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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	54413
Gene name Gene Name - the full gene name approved by the HGNC.	Neuroligin 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NLGN3
Synonyms (NCBI Gene) Gene synonyms aliases	HNL3
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xq13.1
Summary Summary of gene provided in NCBI Entrez Gene.	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(46)

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
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	IBA	21873635
GO:0006898	Process	Receptor-mediated endocytosis	ISS
GO:0007158	Process	Neuron cell-cell adhesion	IBA	21873635
GO:0007158	Process	Neuron cell-cell adhesion	ISS
GO:0007268	Process	Chemical synaptic transmission	IBA	21873635
GO:0007416	Process	Synapse assembly	ISS
GO:0007612	Process	Learning	IMP	12669065
GO:0009986	Component	Cell surface	IBA	21873635
GO:0009986	Component	Cell surface	IDA	15150161, 17292328
GO:0030139	Component	Endocytic vesicle	ISS
GO:0030534	Process	Adult behavior	IMP	12669065
GO:0035176	Process	Social behavior	IMP	12669065
GO:0038023	Function	Signaling receptor activity	IBA	21873635
GO:0038023	Function	Signaling receptor activity	ISS
GO:0042043	Function	Neurexin family protein binding	IBA	21873635
GO:0042043	Function	Neurexin family protein binding	ISS	15152050
GO:0045202	Component	Synapse	IBA	21873635
GO:0045202	Component	Synapse	ISS
GO:0048488	Process	Synaptic vesicle endocytosis	IBA	21873635
GO:0048675	Process	Axon extension	ISS
GO:0050804	Process	Modulation of chemical synaptic transmission	IBA	21873635
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:0089717	Component	Spanning component of membrane	TAS	21838267
GO:0097104	Process	Postsynaptic membrane assembly	IBA	21873635
GO:0097104	Process	Postsynaptic membrane assembly	ISS
GO:0097105	Process	Presynaptic membrane assembly	IBA	21873635
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:0098985	Component	Asymmetric, glutamatergic, excitatory synapse	TAS	21838267
GO:0099054	Process	Presynapse assembly	TAS	21838267
GO:0099055	Component	Integral component of postsynaptic membrane	ISS
GO:2000463	Process	Positive regulation of excitatory postsynaptic potential	ISS
GO:2000969	Process	Positive regulation of AMPA receptor activity	ISS

MIM	HGNC	e!Ensembl
300336	14289	ENSG00000196338

Protein

UniProt ID

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

Show/Hide Causal Diseases (3)

Disease term	Disease name	dbSNP ID	References
Causal
Autism	NON RARE IN EUROPE: Autism, Autistic Disorder, Autistic behavior	rs121964908, rs62643608, rs181327458, rs797046134, rs869312704, rs1555013332, rs876657679, rs1057518999, rs1057518658, rs771827120, rs1555187899, rs773080572, rs753871454, rs1684130791, rs1684180699 View all (8 more)	12669065, 18621663
Autism spectrum disorder	Autism Spectrum Disorders	rs724159978, rs75184679, rs119103221, rs9332964, rs121912562, rs1594344233, rs727504317, rs111033204, rs1801086, rs587784464, rs724159948, rs764659822, rs794727977, rs796052733, rs796052728 View all (51 more)
Mental retardation	Mental Retardation, Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)

Show/Hide Unknown Diseases (2)

Disease term	Disease name	Evidence	Source
Unknown
Autism, X-Linked	autism, susceptibility to, X-linked 1		GenCC
Prostate cancer	Prostate cancer	Together, these results show that PRRX2 is an oncogene and might play a role in the aggressiveness of PC within the DNPC population.	GWAS, CBGDA

Show/Hide Text Mining Associations (10)

Disease Name	Relationship Type	References
Associations from Text Mining
Autism Spectrum Disorder	Associate	12669065, 16648374, 18555979, 21569590, 22892527, 27782075, 34893870
Autistic Disorder	Associate	12669065, 16648374, 18555979, 20227402, 25167861, 27897003
Fragile X Syndrome	Associate	34893870
Glioblastoma	Associate	37443071
Glioma	Associate	30094719, 30636076, 31410219, 32372724, 35148403
Hirschsprung Disease	Associate	29622757
Intellectual Disability	Associate	23871722
Neoplasms	Associate	37443071
Prader Willi Syndrome	Associate	34893870
Proteostasis Deficiencies	Associate	20227402

NLGN3 (neuroligin 3)