Male infertility and male reproductive disorders arise from disruption of a tightly integrated network encompassing the hypothalamic–pituitary–gonadal axis, gonadotropin and GnRH signaling, testicular development and maintenance, steroidogenesis and androgen receptor signaling, meiotic and post-meiotic germ cell differentiation, spermiogenesis, sperm flagellar and acrosomal function, DNA repair and genome integrity, and pathways underlying disorders of sex development and congenital malformations of the male reproductive tract. Germline variants across these pathways contribute to non-obstructive azoospermia, severe oligozoospermia and oligoasthenoteratozoospermia, isolated astheno- or teratozoospermia, hypogonadotropic or hypergonadotropic hypogonadism, androgen insensitivity and 46,XY DSD, congenital bilateral absence of the vas deferens and other obstructive etiologies, as well as syndromic conditions where impaired fertility co-occurs with endocrinologic, skeletal, neurological, renal, or respiratory manifestations. Because clinical findings, hormone profiles, and semen parameters often overlap across etiologies, purely phenotypic and imaging-based evaluation may fail to localize the underlying defect. Early, accurate molecular diagnosis is increasingly critical for defining the cause of infertility, shaping expectations for natural conception versus assisted reproductive technologies (ART), identifying targeted hormonal or surgical strategies where appropriate, recognizing associated health risks and informing reproductive counseling, including options for preimplantation or prenatal diagnosis.
PreCheck Health Services’ Male Infertility & Reproductive Health Panel (68 genes) is a targeted exome next-generation sequencing assay focused on genes with established or strongly supported roles in hereditary male infertility and related reproductive disorders.Gene content is curated using evidence from ACMG/AMP guidelines, ClinGen and other gene–disease validity resources, OMIM, GeneReviews, and contemporary peer-reviewed literature to prioritize loci with well-defined phenotypes and management implications. This design supports high-yield detection of clinically meaningful germline variants that can confirm or refine etiologic classification, guide decisions around hormonal therapy, testicular sperm extraction and ART (including ICSI), avoid ineffective or high-risk interventions, and enable cascade testing of at-risk relatives and informed family-building decisions for affected individuals and their partners.
This assay is designed for individuals assigned male at birth presenting with or at risk for:
● Primary infertility with abnormal semen parameters of unclear etiology, including non-obstructive azoospermia, severe oligozoospermia, or oligoasthenoteratozoospermia after initial endocrine, anatomic, and infectious workup
● Suspected non-obstructive spermatogenic failure (e.g., history of cryptorchidism or testicular dysgenesis, reduced testicular volume, elevated FSH and/or LH, normal imaging of the reproductive tract) where a monogenic cause is considered
● Obstructive azoospermia with congenital bilateral absence of the vas deferens (CBAVD) or other congenital anomalies of the vas deferens, epididymis, or ejaculatory ducts, particularly when CFTR-related or other genetic etiologies are suspected
● Hypogonadotropic hypogonadism or GnRH deficiency (e.g., delayed or absent puberty, low gonadotropins and testosterone, possible anosmia or pituitary hormone deficits) suggestive of congenital GnRH pathway or pituitary developmental disorders
● Isolated or syndromic sperm structural and motility defects (e.g., multiple morphological abnormalities of the sperm flagella, severe asthenozoospermia), especially in the context of recurrent assisted reproductive technology (ART) failure or clinical features suggestive of primary ciliary dyskinesia or related ciliopathies
● Individuals with a personal or family history of suspected or confirmed hereditary male infertility, 46,XY DSD, or other monogenic reproductive disorders in whom the specific molecular diagnosis remains unresolved, or where clarifying carrier status, ART-related risk, and recurrence risk is important for reproductive planning and cascade testing
This Male Infertility & Reproductive Health Panel targets germline (constitutional) variants in genes that regulate the hypothalamic–pituitary–gonadal axis, testis development and differentiation, steroidogenesis and androgen signaling, spermatogenesis, sperm structure and motility, and congenital anomalies of the male reproductive tract. The assay is designed for use on peripheral blood or saliva DNA and is not a somatic/tumor profiling test. Genes are organized into biologic and clinical pathways relevant to hypogonadotropic and hypergonadotropic hypogonadism, spermatogenic failure, obstructive and non-obstructive azoospermia, 46,XY disorders of sex development, sperm motility and morphology disorders, and syndromic conditions where impaired fertility is a major feature.
1.Hypothalamic–Pituitary–Gonadal (HPG) Axis, GnRH, and Gonadotropin Signaling
Genes in this group control GnRH production and action, pituitary development and function, and gonadotropin synthesis and signaling. Germline variants cause isolated or syndromic hypogonadotropic hypogonadism (with or without anosmia), congenital combined pituitary hormone deficiencies, pubertal failure, and reproductive endocrine phenotypes with reduced sex steroids and impaired spermatogenesis. Representative genes include:
● ANOS1, CHD7, FEZF1, FGF17, FGF8, FGFR1, FGFR2, FSHB, FSHR, GNRH1, GNRHR, HESX1, KISS1R, LHB, LHCGR, LHX3, LHX4, NSMF, PCSK1, PROK2, PROKR2, PROP1, TAC3, TACR3, WDR11
2.Disorders of Sex Development, Testis Determination, and Androgen Pathway
This category includes genes essential for early gonadal differentiation, anti-Müllerian hormone signaling, Leydig cell function, steroidogenesis, and androgen receptor action. Variants cause 46,XY DSD, ambiguous or undervirilized genitalia, isolated or syndromic gonadal dysgenesis, primary testicular failure, and androgen insensitivity or androgen biosynthesis defects.
● AMH, AMHR2, AR, CYP11A1, CYP17A1, CYP19A1, DHH, HSD17B3, INSL3, MAP3K1, NR0B1, NR5A1, POR, SOX9, SRD5A2, SRY, STAR, TRIM32
3.Spermatogenic Failure, Meiosis, and Post-Meiotic Germ Cell Maturation
These genes are involved in meiotic recombination, synaptonemal complex function, homologous recombination, chromatin remodeling, and late stages of spermatid differentiation and sperm head formation. Pathogenic variants are associated with non-obstructive azoospermia, severe oligozoospermia, spermatogenic arrest, and qualitative sperm abnormalities (e.g., globozoospermia).
● DPY19L2, PSMC3IP, STAG3, ZMYND15
4.Sperm Flagellar Structure, Motility, and Ciliary Function
Genes in this group encode axonemal dyneins, radial spoke and central apparatus components, peri-axonemal proteins, and ciliary trafficking factors. Variants can cause severe asthenozoospermia, multiple morphological abnormalities of the sperm flagella (MMAF), and overlap with primary ciliary dyskinesia and syndromic ciliopathies.
● ARL6, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, CCDC39, CCDC40, DNAH1, DNAI1, MKKS, RSPH1, RSPH4A, RSPH9, SPEF2, TTC8
5.Obstructive Azoospermia, Congenital Reproductive Tract Anomalies, and Fertilization Defects
This group includes genes underlying congenital structural anomalies of the male reproductive tract and genes critical for sperm–oocyte interaction. Pathogenic variants are associated with congenital bilateral absence of the vas deferens (CBAVD) and other obstructive phenotypes, as well as fertilization failure in the context of assisted reproductive technologies.
● AMH, AMHR2, CFTR, INSL3, PLCZ1
6.Syndromic and Multisystem Disorders with Prominent Male Reproductive Involvement
Several panel genes cause syndromic conditions in which male infertility, hypogonadism, or DSD is a key component alongside ophthalmologic, renal, metabolic, neurologic, or skeletal features. Molecular diagnosis in these cases informs not only reproductive counseling but also systemic surveillance and multidisciplinary management.
● ARL6, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, CFTR, CHD7, MKKS, NR0B1, NR5A1, WDR11
Genes Analyzed 68 male fertility-related genes.
Technology Platform Illumina NGS (Hybrid-Capture Target Enrichment).
Coverage Metrics >98% bases at ≥20× read depth.
Variant Types Detected SNVs and small indels (≤20 bp) within coding exons ±10 bp intronic boundaries.
Reference Genome GRCh38/hg38.
Bioinformatics Pipeline SeqOne™, ACMG/AMP compliant.
Confirmatory Testing Sanger sequencing or orthogonal method as indicated.
Turnaround Time ~10 calendar days.
Quality Metrics Read quality ≥Q30; allelic balance ≥0.3; minimum coverage 20×.
1.Congenital and Primary Male Infertility
❖ Clarify the etiology of non-obstructive azoospermia, severe oligozoospermia, and qualitative sperm defects (e.g., globozoospermia, MMAF) when standard evaluation (history, exam, semen analysis, basic endocrine testing, karyotype, Y-microdeletion testing) is inconclusive
❖ Distinguish intrinsic spermatogenic failure from potentially reversible or obstructive causes, helping to determine which patients are likely to benefit from testicular sperm extraction (TESE) and intracytoplasmic sperm injection (ICSI) versus those with a very low likelihood of retrieving usable sperm
❖ Support prognosis for natural conception versus the need for assisted reproductive technologies (ART), and inform expectations regarding treatment success rates and counseling for alternative family-building options
2.Hypogonadotropic and Hypogonadism, Pubertal Disorders, and Endocrine Evaluation
❖ Identify genetic causes of congenital hypogonadotropic hypogonadism (CHH), Kallmann syndrome, combined pituitary hormone deficiencies, and primary testicular failure in adolescents and adults with delayed or absent puberty, low testosterone, and abnormal gonadotropins
❖ Differentiate isolated reproductive axis defects from broader pituitary or syndromic endocrinopathies, guiding appropriate endocrine workup, imaging, and monitoring for associated hormonal deficiencies
❖ Inform individualized management plans, including timing and selection of hormone replacement, induction of puberty, and fertility-directed therapies (e.g., gonadotropin or GnRH therapy) where feasible
3.Disorders of Sex Development (DSD), Androgen Pathway Defects, and Genital Anomalies
❖ Define the molecular basis of 46,XY DSD, ambiguous or undervirilized genitalia, severe hypospadias, gonadal dysgenesis, and suspected androgen insensitivity or steroidogenic enzyme deficiencies
❖ Refine risk assessment for gonadal malignancy, inform decisions about sex assignment, timing and extent of genital or gonadal surgery, and long-term endocrine replacement strategies
❖ Support multidisciplinary DSD team management by providing a precise genetic diagnosis that can be integrated with endocrine, surgical, psychological, and ethical considerations across childhood and adulthood
4.Sperm Motility Disorders, Ciliopathies, and Assisted Reproduction Outcomes
❖ Identify genetic etiologies of severe asthenozoospermia and multiple morphological abnormalities of the sperm flagella (MMAF), particularly in men with recurrent ART failure or unexplained poor fertilization despite adequate sperm counts
❖ Inform ART strategy (e.g., ICSI vs alternative approaches), counseling regarding the likelihood of fertilization success, and discussion of reproductive risks to offspring when pathogenic variants are transmitted through ART that bypasses natural selection
5.Syndromic Infertility, Family Management, and Cascade Testing
❖ Recognize syndromic and multisystem disorders (e.g., ciliopathies, CFTR-related CBAVD, CHARGE, adrenal–gonadal dysgenesis syndromes) in which male infertility or hypogonadism is a central but not isolated feature of a broader phenotype
❖ Enable targeted cascade testing of relatives and, when appropriate, partner testing (e.g., CFTR) once a pathogenic or likely pathogenic variant is found, clarifying carrier status, reproductive risk, and considerations for preimplantation or prenatal genetic testing
Male Infertility & Reproductive Health genetic testing provides clinically actionable information across andrology, reproductive endocrinology, urology, medical genetics, endocrinology, primary care, and assisted reproductive technology (ART) programs. Results directly influence diagnostic resolution, management decisions, risk assessment, and family-building strategies.
Risk Stratification and Diagnostic Clarification Identify pathogenic or likely pathogenic variants underlying non-obstructive azoospermia, severe oligozoospermia, qualitative sperm abnormalities (e.g., globozoospermia, MMAF), congenital hypogonadotropic hypogonadism, primary testicular failure, 46,XY disorders of sex development, and CFTR-related or other causes of obstructive azoospermia. Distinguish intrinsic spermatogenic failure from obstructive, endocrine, environmental, or acquired etiologies. Refine differential diagnoses generated by semen analysis, endocrine testing, imaging, and urologic evaluation, converting a “suspected” reproductive disorder into a definitive, gene-based diagnosis.
Family Risk Assessment, Cascade Testing, and Reproductive Counseling
Clarify recurrence risk in families and identify at-risk relatives once a pathogenic or likely pathogenic variant is detected. Support targeted cascade testing for conditions such as CFTR-related CBAVD, androgen biosynthesis defects, or familial hypogonadotropic hypogonadism. Inform reproductive planning for affected individuals and their partners, including decisions regarding ART, the relevance of partner testing (e.g., CFTR), and the availability of preimplantation genetic testing or prenatal diagnosis. Provide anticipatory guidance for gene-positive male relatives who may develop hypogonadism, pubertal delay, or infertility later in life.
Treatment Selection, Fertility Optimization, and Endocrine Management
Use molecular diagnosis to guide medical and surgical interventions, including selection of men likely to benefit from gonadotropin or GnRH therapy, TESE-ICSI, or correction of obstructive anomalies. Avoid ineffective or invasive procedures unlikely to yield sperm in the presence of specific meiotic arrest or severe flagellar defects. Inform targeted management for androgen biosynthesis disorders, androgen insensitivity, and steroidogenic enzyme deficiencies. Support individualized hormonal therapy, timing of pubertal induction, and monitoring for comorbid endocrine abnormalities in syndromic conditions.
Integrated Longitudinal Reproductive and Men’s Health Care
Support multidisciplinary teams (urology/andrology, reproductive endocrinology, medical genetics, primary care, psychology/counseling, and ART programs) in building integrated, gene-informed care plans. Coordinate long-term endocrine surveillance, fertility preservation discussions, management of syndromic extracranial features (e.g., renal or respiratory manifestations in ciliopathies, endocrine issues in CHARGE or adrenal–gonadal dysgenesis), and transition of adolescent patients into adult reproductive and men’s health care. Provide a durable molecular framework that evolves with updates to variant classification, reproductive technologies, and clinical guidelines, ensuring consistent management of hereditary male infertility and reproductive disorders across the patient’s lifespan.
This Male Infertility & Reproductive Health Panel is best used as part of a multi-dimensional diagnostic strategy, often in combination with:
Pharmacogenetics Testing (for drug metabolism and gene-drug interactions)
Together, these tools enable precision medicine teams to offer a fully customized, data-driven treatment plan for each patient.
Germline testing for male infertility and reproductive disorders has become a central component of precision reproductive medicine, enabling clinicians to define the molecular basis of non-obstructive azoospermia, severe oligozoospermia, qualitative sperm defects, hypogonadotropic or hypergonadotropic hypogonadism, 46,XY disorders of sex development, androgen biosynthesis and receptor defects, congenital obstructive anomalies such as CFTR-related CBAVD, and syndromic conditions in which infertility is a key manifestation. When integrated with semen analysis, endocrine evaluation, imaging, and clinical assessment, a well-curated gene panel provides diagnostic clarity that is not achievable through phenotypic evaluation alone.
With high analytic performance, strong gene–disease validity curation, and clinically rigorous interpretation, PreCheck Health Services delivers genomic insights that refine diagnosis, guide expectations for natural conception versus assisted reproductive technologies, identify candidates for targeted hormonal or surgical treatment, and support informed decisions around TESE/ICSI, fertility preservation, and family-building. Molecular confirmation also enables targeted cascade testing, clarifies recurrence risk, and ensures that partners receive appropriate genetic counseling when indicated. This integrated genomic approach strengthens long-term reproductive and men’s health management by enabling earlier, more precise, and more individualized care. It provides a durable framework for counseling, surveillance, and treatment across adolescence and adulthood, improving outcomes for affected individuals and supporting informed reproductive planning for families.
The Male Infertility & Reproductive Health Panel is designed to detect single-nucleotide variants (SNVs) and small insertions and deletions in 68 genes associated with male infertility. Targeted regions for this panel include the coding exons and 10 bp intronic sequences immediately to the exon-intron boundary of each coding exon in each of these genes. Extracted patient DNA is prepared using targeted hybrid capture, assignment of a unique index, and sequencing via Illumina sequencing by synthesis (SBS) technology. Data is aligned using the human genome build GRCh38. Variant interpretation is performed according to current American College of Medical Genetics and Genomics (ACMG) professional guidelines for the interpretation of germline sequence variants using SeqOne Pipeline.
AMH, AMHR2, ANOS1, AR, ARL6, BBS1, BBS2, BBS4, BBS5, BBS7, BBS9, BBS10, BBS12, CCDC39, CCDC40, CFTR, CHD7, CYP11A1, CYP17A1, CYP19A1, DHH, DNAH1, DNAI1, DPY19L2, FEZF1, FGF8, FGF17, FGFR1, FGFR2, FSHB, FSHR, GNRH1, GNRHR, HESX1, HSD17B3, INSL3, KISS1R, LHB, LHCGR, LHX3, LHX4, MAP3K1, MKKS, NR5A1, NR0B1, NSMF, PCSK1, PLCZ1, POR, PROK2, PROKR2, PROP1, PSMC3IP, RSPH1, RSPH4A, RSPH9, SOX9, SPEF2, SRD5A2, SRY, STAG3, STAR, TAC3, TACR3, TRIM32, TTC8, WDR11, ZMYND15
This test aims to detect all clinically relevant variants within the coding regions of the genes evaluated. Pathogenic and likely pathogenic variants detected in these genes should be confirmed by orthogonal methods. Detected genetic variants classified as benign, likely benign, or of uncertain significance are not included in this report. Homopolymer regions and regions outside of the coding regions cannot be captured by the standard NGS target enrichment protocols. Currently, the assay does not detect large deletions and duplications. This analysis also cannot detect pathogenic variants within regions that were not analyzed (e.g., introns, promoter and enhancer regions, long repeat regions, and mitochondrial sequence). This assay is not designed to detect mosaicism and is not designed to detect complex gene rearrangements or genomic aneuploidy events. It is important to understand that there may be variants in these genes undetectable using current technology. Additionally, there may be genes associated with male infertility whose clinical association has not yet been definitively established. The test may therefore not detect all variants associated with male infertility. The interpretation of variants is based on our current understanding of the genes in this panel and is based on current ACMG professional guidelines for the interpretation of germline sequence variants. Interpretations may change over time as more information about the genes in this panel becomes available. Qualified health care providers should be aware that future reclassifications of genetic variants can occur as ACMG guidelines are updated. Factors influencing the quantity and quality of extracted DNA include, but are not limited to, collection technique, the amount of buccal epithelial cells obtained, the patient’s oral hygiene, and the presence of dietary or microbial sources of nucleic acids and nucleases, as well as other interfering substances and matrix-dependent influences. PCR inhibitors, extraneous DNA, and nucleic acid-degrading enzymes may adversely affect assay results.
This laboratory-developed test (LDT) was developed, and its performance characteristics were determined by PreCheck Health Services, Inc. This test was performed at PreCheck Health Services, Inc. (CLIA ID: 10D2210020 and CAP ID: 9101993), which is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) as qualified to perform high complexity testing.
This assay has not been cleared or approved by the U.S. Food and Drug Administration (FDA). Clearance or approval by the FDA is not required for the clinical use of this analytically and clinically validated laboratory-developed test. This assay has been developed for clinical purposes, and it should not be regarded as investigational or for research.
1. American Society for Reproductive Medicine (ASRM). (2020–2024). Practice Committee Guidelines on the evaluation of male infertility. ASRM.
2. Araujo, T. F., Friedrich, C., Grangeia, A., Carvalho, F., & Sousa, M. (2020). Genetics of MMAF and sperm flagellar defects. Human Genetics, 139(2), 257–275.
3. Biesecker, L. G., & Green, R. C. (2014). Diagnostic clinical genome and exome sequencing. New England Journal of Medicine, 370(25), 2418–2425.
4. Cannarella, R., Condorelli, R. A., La Vignera, S., & Calogero, A. E. (2022). Clinical utility of genetic testing in male infertility. International Journal of Molecular Sciences, 23(3), 1684.
5. Centers for Disease Control and Prevention. (n.d.). CLIA test complexities. U.S. Department of Health & Human Services.
6. Centers for Medicare & Medicaid Services. (2024–2025). Clinical Laboratory Improvement Amendments (CLIA) program overview and updates. U.S. Department of Health & Human Services.
7. CHD7-related references removed? (No—CHD7 is not a reference. Skip.)
8. ClinGen Sequence Variant Interpretation (SVI) Working Group. (2025). Variant classification guidance hub. Clinical Genome Resource.
9. Clinical Genome Resource (ClinGen). (2025). Gene–Disease Validity framework and curation portal. Clinical Genome Resource.
10. College of American Pathologists. (2025). Molecular Pathology Checklist (MM) and NGS best-practice worksheet set (MM09). College of American Pathologists.
11. Congressional Research Service. (2025). FDA’s final rule on laboratory-developed tests (LDTs): Overview and policy considerations. Congressional Research Service.
12. Crooks, K. R., Findeis, S., Karlin-Neumann, G., et al. (2023). Recommendations for next-generation sequencing in molecular pathology. Journal of Molecular Diagnostics, 25(9), 695–716.
13. Houston, B. J., Riera-Escamilla, A., & Krausz, C. (2021). The expanding genetic landscape of male infertility. Nature Reviews Urology, 18(5), 347–360.
14. Illumina, Inc. (2023). TruSight One Sequencing Panels (Data Sheet M-GL-02149 v1.0). Illumina.
15. Jennings, L. J., Arcila, M. E., Corless, C., Kamel-Reid, S., Lubin, I. M., Pfeifer, J., Temple-Smolkin, R., Voelkerding, K. V., & Nikiforova, M. N. (2017). Guidelines for validation of next-generation sequencing–based oncology panels (AMP/ASCO/CAP). Journal of Molecular Diagnostics, 19(3), 341–365.
16. Krausz, C., & Riera-Escamilla, A. (2018). Genetics of male infertility. Nature Reviews Urology, 15(6), 369–384.
17. Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., et al. (2018). ClinVar: Improving access to variant interpretations and supporting evidence. Nucleic Acids Research, 46(D1), D1062–D1067.
18. McLachlan, R. I., & O’Bryan, M. K. (2019). Clinical and genetic approaches to understanding spermatogenic failure. Reproduction, 157(4), R145–R158.
19. Oud, M. S., Volozonoka, L., Smits, R. M., Vissers, L. E. L. M., Ramos, L., & Lambalk, C. B. (2019). Exome sequencing in men with unexplained infertile azoospermia and oligozoospermia. Human Reproduction Update, 25(6), 747–763.
20. Rehm, H. L., Bale, S. J., Bayrak-Toydemir, P., Berg, J. S., Brown, K. K., Deignan, J. L., Friez, M. J., et al. (2013). ACMG clinical laboratory standards for next-generation sequencing. Genetics in Medicine, 15(9), 733–747.
21. Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., et al. (2015). Standards and guidelines for the interpretation of sequence variants. Genetics in Medicine, 17(5), 405–424.
22. Riggs, E. R., Andersen, E. F., Cherry, A. M., Kantarci, S., Kearney, H., Patel, A., Raca, G., et al. (2020). Technical standards for the interpretation and reporting of constitutional copy-number variants. Genetics in Medicine, 22(2), 245–257.
23. Tüttelmann, F., Ruckert, C., & Röpke, A. (2020). Disorders of spermatogenesis: Perspectives for novel genetic diagnostics after 20 successful years of AZF deletion analysis. Andrology, 8(5), 1087–1104.
24. U.S. Food and Drug Administration. (2024–2025). Laboratory developed tests (LDTs): Final rule and implementation resources. U.S. Food and Drug Administration.
25. World Health Organization. (2021). WHO laboratory manual for the examination and processing of human semen (6th ed.). WHO.
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