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Hypospadias Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
AR 81173,81479
ARX 81404,81403
ATF3 81479,81479
ATRX 81479,81479
B3GLCT 81479,81479
BCOR 81479,81479
BMP4 81479,81479
BMP7 81479,81479
BNC2 81479,81479
CDKN1C 81479,81479
CILK1 81479,81479
CREBBP 81407,81406
CUL7 81479,81479
CYP11A1 81479,81479
DHCR7 81405,81479
DNMT3B 81479,81479
EFNB1 81479,81479
EPG5 81479,81479
ESCO2 81479,81479
EVC 81479,81479
EVC2 81479,81479
FBXL4 81479,81479
FGF10 81479,81479
FGF8 81479,81479
FGFR1 81405,81479
FGFR2 81479,81479
FGFR3 81479,81479
FIG4 81406,81479
FLNA 81479,81479
FRAS1 81479,81479
FREM2 81479,81479
GATA4 81479,81479
GLI3 81479,81479
GNRHR 81479,81479
GPC3 81479,81479
GRIP1 81479,81479
HBA1 81479,81479
HCCS 81479,81479
HNF1B 81405,81404
HOXA13 81479,81479
HOXA4 81479,81479
HOXB6 81479,81479
HSD17B3 81479,81479
HSD3B2 81479,81479
IRF6 81479,81479
MAMLD1 81479,81479
MAP3K1 81479,81479
MED12 81479,81479
MID1 81479,81479
MKKS 81479,81479
NR5A1 81479,81479
PCNT 81479,81479
PDE4D 81479,81479
PEX1 81479,81479
PITX2 81479,81479
POR 81479,81479
PTDSS1 81479,81479
PTPN11 81406,81479
RBBP8 81479,81479
SALL1 81479,81479
SETBP1 81479,81479
SOX2 81479,81479
SPECC1L 81479,81479
SRD5A2 81479,81479
TMEM70 81479,81479
TP63 81479,81479
UBR1 81479,81479
WDR11 81479,81479
WDR35 81479,81479
WNT7A 81479,81479
WT1 81405,81479
ZEB2 81405,81404
ZFPM2 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
6905Genes x (73)81479 81173(x1), 81403(x1), 81404(x3), 81405(x5), 81406(x3), 81407(x1), 81479(x132) $990 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 Custom Panel tool.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

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.


Genetic Counselors


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Hypospadias is one of the most common congenital malformations of the male external genitalia, affecting one in 200-300 boys (Blaschko et al. 2012. PubMed ID: 22790208). It is defined as a defect in the development of the ventral aspect of the penis along with an ectopic opening of the urethral meatus (Kalfa et al. 2011. PubMed ID: 21256920). Hypospadias is considered to be a mild form of the 46,XY disorder of sex development (DSD) (Hughes et al. 2006. PubMed ID: 18947601). Hypospadias can present as an isolated condition or can be accompanied by additional abnormalities, most commonly other genitourinary abnormalities including cryptorchidism, bifid scrotum, vesicoureteral reflux, and inguinal hernia (Holmes. 2012). In addition, Hypospadias can be associated with various syndromic disorders, including the androgen insensitivity syndrome, Denys-Drash syndrome, Opitz syndrome, Smith-Lemli-Opitz syndrome, and WAGR syndrome (van der Zanden et al. 2012. PubMed ID: 22371315; Shih et al. 2014. PubMed ID: 24657417; Bouty et al. 2015. PubMed ID:26613581).


Hypospadias is a multifactorial complex condition with both genetic and environmental factors involved in the pathogenesis. Genetic abnormalities, including both chromosomal and single-gene alterations, have been reported to account for about 30% of hypospadias cases (Ságodi et al. 2014. PubMed ID: 24936573). They can be inherited in an autosomal dominant, autosomal recessive, X-linked, or Y-linked manner depending on the gene involved. Genes and genomic regulation involved in the development of the male external genitalia (WT1 and SF1), patterning of genital tubercle (BMP4, BMP7, HOXA4, HOXB6, FGF8, FGFR2), and masculinization (SRY, SOX9, AR, SRD5A, HSD3B2) have all been associated with hypospadias (van der Zanden et al. 2012. PubMed ID: 22371315; Shih et al. 2014. PubMed ID: 24657417; Bouty et al. 2015. PubMed ID: 26613581). See individual gene test descriptions for information on molecular biology of gene products and mutation spectra.

Copy number variants (CNVs) are a common genetic cause of hypospadias. Clinically significant CNVs were detected in 17.2% of patients with hypospadias (Tannour-Louet et al. 2010. PubMed ID: 21048976). For this reason, genetic testing to detect large cytogenetic events and CNVs is recommended in the case of a patient with hypospadias. Our CNV analysis enables these large cytogenetic abnormalities as well as some exon level CNVs to be identified from NGS data.

Clinical Sensitivity - Sequencing with CNV PGxome

This multi-gene panel analyzes genes involved in both syndromic and non-syndromic hypospadias. Genes in this panel account for approximately 20-30% of cases of 46,XY DSD (Baxter et al. 2015. PubMed ID: 25383892). In one cohort, clinically significant deletions and duplications were detected in 17.2% of patients with hypospadias (Tannour-Louet et al. 2010. PubMed ID: 21048976).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.7% 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. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are individuals with hypospadias.


Name Inheritance OMIM ID
3-Beta-Hydroxysteroid Dehydrogenase, Type II, Deficiency Of AR 201810
3-Oxo-5 Alpha-Steroid Delta 4-Dehydrogenase Deficiency AR 264600
46, XX sex reversal 4 AD 617480
46,XY Sex Reversal, Type 3 AD 612965
46,XY Sex Reversal, Type 6 AD 613762
46XY Sex Reversal 9 AD 616067
Achondroplasia AD 100800
Acrodysostosis 2, with or without Hormone Resistance AD 614613
Adrenal Insufficiency, Congenital, With 46,XY Sex Reversal, Partial Or Complete AR 613743
ADULT Syndrome AD 103285
Alpha Thalassemia AD 604131
Amyotrophic Lateral Sclerosis Type 11 AD 612577
Androgen Resistance Syndrome XL 300068
Antley-Bixler Syndrome AD 207410
Antley-Bixler Syndrome With Genital Anomalies And Disordered Steroidogenesis AR 201750
Apert Syndrome AD 101200
Aplasia Of Lacrimal And Salivary Glands AD 180920
ATR-X Syndrome XL 301040
Atrial Septal Defect 2 AD 607941
Atrioventricular Septal Defect 4 AD 614430
Axenfeld-Rieger syndrome, type 1 AD 180500
Bardet-Biedl Syndrome 6 AR 605231
Beckwith-Wiedemann Syndrome AD 130650
Bent bone dysplasia syndrome AD 614592
Bladder Cancer AD 109800
Camptodactyly, Tall Stature, And Hearing Loss Syndrome AR, AD 610474
Cardiac Valvular Dysplasia, X-Linked XL 314400
Centromeric Instability Of Chromosomes 1,9 And 16 And Immunodeficiency AR 242860
Cervical Cancer AR, AD 603956
Charcot-Marie-Tooth Disease, Type 4J AR 611228
Cranioectodermal Dysplasia 2 AR 613610
Craniofrontonasal Dysplasia XL 304110
Crouzon Syndrome AD 123500
Crouzon Syndrome With Acanthosis Nigricans AD 612247
Cutis Gyrata Syndrome Of Beare And Stevenson AD 123790
Diabetes Mellitus, Noninsulin-Dependent AD 125853
Disordered Steroidogenesis Due To Cytochrome P450 Oxidoreductase Deficiency AR 613571
Drash Syndrome AD 194080
Ectrodactyly, Ectodermal Dysplasia, And Cleft Lip/Palate Syndrome 3 AD 604292
Ellis-van Creveld Syndrome AR 225500
Endocrine-Cerebroosteodysplasia AR 612651
Epidermal Nevus AD 162900
Epilepsy, juvenile myoclonic, susceptibility to, 10 AD 617924
Fallot Tetralogy AD 187500
Familial Colorectal Cancer AR, AD 114500
Fg Syndrome XL 305450
FG Syndrome 2 XL 300321
Fraser Syndrome AR 219000
Fraser Syndrome 2 AR 617666
Fraser Syndrome 3 AR 617667
Frasier Syndrome AD 136680
Frontometaphyseal Dysplasia XL 305620
Fuhrmann Syndrome AR 228930
Greig Cephalopolysyndactyly Syndrome AD 175700
Hand Foot Uterus Syndrome AD 140000
Hartsfield syndrome AD 615465
Hay-Wells Syndrome AD 106260
Heimler syndrome 1 AR 234580
Heinz Body Anemias AD 140700
Hemoglobin H Disease AD 613978
Hypochondroplasia AD 146000
Hypogonadotropic Hypogonadism 14 with or without Anosmia AD 614858
Hypogonadotropic Hypogonadism 7 with or without Anosmia AR 146110
Hypospadias 1, X-Linked XL 300633
Hypospadias 2, X-Linked XL 300758
Hypothalamic Hamartomas AD 241800
IMAGE Syndrome AD 614732
Intestinal Pseudoobstruction Neuronal Chronic Idiopathic X-Linked XL 300048
Iridogoniodysgenesis, Dominant Type AD 137600
Jackson-Weiss Syndrome AD 123150
Jawad syndrome AR 251255
Johanson-Blizzard Syndrome AR 243800
Juvenile Myelomonocytic Leukemia AD 607785
Kallmann Syndrome 2 AD 147950
Kallmann Syndrome 6 AD 612702
Lacrimoauriculodentodigital Syndrome AD 149730
Lenz-Majewski Hyperostotic Dwarfism AD 151050
LEOPARD Syndrome AD 151100
Limb-Mammary Syndrome AD 603543
Lujan-Fryns Syndrome XL 309520
Malignant Mesothelioma AD 156240
Maturity-Onset Diabetes Of The Young, Type 5 AD 137920
Mckusick Kaufman Syndrome AR 236700
Meacham Syndrome AD 608978
Melnick-Needles Syndrome XL 309350
Mental Retardation, Autosomal Dominant 29 AD 616078
Mental Retardation-Hypotonic Facies Syndrome X-Linked, 1 XL 309580
Metachondromatosis AD 156250
Methemoglobinemia, alpha type AD 617973
Microcephalic Osteodysplastic Primordial Dwarfism Type 2 AR 210720
Microphthalmia Syndromic 3 AD 206900
Microphthalmia Syndromic 6 AD 607932
Microphthalmia Syndromic 7 XL 309801
Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 2 AR 614052
Mitochondrial DNA depletion syndrome 13 (encephalomyopathic type) AR 615471
Mowat-Wilson Syndrome AD 235730
Muenke Syndrome AD 602849
Neoplasm Of Stomach AD 613659
Nephrotic syndrome, type 4 AD 256370
Noonan Syndrome 1 AD 163950
Oculofaciocardiodental Syndrome XL 300166
Oculomaxillofacial Dysostosis AD 600251
OHDO Syndrome, X-linked; OHDOX XL 300895
Opitz G/BBB Syndrome, Type I XL 300000
Opitz GBBB syndrome, type II AD 145410
Orofacial Cleft 11 AD 600625
Osteoglophonic Dysplasia AD 166250
Oto-Palato-Digital Syndrome Type 1 XL 311300
Oto-Palato-Digital Syndrome, Type II XL 304120
Pallister-Hall Syndrome AD 146510
Partington X-Linked Mental Retardation Syndrome XL 309510
Peroxisome biogenesis disorder 1A (Zellweger) AR 214100
Peroxisome biogenesis disorder 1B (NALD/IRD) AR 601539
Peters Plus Syndrome AR 261540
Pfeiffer Syndrome AD 101600
Polydactyly Preaxial Type 4 AD 174700
Polydactyly, Postaxial, Type A1 AD 174200
Polymicrogyria, bilateral temporooccipital AR 612691
Popliteal Pterygium Syndrome AD 119500
Preaxial Deficiency, Postaxial Polydactyly And Hypospadias AD 176305
Premature Ovarian Failure 7 AD 612964
Proud Levine Carpenter Syndrome XL 300004
Rapp-Hodgkin Ectodermal Dysplasia Syndrome AD 129400
Reifenstein Syndrome XL 312300
Renal Cell Carcinoma, Nonpapillary AD 144700
Ring Dermoid Of Cornea AD 180550
Roberts Syndrome AR 268300
Roberts-SC Phocomelia Syndrome AR 269000
Rubinstein-Taybi Syndrome AD 180849
SADDAN AD 616482
Saethre-Chotzen Syndrome AD 101400
Scaphocephaly, Maxillary Retrusion, And Mental Retardation AD 609579
Schinzel-Giedion Midface Retraction Syndrome AD 269150
Seckel Syndrome 2 AR 606744
Short-Rib Thoracic Dysplasia 7 with or without Polydactyly AR 614091
Simpson-Golabi-Behmel Syndrome XL 312870
Smith-Lemli-Opitz Syndrome AR 270400
Spermatogenic Failure 8 AD 613957
Split-Hand/Foot Malformation 4 AD 605289
Stroke 1 AD 606799
Terminal Osseous Dysplasia XL 300244
Testicular Anomalies with or without Congenital Heart Disease AD 615542
Testicular Cancer AD 273300
Testosterone 17-Beta-Dehydrogenase Deficiency AR 264300
Thanatophoric Dysplasia Type 1 AD 187600
Thanatophoric Dysplasia Type 2 AD 187601
Three M Syndrome 1 AR 273750
Townes-Brocks Syndrome AD 107480
Trigonocephaly, Nonsyndromic AD 190440
Ulna And Fibula Absence Of With Severe Limb Deficiency AR 276820
Van Der Woude Syndrome AD 119300
Ventricular Septal Defect 1 AD 614429
Vici Syndrome AR 242840
Weyers Acrofacial Dysostosis AD 193530
Wilms' Tumor XL 194070
X-Linked Periventricular Heterotopia XL 300049
Yunis-Varon Syndrome AR 216340

Related Test



  • Baxter et al. 2015. PubMed ID: 25383892
  • Blaschko et al. 2012. PubMed ID: 22790208
  • Bouty et al. 2015. PubMed ID: 26613581
  • Holmes et al. 2012. Common Malformations.
  • Hughes et al. 2006. PubMed ID: 18947601
  • Kalfa et al. 2011. PubMed ID: 21256920
  • Ságodi et al. 2014. PubMed ID: 24936573
  • Shih et al. 2014. PubMed ID: 24657417
  • Tannour-Louet et al. 2010. PubMed ID: 21048976
  • van der Zanden. et al. 2012. PubMed ID: 22371315


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.
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  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

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  • Billing information along with specimen and shipping instructions are within the requisition form.
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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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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