NLGN3-related X-linked Susceptibility to Autism Spectrum Disorder: NLGN3 Gene Sequencing

Condition Description

Mutations in the NLGN3 (Xq13) and NLGN4X (Xq22.33 – also referred to as NLGN4) genes have been found in less than 1% of individuals with autism spectrum disorder (ASD).  The clinical phenotype of affected individuals varies widely and can include autism of variable severity, X-linked intellectual disability without autism, Asperger syndrome, and pervasive developmental delay not otherwise specified (PDD-NOS).  Onset may be gradual or abrupt and regression of milestones may occur.  There are usually no dysmorphic features present.  Carrier females are often unaffected, but neuropsychiatric disorders have been reported in a female carrying a deletion of exons 4-6 of NLGN4X.

For patients with suspected  NLGN3-Related X-Linked Susceptibility to Autism Spectrum Disorder, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.

This testing is for mutations in the NLGN3 gene only.


Genes (1)


This test is indicated for:
  • Confirmation of a clinical diagnosis of NLGN3-Related X-Linked Susceptibility to Autism Spectrum Disorder.
  • Carrier testing in adults with a family history of NLGN3-Related X-Linked Susceptibility to Autism Spectrum Disorder.


PCR amplification of 6 exons contained in the NLGN3 gene is performed on the patient's genomic DNA. Direct sequencing of amplification products is performed in both forward and reverse directions, using automated fluorescence dideoxy sequencing methods. The patient's gene sequences are then compared to a normal reference sequence. Sequence variations are classified as mutations, benign variants unrelated to disease, or variations of unknown clinical significance. Variants of unknown clinical significance may require further studies of the patient and/or family members. This assay does not interrogate the promoter region, deep intronic regions, or other regulatory elements, and does not detect large deletions.


Clinical Sensitivity: Mutations in the NLGN3 and NLGN4X genes have been found in less than 1% of individuals with ASD. Mutations in the promoter region, some mutations in the introns and other regulatory element mutations cannot be detected by this analysis. Large deletions will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient's clinical and/or biochemical phenotype.

Analytical Sensitivity: ~99%

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (
Submit only 1 of the following specimen types

Oragene™ Saliva Collection Kit
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
Collection and Shipping
Please do not refrigerate or freeze saliva sample. Please store and ship at room temperature.
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.
  • Deletion/duplication analysis of the NLGN3 gene by CGH array is available for those individuals in whom sequence analysis is negative.
  • Custom diagnostic mutation analysis (KM) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.
  • Prenatal testing is available only for known familial mutations to individuals who are confirmed carriers of mutations. Please contact the laboratory genetic counselor to discuss appropriate testing prior to collecting a prenatal specimen.
  • X-Linked Intellectual Disability panels are available for 30, 60, and 90 genes.
  • Sequencing and deletion/duplication analysis are also available for the NLGN4X gene.

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