NLGN3 (neuroligin 3)

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
SNPs SNP information provided by dbSNP.
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.
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 information of associated ontologies with gene provided by GO database.
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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
300336 14289 ENSG00000196338
Protein
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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
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
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (1)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Mental retardation intellectual disability rs878853147 N/A
Show/Hide Unknown Diseases (2)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Autism, X-Linked Autism, susceptibility to, X-linked 1, autism, susceptibility to, X-linked 1 N/A N/A ClinVar, GenCC
Prostate cancer Prostate cancer N/A N/A GWAS
Show/Hide Text Mining Associations (10)
Associations from Text Mining Disease 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