Summary Statistics:
ASD Reports: 44
Recent Reports: 10
Annotated variants: 55
Associated CNVs: 17
Evidence score: 4
Gene Score: 3
Relevance to Autism
Several studies have found rare variants in the NLGN4X gene in autism. Association was seen in Finnish and Caucasian population cohorts. However, several studies have found no rare variants in the NLGN4X gene in autistic patients in their cohorts (including Quebec population and IMGSAC cohorts).
Molecular Function
Neuroligins are cell-adhesion molecules at the postsynaptic side of the synapse .
References
Primary
Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism.
ASD
Positive Association
Genes related to sex steroids, neural growth, and social-emotional behavior are associated with autistic traits, empathy, and Asperger syndrome.
ASD
Positive Association
Analysis of four neuroligin genes as candidates for autism.
ASD
Positive Association
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.
SCZ
Positive Association
Variations analysis of NLGN3 and NLGN4X gene in Chinese autism patients.
ASD
Positive Association
A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population.
ASD
Negative Association
Absence of coding mutations in the X-linked genes neuroligin 3 and neuroligin 4 in individuals with autism from the IMGSAC collection.
ASD
Negative Association
NLGN3/NLGN4 gene mutations are not responsible for autism in the Quebec population.
ASD
Negative Association
Mutation screening of X-chromosomal neuroligin genes: no mutations in 196 autism probands.
ASD
Negative Association
Analysis of the SNP rs3747333 and rs3747334 in NLGN4X gene in autism spectrum disorder: a meta-analysis.
ASD
Negative Association
Not all neuroligin 3 and 4X missense variants lead to significant functional inactivation.
ASD
Support
Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders an...
DD, ID
ASD, ADHD
Support
High diagnostic yield of syndromic intellectual disability by targeted next-generation sequencing.
ID
Autistic behavior
Support
Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder
ASD
ADHD, TS
Support
A neuroligin-4 missense mutation associated with autism impairs neuroligin-4 folding and endoplasmic reticulum export.
ASD
Support
GABA/Glutamate synaptic pathways targeted by integrative genomic and electrophysiological explorations distinguish autism from intellectual disabil...
ASD, ID
Support
Integrating de novo and inherited variants in 42
ASD
Support
Autism and nonsyndromic mental retardation associated with a de novo mutation in the NLGN4X gene promoter causing an increased expression level.
ASD
MR
Support
Using whole-exome sequencing to identify inherited causes of autism.
ASD
Support
New Candidates for Autism/Intellectual Disability Identified by Whole-Exome Sequencing
DD, ID
Stereotypy
Support
Familial deletion within NLGN4 associated with autism and Tourette syndrome.
ASD
TS
Support
ID, epilepsy/seizures
Support
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
ASD
Support
Next-Generation Sequencing in Korean Children With Autism Spectrum Disorder and Comorbid Epilepsy
ASD
ID, epilepsy/seizures
Support
Analysis of the neuroligin 3 and 4 genes in autism and other neuropsychiatric patients.
ASD
Support
Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder.
ASD
Support
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
TS
Support
Identification of Four Novel Synonymous Substitutions in the X-Linked Genes Neuroligin 3 and Neuroligin 4X in Japanese Patients with Autistic Spect...
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Highly Cited
X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family.
ID
ASD
Recent Recommendation
Structure function and splice site analysis of the synaptogenic activity of the neurexin-1 beta LNS domain.
Recent Recommendation
Pathogenic mechanism of an autism-associated neuroligin mutation involves altered AMPA-receptor trafficking.
Recent Recommendation
Autism-associated mutation inhibits protein kinase C-mediated neuroligin-4X enhancement of excitatory synapses.
Recent Recommendation
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.
ASD
Recent Recommendation
The functional genetic link of NLGN4X knockdown and neurodevelopment in neural stem cells.
Recent Recommendation
Autism-associated variants of neuroligin 4X impair synaptogenic activity by various molecular mechanisms
ASD
Recent Recommendation
Unusually rapid evolution of Neuroligin-4 in mice.
Recent Recommendation
A Cluster of Autism-Associated Variants on X-Linked NLGN4X Functionally Resemble NLGN4Y
ASD, ID
Recent Recommendation
Reduced social interaction and ultrasonic communication in a mouse model of monogenic heritable autism.
Recent Recommendation
Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons.
GEN172R001
frameshift_variant
c.1186_1187insT
p.Asp396ValfsTer16
Familial
Maternal
Multiplex
GEN172R002
missense_variant
c.1133A>G
p.Lys378Arg
Familial
Maternal
GEN172R003
synonymous_variant
c.1397C>T
p.Pro466Leu
GEN172R004
synonymous_variant
c.1310G>A
p.Arg437Gln
GEN172R005
synonymous_variant
c.1805C>T
p.(=)
GEN172R006
synonymous_variant
C2241TC2243G
p.(=)
GEN172R007
2KB_upstream_variant
c.-335G>A
De novo
Simplex
GEN172R008
copy_number_loss
Familial
Maternal
Multiplex
GEN172R009
copy_number_gain
Familial
Maternal
GEN172R010
synonymous_variant
c.297C>T
p.Gly99=
Unknown
Unknown
GEN172R011
synonymous_variant
c.516C>T
p.Ile172=
Unknown
Unknown
GEN172R012
synonymous_variant
c.1590C>T
p.Phe530=
Unknown
Unknown
GEN172R013
3_prime_UTR_variant
c.1601+2982T>C
Familial
Maternal
Multiplex
GEN172R014
3_prime_UTR_variant
c.1601+969del
Familial
Maternal
Multiplex
GEN172R015
copy_number_gain
Unknown
Unknown
GEN172R016
stop_gained
c.985C>T
p.Gln329Ter
Familial
Maternal
Simplex
GEN172R017
missense_variant
c.2297G>A
p.Arg766Gln
Familial
Maternal
Simplex
GEN172R018
missense_variant
c.250G>A
p.Gly84Arg
Familial
Maternal
Simplex
GEN172R019
missense_variant
c.484C>A
p.Gln162Lys
De novo
Simplex
GEN172R020
missense_variant
c.847G>A
p.Ala283Thr
Familial
Maternal
Simplex
GEN172R021
missense_variant
c.392A>G
p.Asn131Ser
Unknown
Unknown
GEN172R022
missense_variant
c.295G>A
p.Gly99Ser
Familial
Maternal
Multiplex
GEN172R023
missense_variant
c.1133A>G
p.Lys378Arg
Familial
Maternal
Simplex
GEN172R024
missense_variant
c.1207G>A
p.Val403Met
Familial
Maternal
Multiplex
GEN172R025
missense_variant
c.2110C>T
p.Arg704Cys
Familial
Maternal
Multiplex
GEN172R026
frameshift_variant
c.1254_1255del
p.Glu418AspfsTer12
Familial
Maternal
Multi-generational
GEN172R027
inframe_deletion
c.1361_1372del
p.Val454_Ala457del
De novo
GEN172R028
stop_gained
c.820C>T
p.Gln274Ter
Familial
Maternal
Simplex
GEN172R029
frameshift_variant
c.632del
p.Leu211Ter
Unknown
Simplex
GEN172R030
missense_variant
c.1564G>A
p.Val522Met
De novo
Simplex
GEN172R031
missense_variant
c.259C>T
p.Arg87Trp
De novo
Multiplex
GEN172R032
missense_variant
c.281C>T
p.Pro94Leu
Unknown
Unknown
GEN172R033
missense_variant
c.302G>A
p.Arg101Gln
Familial
Maternal
Unknown
GEN172R034
missense_variant
c.325G>C
p.Val109Leu
Familial
Maternal
Unknown
GEN172R035
copy_number_loss
Unknown
GEN172R036
copy_number_loss
Unknown
GEN172R037
missense_variant
c.2167C>T
p.His723Tyr
De novo
Simplex
GEN172R038
splice_site_variant
c.1601+5G>A
De novo
GEN172R039
frameshift_variant
c.659del
p.Gly220AlafsTer29
Unknown
GEN172R040
inframe_indel
c.1581_1582delinsTT
p.Trp527_Thr528delinsCysSer
Familial
Maternal
Simplex
GEN172R041
missense_variant
c.1271A>C
p.Tyr424Ser
De novo
GEN172R042
missense_variant
c.295G>A
p.Gly99Ser
Familial
Maternal
GEN172R043
missense_variant
c.1360G>C
p.Val454Leu
Familial
Maternal
Multiplex
GEN172C001
intron_variant, microsatellite
Finnish
Discovery
GEN172C002
intron_variant
rs12836764
c.-306+6390T>C;c.-305-29322T>C;c.-306+5679T>C
Caucasian
Discovery
GEN172C003
missense_variant
rs3747333
c.1777C>T;c.1837C>T
p.Leu593Phe;p.Leu613Phe
Quebec
Discovery
GEN172C004
synonymous_variant
rs3747334
c.1779C>G;c.1839C>G
p.(=)
Quebec
Discovery
GEN172C005
intron_variant, 2KB_upstream_variant
rs2290487
c.-613+640G>A;c.-1327G>A;c.-518G>A;c.-306+640G>A;c.-1572G>A;c.-1341G>A;c.-2250G>A
G to A
IMGSAC
Discovery
GEN172C006
intron_variant, 2KB_upstream_variant, 5_prime_UTR_variant
rs2290488
c.-613+727G>C;c.-1240G>C;c.-431G>C;c.-306+727G>C;c.-1485G>C;c.-1254G>C;c.-2163G>C
G34C
IMGSAC
Discovery
GEN172C007
synonymous_variant
rs7049300
c.1397C>T;c.933C>T;c.993C>T
p.(=)
IMGSAC
Discovery
GEN172C008
missense_variant
rs3747333
c.1777C>T;c.1837C>T
p.Leu593Phe;p.Leu613Phe
IMGSAC
Discovery
GEN172C009
synonymous_variant
rs3747334
c.1779C>G;c.1839C>G
p.(=)
IMGSAC
Discovery
GEN172C010
missense_variant
rs3747333
c.1777C>T;c.1837C>T
p.Leu593Phe;p.Leu613Phe
318 Chinese ASD cases, 453 Chinese controls
Replication
GEN172C011
synonymous_variant
rs3747334
c.1779C>G;c.1839C>G
p.(=)
319 Chinese ASD cases, 453 Chinese controls
Replication
GEN172C012
intron_variant
rs12009217
c.625+26439T>C;c.685+26439T>C
40,675 SCZ cases and 64,643 controls (CLOZUK and independent PGC datasets)
Discovery
X
Deletion-Duplication
45
X
Deletion-Duplication
11
X
Deletion-Duplication
21
Summary Statistics:
# of Reports: 2
# of Models: 2
External Links
Model Summary
Nlg4 mutant flies show impairments in olfactory associative learning as well as a severe decrease in reversal learning task, a measure of behavioral flexibility. This deficit seems to be due to enhanced old memories, driven by inability to active Rac1-dependent forgetting. Nlg4-deficient mutant flies show decreased anxiety and altered sleep/activity patterns. Moreover, Nlg4 mutant flies show an increased probability to form groups which also are larger in size and less probability for males to remain single. When in groups, male Nlg4 mutants are more likely to form chains. When exposed to male courtship songs, mutant males are more like to show aggression towards other males.
References
Primary
Inability to activate Rac1-dependent forgetting contributes to behavioral inflexibility in mutants of multiple autism-risk genes.
Primary
Neuroligins Nlg2 and Nlg4 Affect Social Behavior in Drosophila melanogaster.
Model Type:
Genetic
Model Genotype:
Homozygous
Mutation:
.
Allele Type: Loss-of-function
Strain of Origin:
Genetic Background: w^1118
ES Cell Line:
Mutant ES Cell Line:
Model Source: Bloomington Drosophila Stock Center
Model Type:
Genetic
Model Genotype:
Homozygous
Mutation:
Nlg4^del/LL01874 compound heterozygotes were generated by crossing an Nlg4^del deletion and an Nlg4 point mutation (Nlg4^LL01874) line. This strategy was adopted as each individual line leads to lethality in the homozygous state. .
Allele Type: Partial knockout
Strain of Origin: Unreported
Genetic Background: Canton S
ES Cell Line:
Mutant ES Cell Line:
Model Source: Junhai Han, Southeast University, Nanjing, China (PMID 24068821)
Cued or contextual fear conditioning: memory of cue: long term recall1
Increased
View More
Description: Nlg4 mutants showed an increase in olfactory associative aversive learning compared to controls.
Olfactory classical conditioning
Adult stage
Cognitive flexibility: associative learning1
Decreased
View More
Description: Nlg4 mutants showed a severe decrease in olfactory reversal learning compared to controls.
Reversal learning of olfactory classical conditioning
Adult stage
Olfactory learning and memory1
Decreased
View More
Description: Nlg4 mutants showed a decrease in olfactory associative aversive learning compared to controls.
Olfactory classical conditioning
Adult stage
Not Reported:
Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure, Sensory, Social behavior
Locomotor activity in diurnal cycle1
Decreased
View More
Description: Nlg4 mutant flies showed a decrease in locomotor activity during light periods compared to controls.
Exp Paradigm: Locomotor activity measured in median beam crossings per hour for 10 hours around noon.
General observations
5 7 days
Circadian rhythms: timing/phases of locomotor activity1
Abnormal
View More
Description: Nlg4 mutant flies showed altered sleep/activity patterns compared to controls. Specifically, Nlg4 mutants showed less frequent but longer sleep episodes compared to wild-type controls.
General observations
5 7 days
Locomotor activity in diurnal cycle: dark phase1
Decreased
View More
Description: Nlg4 mutant flies showed a decrease in locomotor activity during dark periods compared to controls.
Exp Paradigm: Locomotor activity measured in median beam crossings per hour for 10 hours around midnight.
General observations
5 7 days
General locomotor activity1
Decreased
View More
Description: Nlg4 mutant flies showed a decrease in overall locomotor activity compared to controls.
Exp Paradigm: Locomotor activity measured in median beam crossings
Beam crossing
5 7 days
Increased
View More
Description: Nlg4 mutant flies showed an increased probability to form a group compared to controls. Specifically, Nlg4 mutants showed a decreased probability of remaining single (24%), an increase in preferred group size, and a decrease in distance to next neighbor compared to controls.
Group behavior analysis
5 7 days
Mating behavior: male courtship behavior: chaining1
Increased
View More
Description: Nlg4 mutant flies showed a significant increase in male chaining behavior compared to controls.
General observations
5 7 days
Aggression: auditory stimulus induced1
Increased
View More
Description: Nlg4 mutant fly males showed an increased aggression to other males in response to stimulation with courtship song stimulus compared to controls. Nlg4 mutant fly males showed no change in aggressive behavior towards other males in response to either white noise or aggression sound stimulus compared to controls.
Exp Paradigm: Courtship song stimulus (test stimulus); White noise or aggression sound stimulus (control stimuli)
Competitive courtship assay
7 12 days
Decreased
View More
Description: Nlg4 mutant flies showed decreased centrophobia (i.e., avoidance of open areas of an arena) compared to controls.
General observations
5 7 days
Decreased
View More
Description: Nlg4 mutant flies showed reduced levels of Nlg2 transcript (40%) compared controls.
Quantitative pcr (qrt-pcr)
5 7 days
General locomotor activity1
No change
General observations
5 7 days
Sensory-evoked response: excitation: auditory stimulus1
No change
Application of auditory stimuli
5 7 days
Mating behavior: male courtship behavior: audible vocalization1
No change
Sound recordings
5 7 days
Not Reported:
Communications, Developmental profile, Immune response, Learning & memory, Maternal behavior, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure
Summary Statistics:
Total Interactions: 5
Total Publications: 5
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Hide non-ASD
Interactor Symbol
Interactor Name
Interactor Organism
Entrez ID
Uniprot ID
Interaction Type
Evidence
Reference
DLG4
DLG4discs, large homolog 4 (Drosophila)
1742
P78352
IP/WB
Bolliger MF , et al. 2001
FMR1
fragile X mental retardation 1
2332
G8JLE9
PAR-CLIP
Ascano M Jr , et al. 2012
NLGN3
neuroligin 3
54413
D3DVV1
IP; LC-MS/MS
Huttlin EL , et al. 2015
SCN2A
sodium channel, voltage-gated, type II, alpha 1
24766
P04775
IP/WB
Bouzidi M , et al. 2002
SNTG2
syntrophin, gamma 2
54221
Q9NY99
Y2H; IP/WB
Yamakawa H , et al. 2007