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Intellectual Disability via the PAK3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PAK3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9899PAK381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

X-linked Intellectual Disability (XLID) contributes almost 10-15% of intellectual disability (ID) in males. Mental Retardation, X-linked 30 (MRX30) is a condition of non-syndromic XLID that mostly affects males, although carrier females exhibit occasional symptoms (Peippo et al. 2007). The affected individuals display borderline to severe intellectual disability, with sporadic involvement of additional features such as dysmorphic faces with large ears, upslanting palpebral fissures, oromotor impairment (like drooling, speech difficulties), microcephaly, agenesis of corpus callosum, cerebellar hypoplasia, hypotonia, paranoid psychosis, epilepsy, anxiety, aggression, and schizophrenia (Gedeon et al. 2003; Peippo et al. 2007; Rejeb et al. 2008).


Pathogenic variants in PAK3 have been reported in multiple families with MRX30. PAK3 gene maps to Xq21.3-q24 and consists of 18 exons that encode a 544 amino acid polypeptide. PAK3 serine/threonine kinase forms an activated complex with GTP-bound RAS-like (P21), CDC2 and RAC1, which is necessary for dendrite spine morphogenesis as well as synapse formation and plasticity (Boda et al. 2008, Manser et al. 1994, Huang et al. 2011). Loss-of-function variants in p21-activated kinase-3 gene (PAK3) abolish the kinase activity of the PAK3 protein and contribute to MRX30 by affecting the dendritic spine density and morphology via MAPK signaling (Magini et al. 2014). Nonsense, missense and splicing variants have been reported in PAK3. The disease transmission pattern is X-linked recessive.

Clinical Sensitivity - Sequencing with CNV PGxome

This test is predicted to detect pathogenic variants in <0.1% of individuals with intellectual disability (ID). In this context, it is important to note that although pathological variants over 100 genes have been identified in individuals with XLID, a genetic diagnosis is still lacking in most cases due to extreme clinical and genetic heterogeneity of the condition (Vissers et al. 2016). Analytical sensitivity should be high because all pathogenic variants reported to date are detectable by sequencing.

To date, there is no report of any large deletion or duplication involving this gene.

Testing Strategy

This test provides full coverage of all coding exons of the PAK3 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

This test is primarily indicated for patients with intellectual disabilities (mostly non-syndromic) who are negative for any kind of cytogenetic abnormalities, copy number variations, Fragile-X syndrome and also for the family members of the patients who have PAK3 pathogenic variants. Prenatal diagnosis is possible, if the genetic diagnosis has been firmly established in an affected family member.


Official Gene Symbol OMIM ID
PAK3 300142
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Mental Retardation, X-Linked 30 XL 300558


  • Boda B. et al. 2008. Hippocampus. 18:857-61. PubMed ID: 18481281
  • Gedeon A.K. et al. 2003. American Journal of Medical Genetics. Part A. 120A:509-17. PubMed ID: 12884430
  • Huang W. et al. 2011. Molecular and Cellullar Biology. 31:388-403. PubMed ID: 21115725
  • Magini P. et al. 2014. Human Molecular Genetics. 23: 3607-17. PubMed ID: 24556213
  • Manser E. et al. 1994. Nature. 367:40-6. PubMed ID: 8107774
  • Peippo M. et al. 2007. American Journal of Medical Genetics. Part A. 143A: 2406-16. PubMed ID: 17853471
  • Rejeb I. et al. 2008. European Journal of Human Genetics.16:1358-63. PubMed ID: 18523455
  • Vissers L.E. et al. 2016. Nature Reviews. Genetics. 17: 9-18. PubMed ID: 26503795


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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