Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	54413
Gene name	Neuroligin 3
Gene symbol	NLGN3
Synonyms (NCBI Gene)	HNL3
Chromosome	X
Chromosome location	Xq13.1
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. Mutations i

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34927195	->G	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs121917893	C>T	Risk-factor	Coding sequence variant, missense variant
rs143817848	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, intron variant
rs376877146	C>A,T	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, missense variant, intron variant, coding sequence variant
rs878853147	C>T	Likely-pathogenic	Intron variant, missense variant, coding sequence variant
rs1569485503	C>T	Pathogenic	Coding sequence variant, missense variant

Show/Hide all (54)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023264	hsa-miR-122-5p	Microarray	17612493
MIRT516017	hsa-miR-5580-3p	PAR-CLIP	21572407
MIRT516015	hsa-miR-511-3p	PAR-CLIP	21572407
MIRT516014	hsa-miR-4711-3p	PAR-CLIP	21572407
MIRT516013	hsa-miR-6867-5p	PAR-CLIP	21572407
MIRT516012	hsa-miR-574-5p	PAR-CLIP	21572407
MIRT516017	hsa-miR-5580-3p	PAR-CLIP	23446348
MIRT516015	hsa-miR-511-3p	PAR-CLIP	23446348
MIRT516014	hsa-miR-4711-3p	PAR-CLIP	23446348
MIRT516013	hsa-miR-6867-5p	PAR-CLIP	23446348
MIRT516012	hsa-miR-574-5p	PAR-CLIP	23446348
MIRT516017	hsa-miR-5580-3p	PAR-CLIP	21572407
MIRT516015	hsa-miR-511-3p	PAR-CLIP	21572407
MIRT516014	hsa-miR-4711-3p	PAR-CLIP	21572407
MIRT516013	hsa-miR-6867-5p	PAR-CLIP	21572407
MIRT516012	hsa-miR-574-5p	PAR-CLIP	21572407
MIRT516017	hsa-miR-5580-3p	PAR-CLIP	23446348
MIRT516015	hsa-miR-511-3p	PAR-CLIP	23446348
MIRT516014	hsa-miR-4711-3p	PAR-CLIP	23446348
MIRT516013	hsa-miR-6867-5p	PAR-CLIP	23446348
MIRT516012	hsa-miR-574-5p	PAR-CLIP	23446348
MIRT1186767	hsa-miR-1972	CLIP-seq
MIRT1186768	hsa-miR-3176	CLIP-seq
MIRT1186769	hsa-miR-3622a-3p	CLIP-seq
MIRT1186770	hsa-miR-3622b-3p	CLIP-seq
MIRT1186771	hsa-miR-3663-5p	CLIP-seq
MIRT1186772	hsa-miR-3922-3p	CLIP-seq
MIRT1186773	hsa-miR-4435	CLIP-seq
MIRT1186774	hsa-miR-4527	CLIP-seq
MIRT1186775	hsa-miR-4755-3p	CLIP-seq
MIRT2054125	hsa-miR-122	CLIP-seq
MIRT2054126	hsa-miR-3127-5p	CLIP-seq
MIRT2054127	hsa-miR-4270	CLIP-seq
MIRT2054128	hsa-miR-4441	CLIP-seq
MIRT2283271	hsa-miR-1184	CLIP-seq
MIRT2283272	hsa-miR-1205	CLIP-seq
MIRT2283273	hsa-miR-3155	CLIP-seq
MIRT2283274	hsa-miR-3155b	CLIP-seq
MIRT2283275	hsa-miR-3158-5p	CLIP-seq
MIRT2283276	hsa-miR-3194-3p	CLIP-seq
MIRT2283277	hsa-miR-4290	CLIP-seq
MIRT2283278	hsa-miR-4687-5p	CLIP-seq
MIRT2283279	hsa-miR-484	CLIP-seq
MIRT2283280	hsa-miR-760	CLIP-seq
MIRT2581584	hsa-miR-1343	CLIP-seq
MIRT2581585	hsa-miR-193a-5p	CLIP-seq
MIRT2581586	hsa-miR-3667-3p	CLIP-seq
MIRT2581587	hsa-miR-4326	CLIP-seq
MIRT2581588	hsa-miR-637	CLIP-seq
MIRT2581584	hsa-miR-1343	CLIP-seq
MIRT2581585	hsa-miR-193a-5p	CLIP-seq
MIRT2581586	hsa-miR-3667-3p	CLIP-seq
MIRT2581587	hsa-miR-4326	CLIP-seq
MIRT2581588	hsa-miR-637	CLIP-seq

Show/Hide all (54)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002087	Process	Regulation of respiratory gaseous exchange by nervous system process	ISS
GO:0005515	Function	Protein binding	IPI	17292328, 25464930
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006898	Process	Receptor-mediated endocytosis	ISS
GO:0007155	Process	Cell adhesion	IEA
GO:0007158	Process	Neuron cell-cell adhesion	IBA
GO:0007158	Process	Neuron cell-cell adhesion	ISS
GO:0007268	Process	Chemical synaptic transmission	IBA
GO:0007416	Process	Synapse assembly	ISS
GO:0007612	Process	Learning	IMP	12669065
GO:0009986	Component	Cell surface	IBA
GO:0009986	Component	Cell surface	IDA	15150161, 17292328
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	21838267
GO:0030139	Component	Endocytic vesicle	ISS
GO:0030534	Process	Adult behavior	IMP	12669065
GO:0035176	Process	Social behavior	IMP	12669065
GO:0035176	Process	Social behavior	ISS
GO:0038023	Function	Signaling receptor activity	IBA
GO:0038023	Function	Signaling receptor activity	ISS
GO:0042043	Function	Neurexin family protein binding	IBA
GO:0042043	Function	Neurexin family protein binding	IEA
GO:0042043	Function	Neurexin family protein binding	ISS	15152050
GO:0045202	Component	Synapse	IBA
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS
GO:0045211	Component	Postsynaptic membrane	ISS
GO:0048488	Process	Synaptic vesicle endocytosis	IBA
GO:0048675	Process	Axon extension	ISS
GO:0050804	Process	Modulation of chemical synaptic transmission	IBA
GO:0050804	Process	Modulation of chemical synaptic transmission	ISS
GO:0050808	Process	Synapse organization	IMP	15150161
GO:0050839	Function	Cell adhesion molecule binding	ISS	15152050
GO:0051965	Process	Positive regulation of synapse assembly	ISS
GO:0051968	Process	Positive regulation of synaptic transmission, glutamatergic	ISS
GO:0060024	Process	Rhythmic synaptic transmission	ISS
GO:0060076	Component	Excitatory synapse	IDA	15620359
GO:0060080	Process	Inhibitory postsynaptic potential	ISS
GO:0071625	Process	Vocalization behavior	IMP	12669065
GO:0097104	Process	Postsynaptic membrane assembly	IBA
GO:0097104	Process	Postsynaptic membrane assembly	ISS
GO:0097105	Process	Presynaptic membrane assembly	IBA
GO:0097105	Process	Presynaptic membrane assembly	ISS
GO:0097110	Function	Scaffold protein binding	IPI	17292328
GO:0098793	Component	Presynapse	IEA
GO:0098983	Component	Symmetric, GABA-ergic, inhibitory synapse	TAS	21838267
GO:0098984	Component	Neuron to neuron synapse	IEA
GO:0098985	Component	Asymmetric, glutamatergic, excitatory synapse	TAS	21838267
GO:0099054	Process	Presynapse assembly	IEA
GO:0099054	Process	Presynapse assembly	TAS	21838267
GO:1900451	Process	Positive regulation of glutamate receptor signaling pathway	ISS
GO:2000463	Process	Positive regulation of excitatory postsynaptic potential	ISS

MIM	HGNC	e!Ensembl
300336	14289	ENSG00000196338

Q9NZ94

Protein name

Neuroligin-3 (Gliotactin homolog)

Protein function

Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and may mediate its effects by clustering other synaptic proteins. May

PDB

8GS3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00135	COesterase	40 → 624	Carboxylesterase family	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in the blood vessel walls (at protein level). Detected in throughout the brain and in spinal cord. Detected in brain, and at lower levels in pancreas islet beta cells. {ECO:0000269|PubMed:10767552, ECO:0000269|PubMed:18755801

Sequence

MWLRLGPPSLSLSPKPTVGRSLCLTLWFLSLALRASTQAPAPTVNTHFGKLRGARVPLPS
EILGPVDQYLGVPYAAPPIGEKRFLPPEPPPSWSGIRNATHFPPVCPQNIHTAVPEVMLP
VWFTANLDIVATYIQEPNEDCLYLNVYVPTEDVKRISKECARKPNKKICRKGGSGAKKQG
EDLADNDGDEDEDIRDSGAKPVMVYIHGGSYMEGTGNMIDGSILASYGNVIVITLNYRVG
VLGFLSTGDQAAKGNYGLLDQIQALRWVSENIAFFGGDPRRITVFGSGIGASCVSLLTLS
HHSEGLFQRAIIQSGSALSSWAVNYQPVKYTSLLADKVGCNVLDTVDMVDCLRQKSAKEL
VEQDIQPARYHVAFGPVIDGDVIPDDPEILMEQGEFLNYDIMLGVNQGEGLKFVEGVVDP
EDGVSGTDFDYSVSNFVDNLYGYPEGKDTLRETIKFMYTDWADRDNPETRRKTLVALFTD
HQWVEPSVVTADLHARYGSPTYFYAFYHHCQSLMKPAWSDAAHGDEVPYVFGVPMVGPTD
LFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNKPVPQDTKFIHTKANRFEEVAWSKYNPRD
QLYLHIGLKPRVRDHYRATKVAFWKHLVPHLYNLHDMFHYTSTTTKVPPPDTTHSSHITR
RPNGKTWSTKRPAISPAYSNENAQGSWNGDQDAGPLLVENPRDYSTELSVTIAVGASLLF
LNVLAFAALYYRKDKRRQEPLRQPSPQRGAGAPELGAAPEEELAALQLGPTHHECEAGPP
HDTLRLTALPDYTLTLRRSPDDIPLMTPNTITMIPNSLVGLQTLHPYNTFAAGFNSTGLP
HSHSTTRV

Sequence length

848

Interactions

View interactions

	KEGG		Reactome
	Cell adhesion molecules		Neurexins and neuroligins

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism, susceptibility to, X-linked 1	Likely pathogenic; Pathogenic	rs2147900685, rs2147908798, rs2519748934, rs1460006418	RCV001787304 RCV001794857 RCV002291239 RCV002470678	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autistic behavior	Pathogenic	rs1569485503	RCV000778067	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypogonadotropic hypogonadism	Pathogenic	rs2519735876	RCV003151703	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic; Pathogenic	rs878853147, rs1569485503	RCV000224769 RCV000778067	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Adrenocortical carcinoma, hereditary	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complex neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cone-rod dystrophy	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NLGN3-related disorder	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen, ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (47)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Anxiety	Anxiety Disorder	BEFREE	25299583		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	25299583		★★★★★ ★☆☆☆☆ Found in Text Mining only
ASPERGER SYNDROME, X-LINKED, SUSCEPTIBILITY TO, 1 (disorder)	Asperger Syndrome	UNIPROT_DG	12669065		★★★★★ ★☆☆☆☆ Found in Text Mining only
ASPERGER SYNDROME, X-LINKED, SUSCEPTIBILITY TO, 1 (disorder)	Asperger Syndrome	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
ASPERGER SYNDROME, X-LINKED, SUSCEPTIBILITY TO, 1 (disorder)	Asperger Syndrome	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	12669065, 16648374, 18555979, 21569590, 22892527, 27782075, 34893870	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	12669065, 15152050, 16077734, 16508939, 18189281, 18555979, 21364653, 21569590, 22892527, 24995974, 25299583, 27743928, 28255463, 28385162, 28841651 View all (9 more)		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic behavior	Autism	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autistic Disorder	Autism	BEFREE	12669065, 15152050, 15389766, 16077734, 16508939, 16648374, 17823315, 19406211, 19645625, 20615874, 21130222, 22106001, 22671294, 23851596, 24570023 View all (11 more)		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	CTD_human_DG	12669065, 18621663		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	Pubtator	12669065, 16648374, 18555979, 20227402, 25167861, 27897003	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	LHGDN	16077734, 16508939, 16648374		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Neoplasms	Brain Neoplasms	BEFREE	28959975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Hypothyroidism	Congenital Hypothyroidism	BEFREE	20615874		★★★★★ ★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	BEFREE	29775613		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29474958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diffuse Intrinsic Pontine Glioma	Diffuse Intrinsic Pontine Glioma	BEFREE	28959975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	12669065, 15150161, 23849776, 24570023		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	28959975, 29777576		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	37443071	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	28959975, 29777576		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	28959975, 30094719, 30242227, 31150649, 31410219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	30094719, 30636076, 31410219, 32372724, 35148403	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	29622757		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung disease	Pubtator	29622757	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	29474958, 31184401		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	16118346, 18628683, 31184401		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Intellectual developmental disorder	Pubtator	23871722	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Kidney Failure	Kidney Failure	BEFREE	29474958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Glioma	Glioma	BEFREE	28959975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	28959975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental Depression	Mental Depression	BEFREE	29775613		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	16118346, 18628683		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28959975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	31150649		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	31184401		★★★★★ ★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Asperger syndrome	Asperger Syndrome	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Autism	Autism	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	15152050, 18189281, 25299583, 28958035, 31184401		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	27865048		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Disorders	Sleep Disorders	BEFREE	28958035		★★★★★ ★☆☆☆☆ Found in Text Mining only
Social Communication Disorder	Social Communication Disorder	BEFREE	28255463		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stereotyped Behavior	Stereotyped Behavior	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

NLGN3 (neuroligin 3)