DNA icon

Dystroglycanopathies via the POMK 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
POMK 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8981POMK81479 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


  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Pathogenic variants in the POMK gene cause muscular dystrophies in the dystroglycanopathy spectrum. Walker-Warburg syndrome (WWS), a severe congenital muscular dystrophy with defective neuronal migration and associated with structural brain and eye abnormalities, is the most severe manifestation (van Reeuwijk et al. 2005) seen in the dystroglycanopathy spectrum. Several patients with pathogenic POMK variants have presented with typical WWS, including macrocephaly, hypotonia at birth, tonic seizures, ocular abnormalities, elevated CK levels and cobblestone lissencephaly (Jae et al. 2013; Di Costanzo et al. 2014). However, clinical heterogeneity exists and other milder forms of congenital muscular dystrophy (CMD) (von Renesse et al. 2014) or limb girdle muscular dystrophy with cognitive impairment (Di Costanzo et al. 2014) have been observed. In a milder case, the patient presented in infancy with weakness and delayed motor development and at age 22 has proximal weakness, calf pseudohypertrophy, mild facial weakness, mild intellectual disability and elevated CK, but was still ambulatory (Di Costanzo et al. 2014). In a Lebanese family, two affected siblings presented with congenital muscular dystrophy including hypotonia at birth, motor developmental delay, white matter changes, hearing impairment, and myopathic changes and deficient laminin alpha-2 staining on the muscle biopsy. Both siblings have had progressive muscle weakness and are wheelchair dependent in their teens (von Renesse et al. 2014).


Dystroglycanopathies due to POMK pathogenic variants are inherited in an autosomal recessive manner. Protein O-mannose kinase (POMK) activity is necessary for proper post translational processing of the protein, alpha dystroglycan (ADG). The ADG protein is extensively glycosylated, which is essential for binding to extracellular matrix ligands (in particular laminin-alpha 2). In addition, these branched sugars can be further modified through phosphorylation. POMK is an atypical kinase that phosphorylates the 6-position of O-mannose, specifically after the mannose has been modified by the POMGNT2 and B3GALNT2 enzymes (Yoshida-Moriguchi et al. 2013). Molecular diagnosis (and classification) of the dystroglycanopathy subtypes is complex because extensive locus heterogeneity exists for each disorder (Endo 2015), and because the phenotypes caused by the genes involved with post translational processing of ADG are varied. Pathogenic variants in POMK reported to date include missense, nonsense, and a small deletion (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity cannot be estimated because only a small number of patients have been reported. Analytical sensitivity should be almost 100% because all reported pathogenic variants are detectable by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the POMK 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

Individuals with symptoms consistent with Walker-Warburg syndrome, Muscle-Eye-Brain disease, Congenital Muscular Dystrophy or Limb Girdle Muscular Dystrophy with intellectual disability. Individuals with immunofluorescence results demonstrating hypoglycosylation of alpha-dystroglycan or reduced alpha-dystroglycan in muscle. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in POMK.


Official Gene Symbol OMIM ID
POMK 615247
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Di Costanzo S, Balasubramanian A, Pond HL, Rozkalne A, Pantaleoni C, Saredi S, Gupta VA, Sunu CM, Yu TW, Kang PB, Salih MA, Mora M, et al. 2014. POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations. Hum. Mol. Genet. 23:5781-92. PubMed ID: 24925318
  • Endo T. 2015. Glycobiology of -dystroglycan and muscular dystrophy. Journal of Biochemistry 157: 1–12. PubMed ID: 25381372
  • Human Gene Mutation Database (Bio-base).
  • Jae LT, Raaben M, Riemersma M, Beusekom E van, Blomen VA, Velds A, Kerkhoven RM, Carette JE, Topaloglu H, Meinecke P, Wessels MW, Lefeber DJ, et al. 2013. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. Science 340: 479–483. PubMed ID: 23519211
  • van Reeuwijk, J., et.al. (2005). "Glyc-O-genetics of Walker-Warburg syndrome." Clin Genet 67(4): 281-9. PubMed ID: 15733261
  • von Renesse A, Petkova MV, Lützkendorf S, Heinemeyer J, Gill E, Hübner C, Moers A von, Stenzel W, Schuelke M. 2014. POMK mutation in a family with congenital muscular dystrophy with merosin deficiency, hypomyelination, mild hearing deficit and intellectual disability. J. Med. Genet. 51: 275–282. PubMed ID: 24556084
  • Yoshida-Moriguchi T, Willer T, Anderson ME, Venzke D, Whyte T, Muntoni F, Lee H, Nelson SF, Yu L, Campbell KP. 2013. SGK196 Is a Glycosylation-Specific O-Mannose Kinase Required for Dystroglycan Function. Science 341: 896-9. PubMed ID: 23929950


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

loading Loading... ×


An error has occurred while calculating the price. Please try again or contact us for assistance.

View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

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.
Total Price: loading
Patient Prompt Pay Price: loading
A patient prompt pay discount is available if payment is made by the patient and received prior to the time of reporting.
Show Patient Prompt Pay Price
Copy Text to Clipboard