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Deafness, Autosomal Dominant 69 (DFNA69), and Familial Progressive Hyperpigmentation with or without Hypopigmentation via the KITLG 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
KITLG 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
5043KITLG81479 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.

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


  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Nonsyndromic hearing loss is characterized by difficulty or inability to hear that is not associated with any visible defects involving the external ear, other organs, or any other medical condition. Nonsyndromic hearing loss may be associated with abnormalities involving the middle ear and/or the inner ear (Ciuman 2013; Dodson et al. 2011; Hilgert et al. 2009). At least 70% of cases involving hearing loss are nonsyndromic (Van Camp et al. 1997).

Nonsyndromic hearing loss and deafness due to pathogenic variants in the KITLG gene is associated with congenital or prelingual, mild to profound, asymetric, unilateral or bilateral, non-progressive sensorineural hearing impairment with overall variable penetrance. No vestibular abnormalities are present. Furthermore, no pigmentation effects were detected in two families with hearing loss due to variants in the KITLG gene (Zazo Seco et al. 2015).

Pathogenic variants in the KITLG gene also cause familial progressive hyperpigmentation with or without hypopigmentation, associated with diffuse hyperpigmentation, cafe-au-lait macules and larger hypopigmented ash-leaf macules on the face, neck, trunk and limbs. Onset is congenital or early infancy and progressive with large areas of the skin becoming hyperpigmented. Hearing was not reported as being affected in patients with pigmentation effects (Wang et al. 2009; Amyere et al. 2011).

The KITLG gene has also been suggested as the cause of hearing loss, heterochromia iridum with skin hyper- and hypopigmentation in a single Dutch family. These features along with the absence of dystopia canthorum in this family had resulted in a diagnosis of Waardenburg syndrome type II prior to genetic testing, indicating that variants in the KITLG gene may also cause this auditory-pigmentary disorder (Zazo Seco et al. 2015).


The KIT ligand (KITLG) gene is located on chromosome 12q21.32 and spans 91.7 kb, consisting of 9 coding exons that produce a 273 amino acid protein. The KITLG protein (also known as steel factor, stem cell factor, and mast cell growth factor) is the ligand for the KIT tyrosine-kinase receptor. KITLG is involved in proliferation and migration of neural crest cells as well as survival and differentiation of hematopoietic precursor cells, primordial germ cells and melanoblasts (Zazo Seco et al. 2015). KIT signaling causes post-translational modification of the MITF protein, a key transcription factor involved in the survival, proliferation and differentiation of melanoblasts as well as regulating the expression of genes involved in pigment production (Zazo Seco et al. 2015; Lin and Fisher 2007).

The mechanism by which KITLG variants cause sensorineural hearing loss is not completely understood, although it is thought to be mediated by melanocytes in the stria vascularis of the inner ear that are necessary for generating the endocochlear potential involved in the detection of sound (Kim et al. 2015; Cable et al. 1992).

Six missense, one small deletion and one premature protein termination variant in the KITLG gene have been reported as pathogenic, all of which were inherited in an autosomal dominant manner (Wang et al. 2009; Amyere et al. 2011; Cuell et al. 2015; Zazo Seco et al. 2015).

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity of this sequencing test is not precisely known. Only six point and two small insertion/deletion variants in the KITLG gene have been reported as pathogenic (Human Gene Mutation Database). Analytical sensitivity should be high because all reported variants are detectable by sequencing.

Testing Strategy

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

Patients with nonsyndromic hearing loss; skin hyper/hypopigmentation; or both of these in combination with hair and eye pigmentation abnormalities suggestive of Waardenburg syndrome type II.


Official Gene Symbol OMIM ID
KITLG 184745
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Amyere M. et al. 2011. The Journal of Investigative Dermatology. 131: 1234-9. PubMed ID: 21368769
  • Cable J. et al. 1992. Hearing Research. 64:6-20. PubMed ID: 1490901
  • Ciuman R.R. 2013. Medical Science Monitor. 19: 1195-210. PubMed ID: 24362017
  • Cuell A. et al. 2015. Clinical and Experimental Dermatology. 40:860-4. PubMed ID: 26179221
  • Dodson K.M. et al. 2011. American Journal of Medical Genetics. Part A. 155A: 993-1000. PubMed ID: 21465647
  • Hilgert N. et al. 2009. Mutation Research. 681: 189-96. PubMed ID: 18804553
  • Human Gene Mutation Database (Bio-base).
  • Kim S.H. et al. 2015. Medicine. 94:e1817. PubMed ID: 26512583
  • Lin J.Y. and Fisher D.E. 2007. Nature. 445: 843-50. PubMed ID: 17314970
  • Van Camp G. et al. 1997. American Journal of Human Genetics. 60: 758-64. PubMed ID: 9106521
  • Wang Z.Q. et al. 2009. American Journal of Human Genetics. 84:672-7. PubMed ID: 19375057
  • Zazo Seco C. et al. 2015. American Journal of Human Genetics. 97:647-60. PubMed ID: 26522471


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