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Kallmann Syndrome (KS) Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
ANOS1 81406,81479
CHD7 81407,81479
FGF8 81479,81479
FGFR1 81405,81479
GNRHR 81479,81479
IL17RD 81479,81479
PROK2 81479,81479
PROKR2 81479,81479
SOX10 81479,81479
TACR3 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10279Genes x (10)81479 81405(x1), 81406(x1), 81407(x1), 81479(x17) $990 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

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).

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


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Kallmann syndrome (KS) is a genetic disorder that is characterized by delayed or absent puberty along with an impaired or absent sense of smell (hyposmia or anosmia). This disorder is a form of idiopathic hypogonadotropic hypogonadism (IHH), which is a group of reproductive conditions due to gonadotropin-releasing hormone (GnRH) deficiency (Dodé and Hardelin, 2009. PubMed ID: 18985070; Layman, 2013. PubMed ID: 23650337). Patients with IHH usually present with absent or incomplete pubertal development, low levels of circulating gonadotropins LH (luteinizing hormone) and FSH (follicle-stimulating hormone), but no other abnormalities of the hypothalamic-pituitary axis. IHH can be divided into two major phenotypes: normosmic hypogonadotropic hypogonadism (nHH), in which hypothalamic GnRH gene regulation or GnRH synthesis, secretion, or signaling is impaired; and Kallmann syndrome (KS), in which the migratory pathway of GnRH and olfactory neurons from the nasal region into the hypothalamus is disrupted.

Due to hypothalamic GnRH deficiency, infant boys with KS often demonstrate micropenis and cryptorchidism. Adult males with KS present failure to undergo normal puberty and absence of secondary sexual characteristics. Females with KS usually present with primary amenorrhea or infertility. The lack of the sense of smell is the key feature that distinguishes Kallmann syndrome from other forms of hypogonadotropic hypogonadism. The degree of both the hypogonadism and the smell deficiency vary significantly even within affected family members. In addition to reproductive symptoms, many KS patients exhibit a wide variety of additional signs and symptoms. Commonly recognized non-reproductive features that may be present in KS patients include: digital synkinesia, unilateral renal agenesis, cleft lip and /or palate, dental agenesis, hearing loss, and abnormal eye movements (Kaplan et al., 2010. PubMed ID: 20949504; Layman, 2013. PubMed ID: 23650337; Balasubramanian et al., 2017. PubMed ID: 20301509).


KS is caused by pathogenic variants in a number of different genes and to date, ~50% of KS patients are found to have a pathogenic variant that is identifiable. The most common causes of KS are pathogenic variants in the ANOS1 (KAL1), FGFR1, CHD7, PROKR2, PROK2, FGF8, IL17RD, SOX10, GNRHR and TACR3 genes (Balasubramanian et al., 2017. PubMed ID: 20301509). These genes are known to be involved in the formation and migration of GnRH and olfactory neurons. Pathogenic variant in these genes haven been reported to disrupt the migratory pathway of GnRH and olfactory neurons from the nasal region into the hypothalamus. KS can be inherited in an X-linked (ANOS1), autosomal dominant (FGFR1, CHD7, FGF8, IL17RD, SOX10, PROKR2, PROK2), or autosomal recessive manner (PROKR2, PROK2, GNRHR, TACR3). Some of these genes have also been associated with oligogenic inheritance. See individual gene test descriptions for information on molecular biology of gene products.

Clinical Sensitivity - Sequencing with CNV PGxome

This multi-gene panel analyzes 10 most common genes associated with Kallmann syndrome (KS). Clinical sensitivity for this NGS test is ~50% (Balasubramanian et al., 2017. PubMed ID: 20301509).

Gross deletions in ANOS1 (KAL1) have been reported in 5-10% of patients with X-linked recessive inheritance (Ahmadzadeh et al., 2015. PubMed ID: 26629483). Only 4 large deletions and genomic complex rearrangements involving FGFR1 were reported in patients affected with Kallmann syndrome or related disorders (Fukami et al., 2013. PubMed ID: 23657145). Gross deletions or duplications of other genes in this panel have not been reported in patients with KS (Human Gene Mutation Database).

Testing Strategy

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

This panel provides 100% coverage of all coding exons of the genes 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 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 patients with symptoms consistent with Kallmann syndrome.


Official Gene Symbol OMIM ID
ANOS1 300836
CHD7 608892
FGF8 600483
FGFR1 136350
GNRHR 138850
IL17RD 606807
PROK2 607002
PROKR2 607123
SOX10 602229
TACR3 162332
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test



  • Ahmadzadeh et al., 2015. PubMed ID: 26629483
  • Balasubramanian et al., 2017. PubMed ID: 20301509
  • Dodé and Hardelin, 2009. PubMed ID: 18985070
  • Fukami et al., 2013. PubMed ID: 23657145
  • Human Gene Mutation Database (Bio-base).
  • Kaplan et al., 2010. PubMed ID: 20949504
  • Layman, 2013. PubMed ID: 23650337


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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2) Select Additional Test Options

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