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
10279 ANOS1 81406,81479 Order Options and Pricing
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, 81406, 81407, 81479 $1030 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 PGxome Custom Panel tool.

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

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

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

EMAIL CONTACTS

Genetic Counselors

Geneticist

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).

Genetics

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.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Candidates for this test are patients with symptoms consistent with Kallmann syndrome.

Genes

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

Name
PGxome®

Citations

  • 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/Specimens

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.

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


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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