Associated disorders

The SYNGAP1 gene is associated with autosomal dominant intellectual disability (MedGen UID: 382611).

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Pathogenic variants in the SYNGAP1 gene are associated with ~1% of clinical cases of early infantile epileptic encephalopathy (EIEE).

Enzymes that utilize GTP as an energy source often require GTPase activating proteins (GAPs) to catalyze the conversion from GTP to GDP and guanine nucleotide exchange factors (GEFs) to promote turnover of the used GDP molecule and allow new GTP binding. The SYNGAP1 gene encodes a GAP that interacts with the NMDA receptor, a ligand-gated ion channel that allows calcium into the cell after binding to the excitatory neurotransmitter, glutamate.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
SYNGAP1 NM_006772.2