Ordering Recommendation

Aids in determining the cause of azoospermia or oligospermia and helps predict effectiveness of assisted reproductive technologies in men with Y chromosome microdeletions.




Polymerase Chain Reaction/Electrophoresis


Tue, Fri


7-10 days

New York DOH Approval Status

This test is New York DOH approved.

Specimen Required

Patient Preparation

Lavender (EDTA) or pink (K2EDTA). Also acceptable: Yellow (ACD Solution A or B), lt. blue (sodium citrate), green (sodium or lithium heparin).

Specimen Preparation

Do not freeze. Transport 3 mL whole blood. (Min: 1 mL)

Storage/Transport Temperature


Unacceptable Conditions

Serum. Frozen specimens. Severely hemolyzed specimens.


Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable

Reference Interval

By report

Interpretive Data

Background Information: Y Chromosome Microdeletion
Characteristics: Y chromosome microdeletions are typically characterized by azoospermia, severe to moderate oligospermia, or abnormal sperm morphology/motility in men with a normal physical evaluation. Assisted reproductive techniques are contraindicated for men carrying AZFa, AZFb, AZFbc or AZFabc microdeletions, which are classically associated with spermatogenic failure.
Prevalence: 1 in 2,000 to 3,000 males carry Y chromosome deletions/microdeletions.
Penetrance: Approaches 100 percent in males; variable expression may result in intra-familial variation of fertility in men with an identical microdeletion.
Inheritance: Y-linked; microdeletions are typically de novo.
Cause: Microdeletions of the Y chromosome azoospermia factor regions a, b or c (AZFa, AZFb or AZFc).
Mutations Tested: Five common Y chromosome microdeletions: AZFa, AZFb, AZFc, AZFbc, and AZFabc.
Clinical Sensitivity: Estimated at 5 to 10 percent for men with non-obstructive azoospermia or severe oligospermia.
Methodology: Multiplex polymerase chain reaction (PCR) followed by electrophoresis.
Analytical Sensitivity and Specificity: Greater than 99 percent.
Limitations: Diagnostic errors can occur due to rare sequence variations. Mutations within individual genes included in the AZF regions will not be detected.  Breakpoints of identified microdeletions will not be determined. Male infertility due to causes other than Y chromosome microdeletions tested, has not been excluded.

This test was developed and its performance characteristics determined by ARUP Laboratories. It has not been cleared or approved by the US Food and Drug Administration. This test was performed in a CLIA certified laboratory and is intended for clinical purposes.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Compliance Category

Laboratory Developed Test (LDT)


Hotline History


CPT Codes



Component Test Code* Component Chart Name LOINC
2001779 Y CHROM Specimen 31208-2
2001781 Y Chromosome Result 35456-3
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


Y Chromosome Microdeletion