NLGN1 (neuroligin 1)

Gene

• Entrez ID: 22871
• Gene name: Neuroligin 1
• Gene symbol: NLGN1
• Synonyms (NCBI Gene): NL1, NLG1
• Chromosome: 3
• Chromosome location: 3q26.31
• 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. [provided b

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT720878	hsa-miR-5088-5p	HITS-CLIP	19536157
MIRT720877	hsa-miR-4446-3p	HITS-CLIP	19536157
MIRT720876	hsa-miR-3158-3p	HITS-CLIP	19536157
MIRT708819	hsa-miR-4705	HITS-CLIP	19536157
MIRT708818	hsa-miR-31-3p	HITS-CLIP	19536157
MIRT708817	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT708816	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT708815	hsa-miR-1238-3p	HITS-CLIP	19536157
MIRT708819	hsa-miR-4705	HITS-CLIP	19536157
MIRT708818	hsa-miR-31-3p	HITS-CLIP	19536157
MIRT708817	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT708816	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT708815	hsa-miR-1238-3p	HITS-CLIP	19536157
MIRT736302	hsa-miR-128-3p	Western blotting, qRT-PCR	32058631
MIRT720878	hsa-miR-5088-5p	HITS-CLIP	19536157
MIRT720877	hsa-miR-4446-3p	HITS-CLIP	19536157
MIRT720876	hsa-miR-3158-3p	HITS-CLIP	19536157
MIRT708819	hsa-miR-4705	HITS-CLIP	19536157
MIRT708818	hsa-miR-31-3p	HITS-CLIP	19536157
MIRT708817	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT708816	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT708815	hsa-miR-1238-3p	HITS-CLIP	19536157
MIRT708819	hsa-miR-4705	HITS-CLIP	19536157
MIRT708818	hsa-miR-31-3p	HITS-CLIP	19536157
MIRT708817	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT708816	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT708815	hsa-miR-1238-3p	HITS-CLIP	19536157
MIRT1186650	hsa-miR-129-5p	CLIP-seq
MIRT1186651	hsa-miR-145	CLIP-seq
MIRT1186652	hsa-miR-197	CLIP-seq
MIRT1186653	hsa-miR-300	CLIP-seq
MIRT1186654	hsa-miR-3144-3p	CLIP-seq
MIRT1186655	hsa-miR-3149	CLIP-seq
MIRT1186656	hsa-miR-3671	CLIP-seq
MIRT1186657	hsa-miR-369-3p	CLIP-seq
MIRT1186658	hsa-miR-374a	CLIP-seq
MIRT1186659	hsa-miR-374b	CLIP-seq
MIRT1186660	hsa-miR-381	CLIP-seq
MIRT1186661	hsa-miR-4286	CLIP-seq
MIRT1186662	hsa-miR-4659a-3p	CLIP-seq
MIRT1186663	hsa-miR-4659b-3p	CLIP-seq
MIRT1186664	hsa-miR-4666-3p	CLIP-seq
MIRT1186665	hsa-miR-4778-3p	CLIP-seq
MIRT1186666	hsa-miR-496	CLIP-seq
MIRT1186667	hsa-miR-568	CLIP-seq
MIRT1186668	hsa-miR-607	CLIP-seq
MIRT1186669	hsa-miR-875-5p	CLIP-seq
MIRT2054100	hsa-miR-526b	CLIP-seq
MIRT2581563	hsa-miR-33a	CLIP-seq
MIRT2581564	hsa-miR-33b	CLIP-seq
MIRT2581565	hsa-miR-340	CLIP-seq
MIRT2686386	hsa-miR-193a-3p	CLIP-seq
MIRT2686387	hsa-miR-193b	CLIP-seq
MIRT2686388	hsa-miR-2277-3p	CLIP-seq
MIRT2686389	hsa-miR-3128	CLIP-seq
MIRT2581563	hsa-miR-33a	CLIP-seq
MIRT2581564	hsa-miR-33b	CLIP-seq
MIRT2581565	hsa-miR-340	CLIP-seq
MIRT2686390	hsa-miR-3689a-5p	CLIP-seq
MIRT2686391	hsa-miR-3689b	CLIP-seq
MIRT2686392	hsa-miR-3689e	CLIP-seq
MIRT2686393	hsa-miR-3689f	CLIP-seq
MIRT2686394	hsa-miR-4291	CLIP-seq
MIRT2686395	hsa-miR-4310	CLIP-seq
MIRT2686396	hsa-miR-4470	CLIP-seq
MIRT2686397	hsa-miR-4501	CLIP-seq
MIRT2686398	hsa-miR-4722-3p	CLIP-seq
MIRT2686399	hsa-miR-513a-3p	CLIP-seq
MIRT2686400	hsa-miR-892b	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001540	Function	Amyloid-beta binding	NAS	21838267
GO:0005576	Component	Extracellular region	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	28841651
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	NAS	14522992
GO:0005886	Component	Plasma membrane	TAS
GO:0006605	Process	Protein targeting	ISS
GO:0007155	Process	Cell adhesion	IEA
GO:0007157	Process	Heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	ISS
GO:0007158	Process	Neuron cell-cell adhesion	ISS
GO:0007158	Process	Neuron cell-cell adhesion	NAS	16242404, 25428619
GO:0007158	Process	Neuron cell-cell adhesion	TAS	15797875
GO:0007399	Process	Nervous system development	IMP	28841651
GO:0007399	Process	Nervous system development	ISS
GO:0007416	Process	Synapse assembly	ISS
GO:0009986	Component	Cell surface	ISS	26440732
GO:0010841	Process	Positive regulation of circadian sleep/wake cycle, wakefulness	ISS
GO:0014069	Component	Postsynaptic density	IEA
GO:0014069	Component	Postsynaptic density	TAS	15797875
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	21838267
GO:0016080	Process	Synaptic vesicle targeting	ISS
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	ISS
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	NAS	18084303
GO:0023041	Process	Neuronal signal transduction	TAS	15797875
GO:0030165	Function	PDZ domain binding	IDA	17474715
GO:0030425	Component	Dendrite	ISS
GO:0031175	Process	Neuron projection development	IDA	22750515
GO:0031175	Process	Neuron projection development	ISS
GO:0031594	Component	Neuromuscular junction	NAS	28194405
GO:0032230	Process	Positive regulation of synaptic transmission, GABAergic	ISS
GO:0032230	Process	Positive regulation of synaptic transmission, GABAergic	NAS	16846852
GO:0032433	Component	Filopodium tip	ISS
GO:0035418	Process	Protein localization to synapse	ISS
GO:0038023	Function	Signaling receptor activity	ISS
GO:0042043	Function	Neurexin family protein binding	IEA
GO:0042043	Function	Neurexin family protein binding	ISS
GO:0042043	Function	Neurexin family protein binding	NAS	14522992
GO:0042802	Function	Identical protein binding	ISS
GO:0043083	Component	Synaptic cleft	IEA
GO:0043197	Component	Dendritic spine	ISS
GO:0043235	Component	Receptor complex	ISS
GO:0045184	Process	Establishment of protein localization	ISS
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS
GO:0045211	Component	Postsynaptic membrane	TAS	15797875
GO:0045664	Process	Regulation of neuron differentiation	ISS
GO:0048511	Process	Rhythmic process	IEA
GO:0048789	Process	Cytoskeletal matrix organization at active zone	ISS
GO:0048812	Process	Neuron projection morphogenesis	NAS	29504935
GO:0050804	Process	Modulation of chemical synaptic transmission	ISS
GO:0050839	Function	Cell adhesion molecule binding	ISS
GO:0051491	Process	Positive regulation of filopodium assembly	ISS
GO:0051965	Process	Positive regulation of synapse assembly	IDA	24613359
GO:0051965	Process	Positive regulation of synapse assembly	ISS
GO:0051968	Process	Positive regulation of synaptic transmission, glutamatergic	ISS
GO:0051968	Process	Positive regulation of synaptic transmission, glutamatergic	NAS	16846852
GO:0060076	Component	Excitatory synapse	NAS	25428619
GO:0060999	Process	Positive regulation of dendritic spine development	IGI	23143522
GO:0060999	Process	Positive regulation of dendritic spine development	ISS
GO:0061002	Process	Negative regulation of dendritic spine morphogenesis	IGI	23143522
GO:0071277	Process	Cellular response to calcium ion	ISS
GO:0072553	Process	Terminal button organization	ISS
GO:0097060	Component	Synaptic membrane	IEA
GO:0097091	Process	Synaptic vesicle clustering	ISS
GO:0097104	Process	Postsynaptic membrane assembly	ISS
GO:0097105	Process	Presynaptic membrane assembly	ISS
GO:0097110	Function	Scaffold protein binding	IDA	17474715
GO:0097113	Process	AMPA glutamate receptor clustering	ISS
GO:0097114	Process	NMDA glutamate receptor clustering	IGI	23143522
GO:0097114	Process	NMDA glutamate receptor clustering	ISS
GO:0097115	Process	Neurexin clustering involved in presynaptic membrane assembly	ISS
GO:0097119	Process	Postsynaptic density protein 95 clustering	ISS
GO:0097120	Process	Receptor localization to synapse	ISS
GO:0098635	Component	Protein complex involved in cell-cell adhesion	ISO
GO:0098635	Component	Protein complex involved in cell-cell adhesion	NAS	18084303
GO:0098793	Component	Presynapse	IEA
GO:0098794	Component	Postsynapse	NAS	14522992
GO:0098978	Component	Glutamatergic synapse	NAS	16846852
GO:0098982	Component	GABA-ergic synapse	NAS	16846852
GO:0098984	Component	Neuron to neuron synapse	IEA
GO:0098985	Component	Asymmetric, glutamatergic, excitatory synapse	TAS	21838267
GO:0098989	Process	NMDA selective glutamate receptor signaling pathway	ISS
GO:0098990	Process	AMPA selective glutamate receptor signaling pathway	ISS
GO:0099054	Process	Presynapse assembly	IEA
GO:0099054	Process	Presynapse assembly	TAS	21838267
GO:0099634	Component	Postsynaptic specialization membrane	IBA
GO:0099634	Component	Postsynaptic specialization membrane	ISS
GO:0140058	Process	Neuron projection arborization	ISS
GO:1900029	Process	Positive regulation of ruffle assembly	ISS
GO:1900075	Process	Positive regulation of neuromuscular synaptic transmission	NAS	28194405
GO:1900244	Process	Positive regulation of synaptic vesicle endocytosis	ISS
GO:1902533	Process	Positive regulation of intracellular signal transduction	ISS
GO:1904861	Process	Excitatory synapse assembly	ISS	26440732
GO:2000302	Process	Positive regulation of synaptic vesicle exocytosis	ISS
GO:2000463	Process	Positive regulation of excitatory postsynaptic potential	IGI	23143522
GO:2000463	Process	Positive regulation of excitatory postsynaptic potential	ISS

Other IDs

• MIM: 600568
• HGNC: 14291
• e!Ensembl: ENSG00000169760

Protein

• UniProt ID: Q8N2Q7
• Protein name: Neuroligin-1
• 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 probably mediates its effects by recruiting and clustering other sy
• PDB: 5OJ6, 5OJK
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00135	COesterase	51 → 646	Carboxylesterase family	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the blood vessel walls (at protein level). Highly expressed in brain through prenatal stages, and at lower levels in pancreas islet beta cells. {ECO:0000269|PubMed:18755801, ECO:0000269|PubMed:19926856, ECO:0000269|PubMed:
• Sequence:

  MALPRCTWPNYVWRAVMACLVHRGLGAPLTLCMLGCLLQAGHVLSQKLDDVDPLVATNFG
  KIRGIKKELNNEILGPVIQFLGVPYAAPPTGERRFQPPEPPSPWSDIRNATQFAPVCPQN
  IIDGRLPEVMLPVWFTNNLDVVSSYVQDQSEDCLYLNIYVPTEDVKRISKECARKPGKKI
  CRKGGPLTKKQTDDLGDNDGAEDEDIRDSGGPKPVMVYIHGGSYMEGTGNLYDGSVLASY
  GNVIVITVNYRLGVLGFLSTGDQAAKGNYGLLDLIQALRWTSENIGFFGGDPLRITVFGS
  GAGGSCVNLLTLSHYSEGNRWSNSTKGLFQRAIAQSGTALSSWAVSFQPAKYARMLATKV
  GCNVSDTVELVECLQKKPYKELVDQDIQPARYHIAFGPVIDGDVIPDDPQILMEQGEFLN
  YDIMLGVNQGEGLKFVENIVDSDDGISASDFDFAVSNFVDNLYGYPEGKDVLRETIKFMY
  TDWADRHNPETRRKTLLALFTDHQWVAPAVATADLHSNFGSPTYFYAFYHHCQTDQVPAW
  ADAAHGDEVPYVLGIPMIGPTELFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDT
  KFIHTKPNRFEEVAWTRYSQKDQLYLHIGLKPRVKEHYRANKVNLWLELVPHLHNLNDIS
  QYTSTTTKVPSTDITFRPTRKNSVPVTSAFPTAKQDDPKQQPSPFSVDQRDYSTELSVTI
  AVGASLLFLNILAFAALYYKKDKRRHDVHRRCSPQRTTTNDLTHAQEEEIMSLQMKHTDL
  DHECESIHPHEVVLRTACPPDYTLAMRRSPDDVPLMTPNTITMIPNTIPGIQPLHTFNTF
  TGGQNNTLPHPHPHPHSHSTTRV

• Sequence length: 863

Pathways

KEGG:

Cell adhesion molecules

Reactome:

Neurexins and neuroligins

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism, susceptibility to, 20	Conflicting classifications of pathogenicity; Uncertain significance; risk factor	ClinVar ClinVar, GenCC	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
AUTISTIC DISORDER	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRRITABLE BOWEL SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MIGRAINE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NLGN1-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, SPINE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESTLESS LEGS SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	33522967	Inhibit	★☆☆☆☆ Found in Text Mining only
Amnesia	Amnesia	BEFREE	28283575		★☆☆☆☆ Found in Text Mining only
Amyloidosis	Amyloidosis	BEFREE	31311385		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	GWASCAT_DG	27890468		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorder	Autism	Pubtator	21915259, 22952857, 32127416	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	16077734, 21915259, 22952857, 28841651, 31132842		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	16077734, 20010541, 22671294, 27219346, 28841651, 28972980		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	LHGDN	16077734		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	Pubtator	18084303, 19404257, 27219346	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	CTD_human_DG	19404257		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	BEFREE	21915259		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	21915259		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	GWASCAT_DG	27890468		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cognition Disorders	Cognition disorder	Pubtator	33522967	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34340665	Associate	★☆☆☆☆ Found in Text Mining only
Corticobasal Degeneration	Corticobasal degeneration	Pubtator	33522967	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	GWASCAT_DG	28736931		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	26109803, 28656720		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung disease	Pubtator	26109803	Associate	★☆☆☆☆ Found in Text Mining only
Hypertension	Hypertension	Pubtator	33792450	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	15551338		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	15551338		★☆☆☆☆ Found in Text Mining only
Motion Sickness	Motion Sickness	GWASCAT_DG	25628336		★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	22106001		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	33522967	Associate	★☆☆☆☆ Found in Text Mining only
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	31132842		★☆☆☆☆ Found in Text Mining only
Post-Traumatic Stress Disorder	Stress Disorder	BEFREE	27219346, 30873067		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	34911933	Associate	★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	21915259, 26674772		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	21915259		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	22952857	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	GWASCAT_DG	26198764		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Supranuclear Palsy Progressive	Progressive supranuclear palsy	Pubtator	33522967	Associate	★☆☆☆☆ Found in Text Mining only
Thrombophilia due to Activated Protein C Resistance	Thrombophilia	Pubtator	32661233	Associate	★☆☆☆☆ Found in Text Mining only