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Kallmann Syndrome via the KAL1(ANOS1) Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
ANOS1 81406 81406,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4553ANOS181406 81406,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Idiopathic hypogonadotropic hypogonadism (IHH) is a group of reproductive disorders due to gonadotropin-releasing hormone (GnRH) deficiency (Layman 2013). IHH is characterized by absent or incomplete pubertal development, low levels of circulating gonadotropins and testosterone, and 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 this migratory pathway of GnRH and olfactory neurons from the nasal region into the hypothalamus is disrupted.

Kallmann syndrome is characterized by an impaired sense of smell (hyposmia or anosmia) alongside delayed or absent puberty. It is also characterized by a variety of nonreproductive anomalies including involuntary upper limb mirror movements (bimanual synkinesis), abnormal eye movements, congenital ptosis, abnormal visual spatial attention, hearing impairment, agenesis of the corpus callosum, unilateral (occasionally bilateral) renal agenesis, cleft lip or palate, agenesis of one or several teeth (hypodontia), obesity and other less observed anomalies. The degree of both the hypogonadism and the smell deficiency vary significantly even within affected family members.

Kallmann syndrome 1 is an X-linked recessive disorder caused by defects in the KAL1(ANOS1) gene. Since it is X-linked recessive and the ANOS1 gene escapes X-inactivation, there is not convincing evidence that ANOS1 mutations cause KS in females (Layman 2013).

Genetics

Kallmann syndrome 1 is an X-linked recessive disorder caused by defects in the ANOS1 gene. The ANOS1 gene has 14 coding exons that encode the extracellular glycoprotein anosmin-1 (ANOS1). Genetic defects of ANOS1 include missense, nonsense, splicing site mutations and small indels. Large deletions and duplication are commonly found within the ANOS1 gene or encompassing multiple genes including ANOS1 (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

The prevalence of ANOS1 mutations has been estimated to be 5–10% in males KS patients (both sporadic and familial) and much higher (30-70%) in the clearly X-linked recessive families (Layman 2013). Given that large deletions and duplications are common in the ANOS1 region, ANOS1 mutation detection rate through sequencing is expected to be lower than this number.

Testing Strategy

This test provides full coverage of all coding exons of the ANOS1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are male patients with Kallmann syndrome in X-linked recessive families. Testing is also indicated for family members of patients who have known ANOS1 mutations.

Gene

Official Gene Symbol OMIM ID
ANOS1 300836
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Kallmann Syndrome 1 XL 308700

Related Tests

Name
CHARGE and Kallmann Syndromes Panel
Hypogonadotropic Hypogonadism/Kallmann Syndrome Panel
Kallmann Syndrome (KS) Panel

Citations

  • Human Gene Mutation Database (Bio-base).
  • Layman LC. 2013. Clinical genetic testing for Kallmann syndrome. J. Clin. Endocrinol. Metab. 98: 18601862. PubMed ID: 23650337
  • Layman LC. 2013. The genetic basis of female reproductive disorders: etiology and clinical testing. Mol. Cell. Endocrinol. 370: 138148. PubMed ID: 23499866

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.
  • 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

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ORDER OPTIONS

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View Ordering Instructions

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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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