
No Evidence.

Genome-Wide Association Studies(By Ethnic Group) Top

Reference	Stage	#SNPs/ #VNTRs	#Families	Affecteds	Result
#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ (range)
No Evidence.

Reference	Stage	#SNPs/ #VNTRs	ASD Cases	Normal Controls	Result
#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ	#Subjects (% Women)	Age (range)
No Evidence.

Other Low Scale Gene Studies Top

Reference	Orangnism	Tissue	ADI-R	ADOS	Diagnosis	Evidence Level
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	blood			ASD	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 cells			ASD	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

Reference	Population	Tissue	#Subjects (% Women)	ADI-R	ADOS	Endo- pheno	Diagnosis	Normal Controls (% Women)	Fold Change	Up/ Down	P/Q value
No Evidence.

Reference	Population	Tissue	Platform	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Normal Controls(% Women)
No Evidence.

CNV Studies Top

CNV Name	Chr	Band	Gain/Loss	Number of CNVs		Evidence Type	Reference
CNV Name	Chr	Band	Gain/Loss	Case	Control	Evidence Type	Reference
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

Linkage Name	Band	Chr	Marker	LOD	NPL	P_Value	Reference
No Matched Linkage Regions !

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Syndromic Genes

Non-syndromic Genes

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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