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Kabuki Syndrome via the KDM6A 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
KDM6A 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15169KDM6A81479 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


  • Stela Berisha, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Kabuki syndrome is a multiple congenital disorder characterized by arched and broad eyebrows, long palpebral fissures with the everted lateral third of the lower eye lids, depressed nasal tip, large protruding earlobes, persistence of fetal fingertip pads, skeletal defects, developmental delay and mental retardation. Other features include congenital heart defects, genitourinary anomalies, cleft lip and/or palate, gastrointestinal anomalies hearing loss, and widely spaced teeth and hypodontia. Patients may also have frequent infections, seizures, and feeding problems (Miyake et al. 2013; Adam et al. 2013).


Kabuki syndrome can be autosomal dominant (caused by mutations in KMT2D, also called MLL2) or X-linked dominant (caused by mutations in KDM6A). The KDM6A protein coded by exons 1 to 29 of the KDM6A gene on Xp11.2 is histone demethylase that specifically demethylates the Lys-27 position of histone H3. In two cohort studies with 303 and 81 clinically diagnosed Kabuki patients, KMT2D mutations were found in 43% -61% of the studied patients, while KDM6A mutations were identified in approximately 1% to 6% of the studied patients (Miyake et al.; Micale et al. 2014).Pathogenic variants in KDM6A cause X-linked dominant Kabuki syndrome, and can affect both males and females. To date, ~20 unique pathogenic variants have been documented and include small deletions, gross deletions and gross insertions. Large deletions/duplications and complex large rearrangements account for 65% of pathogenic variants found in KDM6A (Lindgren et al. 2013; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

In two cohort studies with 303 and 81 clinically diagnosed Kabuki patients, KMT2D pathogenic variants were found in 43% -61% of the studied patients, while KDM6A pathogenic variants were identified in approximately 1% to 6% of the studied patients (Miyake et al.; Micale et al. 2014).

Testing Strategy

This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the KDM6A gene plus 10 bases flanking noncoding DNA in all available transcripts in addition to 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

Candidates for this test are male or female patients with symptoms consistent with Kabuki syndrome.


Official Gene Symbol OMIM ID
KDM6A 300128
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Kabuki Syndrome 2 XL 300867


  • Adam et al. 2019 PubMed ID: 21882399
  • Human Gene Mutation Database (Bio-base).
  • Lindgren et al. 2013. PubMed ID: 23354975
  • Micale et al. 2014. PubMed ID: 24633898
  • Miyake et al. 2013. PubMed ID: 23913813


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

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.
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