Neurogenetics Reference Lab · Teaching Example
- Panel
- Intellectual Disability / Autism Panel (1,250 genes)
- Report ID
- TEACH-0003
- Indication
- Global developmental delay, intellectual disability, autism, generalized epilepsy.
- Specimen
- Peripheral blood, EDTA · Received 2026-02-04
- Reported
- 2026-02-19
- Methodology
- Targeted capture NGS, mean depth 200×. Trio analysis.
Patient (anonymized teaching example)
Age 5 years · Male · Mixed ancestry
Clinical: Severe developmental delay, non-verbal, generalized tonic-clonic and absence seizures from age 3, autistic features. Normal MRI.
Reportable Variants
| Gene | Variant | Zygosity | Condition (Mode) | Origin | Classification |
|---|---|---|---|---|---|
Interpretation
This individual is heterozygous for the SYNGAP1 variant c.2059_2062del (p.Asp687fs), a 4-bp deletion that and introduces a . The PTC is well upstream of the last exon-exon junction, predicting (NMD) of the transcript and loss of function from the affected allele. The variant arose de novo (trio-confirmed). SYNGAP1 is an established gene causing autosomal-dominant developmental and epileptic encephalopathy. Classification: Pathogenic per ACMG/AMP (, PS2, PM2_Supporting).
Recommendations
- •Genetic counseling. Recurrence risk for future pregnancies <1% given confirmed de novo origin.
- •Antiepileptic therapy guided by seizure type; valproate often effective for SYNGAP1-related epilepsy.
- •Developmental pediatrics, speech/language, occupational therapy.
- •Connect family to the SYNGAP1 patient community (Syngap Research Fund).