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Y Chromosome Deletion Analysis

Summary and Pricing

Test Method

Targeted Deletion Testing via PCR
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
Y Chromosome 81479 81479 $350
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
3740Y Chromosome81479 81479 $350 Order Options and Pricing

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

Turnaround Time

4 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.


Genetic Counselors


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Y chromosome deletions are typically characterized by azoospermia, severe to moderate oligozoospermia, and/or abnormal sperm morphology/motility. Males with Y chromosome deletions usually have no obvious symptoms, although physical examination may reveal small testes. Y chromosome deletions are the most frequent cause of spermatogenic failure in infertile men with normal cytogenetic chromosomes. Incidence of these deletions in infertile men is about 3-10% (Silber and Disteche 2012).

A portion of the Y chromosome has been subdivided in three AZF (Azoospermia Factor) regions: AZFa, AZFb and AZFc. Each AZF region contains several genes associated with normal spermatogenesis. AZFa deletions are rare and usually produce the severe phenotype of Sertoli-cell-only syndrome (SCOS). AZFb and/or AZFb/c deletions are uncommon and usually result in severe azoospermia. AZFc deletions are relatively common and result in a variable infertility phenotype, ranging from azoospermia and SCOS to severe or mild oligozoospermia (Silber 2011).

The correct diagnosis of the genetic cause of infertility is important for the further treatment of patients. Furthermore, Y chromosome deletion testing is recommended before a couple undergoes assisted reproduction in order to prevent the possible transmission of the genetic lesion to the next generation.


Y chromosome deletions inherited in a Y-linked manner. Cases of Y chromosome microdeletions usually occur de novo, and due to the infertile phenotype, they are typically not transmitted. Despite their severely impaired spermatogenesis, some males with deletions in the AZF regions have occasionally spontaneously fathered sons who are infertile. In cases where assisted reproductive technology is used to achieve pregnancy, male offspring have the same deletion as their father, with a high risk of male infertility (Silber 2012).

The AZFa region is about 1100 kb long and contains two single-copy genes USP9Y and DDX3Y. Complete deletion of the AZFa region removes both genes. The AZFb and AZFc regions together encompass 24 genes, most of which are present in multiple copies for a total of 46 copies. Complete deletion of AZFb removes 6.2 Mb (including 32 copies of genes). The AZFc region includes 12 genes, each present in a variable number of copies making a total of 32 copies. The classical complete deletion of AZFc, the most frequent pattern among men with deletions of the Y chromosome, removes 3.5 Mb (Krausz 2014).

Clinical Sensitivity - Targeted Deletion

Y chromosome deletions are estimated in 5%-15% of men with non-obstructive azoospermia or severe oligospermia (Silber and Disteche 2012).

Testing Strategy

Testing for deletions involves investigating for the presence or absence of markers located within nonpolymorphic regions of the AZFa, AZFb, and AZFc regions. Y chromosome deletions are detected by multiplex PCR amplification. Over 99% of the five common microdeletions AZFa, AZFb, AZFbc and AZFabc will be detected by this assay (Krausz 2014).

Indications for Test

This test is indicated for men with infertility due to azoospermia or oligospermia, or otherwise unexplained male factor infertility.


Official Gene Symbol OMIM ID
Y Chromosome 0
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Krausz C. et al. 2014. Andrology. 2(1): 5-19. PubMed ID: 24357628
  • Silber S.J. 2011. Fertility and Sterility. 95: 2439-48. PubMed ID: 21704208
  • Silber S.J., Disteche C.M. 2012. Y Chromosome Infertility. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301513


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

Specimen Types

Specimen Requirements and Shipping Details

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