Test Code: 4927

Early Infantile Epileptic Encephalopathy Type 10: PNKP Gene Deletion/Duplication
Test Code: 4927
Turnaround time: 3 weeks


Shen et al. (2010) describes an autosomal recessive disorder, early infantile epileptic encephalopathy type 10, characterized by microcephaly, early- onset intractable seizures and developmental delay in seven families. Additional variable behavioral problems, especially hyperactivity, were reported. Mutations were identified in all seven families in the PNKP gene (19q13.4). PNKP encodes a protein involved in DNA repair.

For patients with suspected early infantile epileptic encephalopathy, 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.

• Shen et al. (2010) Nat Genet, 42:245-249.
• OMIM #605610: PNKP gene
• OMIM #613402: Early Infantile Epileptic Encephalopathy


This test is indicated for:

  • Confirmation of a clinical diagnosis of early infantile epileptic encephalopathy in an individual in whom sequence analysis was negative.
  • Carrier testing in adults with a family history of early infantile epileptic encephalopathy in whom sequence analysis was negative.


DNA isolated from peripheral blood is hybridized to a CGH array to detect deletions and duplications. The targeted CGH array has overlapping probes which cover the entire genomic region.

Please note that a “backbone” of probes across the entire genome are included on the array for analytical and quality control purposes. Rarely, off- target copy number variants causative of disease may be identified that may or may not be related to the patient’s phenotype. Only known pathogenic off-target copy number variants will be reported. Off-target copy number variants of unknown clinical significance will not be reported.


Detection is limited to duplications and deletions. The CGH array will not detect point or intronic mutations. Results of molecular analysis must be interpreted in the context of the patient’s clinical and/or biochemical phenotype.


Submit only 1 of the following specimen types
* Preferred specimen type: Whole Blood

Type: Whole Blood
Specimen Requirements:
In EDTA (purple top) or ACD (yellow top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Saliva
Specimen Requirements:
OrageneTM Saliva Collection kit (available through CEN4GEN) used according to manufacturer instructions.

Specimen Collection and Shipping: Store sample at room temperature. Ship sample within 5 days of collection at room temperature with overnight delivery.

Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed by another third party provider, please submit a copy of the sequencing report with the test requisition.


  • Sequence analysis of the PNKP gene is available and is required before deletion/duplication analysis.
  • Custom diagnostic mutation analysis (test code: 6875) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.