Associated disorders

The PNKP gene is associated with autosomal recessive early infantile epileptic encephalopathy (EIEE) (MedGen UID: 462017) and ataxia with oculomotor apraxia.

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Invitae tests that include this gene:

Pathogenic variants in the PNKP gene are a rare cause of clinical cases of early infantile epileptic encephalopathy (EIEE).

DNA is regularly damaged by both intracellular and extracellular insults, necessitating repair to maintain genome integrity. The PNKP gene encodes an enzyme that primes regions of DNA for repair by ensuring that the DNA termini remaining after the removal of a DNA lesion are compatible with extension and ligation.

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
PNKP NM_007254.3