Developmental Brain Disorder Gene Database

LoF Variant Gene

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Tier

3

NLGN3

HGNC:14289 (protein-coding gene)

neuroligin 3

Unique Cases:
2
Disorders:
ID, SCZ
Last Updated:
November 4, 2024

Summary
Cases
Publications
External

Gene Summary:

DBD Genes Classification
NLGN3 is an Emerging candidate gene classified as Tier 3. Tier 3 genes have one de novo pathogenic loss-of-function variants.
Gene 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 promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity). {ECO:0000250, ECO:0000269|PubMed:15620359}. (Source: Uniprot)
Previous symbols
No previous symbols
Alias symbols
HNL3, KIAA1480, ASPGX1, AUTSX1
Chromosomal Location
Xq13.1
Genomic Coordinates
GRCh37:chrX:70364681-70391051
GRCh38:chrX:71144389-71175307
Associated Disorders
Intellectual Disability

Predictive Scores:

HI Score (Decipher)

10.65

pLI (gnomAD)

0.98

LOEUF (gnomAD)

0.31

Classifications from External Sources:

SFARI Score (SFARI)

1

DDG2P Classification (DDG2P)

Strong

ClinGen Classification (ClinGen)

Moderate1

GenCC Classification (GenCC)

Moderate3 Strong1 Limited1

Publications:

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.
Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.
DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.
SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.
GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
gnomAD
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Autism & Developmental Medicine Institute