NLGN3 (neuroligin 3)

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
SNPs SNP information provided by dbSNP.
6
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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
miRNA miRNA information provided by mirtarbase database.
54
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
300336 14289 ENSG00000196338
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG  Reactome
  Cell adhesion molecules   Neurexins and neuroligins
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (4)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Autism, susceptibility to, X-linked 1 Likely pathogenic; Pathogenic rs2147900685, rs2147908798, rs2519748934, rs1460006418 RCV001787304
RCV001794857
RCV002291239
RCV002470678
Autistic behavior Pathogenic rs1569485503 RCV000778067
Hypogonadotropic hypogonadism Pathogenic rs2519735876 RCV003151703
Intellectual disability Likely pathogenic; Pathogenic rs878853147, rs1569485503 RCV000224769
RCV000778067
Show/Hide Unknown Diseases (7)
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Adrenocortical carcinoma, hereditary Benign; Likely benign rs151276700 RCV005907361
Autism spectrum disorder Uncertain significance rs2147900298, rs2519775298 RCV002226421
RCV003127421
Complex neurodevelopmental disorder Uncertain significance rs2092463681 RCV001270905
Cone-rod dystrophy Conflicting classifications of pathogenicity rs376877146 RCV005625635
Show/Hide Text Mining Associations (10)
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
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