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Renal Coloboma Syndrome and Isolated Renal Hypoplasia via the PAX2 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PAX2 81406 81406,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11551PAX281406 81406,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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


  • Wuyan Chen, PhD

Clinical Features and Genetics

Clinical Features

Renal coloboma syndrome (also known as papillorenal syndrome; OMIM# 120330) is an autosomal dominant syndrome characterized by optic nerve abnormalities and renal hypoplasia/dysplasia (Sanyanusin et al. 1995; Bower et al. 2011). Other clinical features include hearing loss and central nervous system anomalies. Extremely variable clinical presentations, even within the same family, have been found in renal coloboma syndrome. Classic ophthalmologic findings include optic nerve coloboma, morning glory anomaly, and excavation of the optic disc. The most common renal findings are renal hypodysplasia, vesicoureteral reflux, renal cysts, and multicystic dysplastic kidneys, all of which are within the typical spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). PAX2 and HNF1B are the two major known CAKUT-causing genes to date (Vivante et al. 2014). PAX2 defects can also cause isolated renal hypoplasia (OMIM# 191830) without optic nerve or hearing abnormalities or with subtle features (Nishimoto et al. 2001).


Both renal coloboma syndrome and isolated renal hypoplasia are autosomal dominant disorders caused by defects in the PAX2 gene (Sanyanusin et al. 1995; Nishimoto et al. 2001). PAX2 has 11 coding exons that encode a member of the “paired box” (PAX) family of transcriptional regulator genes. PAX2 contains a paired domain (exons 2 to 4), octapeptide domain (exon 5), a partial homeodomain (exon 7), and the transactivation domain (exons 8 to 10).

Genetic defects of PAX2 throughout the whole coding region include missense, nonsense, splicing mutations, small deletion/insertions and large deletions encompassing the whole PAX2 gene (Human Gene Mutation Database). PAX2 defects have been reported in approximately 50% of patients with classic findings of renal hypoplasia/dysplasia and abnormalities of the optic nerve (Bower et al. 2011). Of note, de novo PAX2 mutations occur in about 50% of patients.

Clinical Sensitivity - Sequencing with CNV PGxome

PAX2 mutations have been reported in approximately 50% of patients with classic findings of renal hypoplasia/dysplasia and abnormalities of the optic nerve (Bower et al. 2011).

PAX2 mutations were found in 4-6% of patients/fetuses with renal hypodysplasia in three large cohort studies (Weber et al. 2006; Thomas et al. 2011; Madariaga et al. 2013). In a small cohort of 20 unrelated Japanese patients with bilateral renal hypoplasia, PAX2 mutations were detected in two patients (10%) (Nishimoto et al. 2001).

Testing Strategy

This test provides full coverage of all coding exons of the PAX2 gene 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 full 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 patients with renal coloboma syndrome or isolated renal hypoplasia or the CAKUT spectrum disorder. Testing is also indicated for family members of patients who have known PAX2 mutations.


Official Gene Symbol OMIM ID
PAX2 167409
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Papillorenal Syndrome AD 120330
Renal Adysplasia AR 191830


  • Bower M, Salomon R, Allanson J, Antignac C, Benedicenti F, Benetti E, Binenbaum G, Jensen UB, Cochat P, DeCramer S, Dixon J, Drouin R, et al. 2012. Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database. Hum. Mutat. 33: 457-466. PubMed ID: 22213154
  • Human Gene Mutation Database (Bio-base).
  • Madariaga L, Morinière V, Jeanpierre C, Bouvier R, Loget P, Martinovic J, Dechelotte P, Leporrier N, Thauvin-Robinet C, Jensen UB, Gaillard D, Mathieu M, et al. 2013. Severe prenatal renal anomalies associated with mutations in HNF1B or PAX2 genes. Clin J Am Soc Nephrol 8: 1179-1187. PubMed ID: 23539225
  • Nishimoto K, Iijima K, Shirakawa T, Kitagawa K, Satomura K, Nakamura H, Yoshikawa N. 2001. PAX2 gene mutation in a family with isolated renal hypoplasia. J. Am. Soc. Nephrol. 12: 1769-1772. PubMed ID: 11461952
  • Sanyanusin P, McNoe LA, Sullivan MJ, Weaver RG, Eccles MR. 1995. Mutation of PAX2 in two siblings with renal-coloboma syndrome. Hum. Mol. Genet. 4: 2183-2184. PubMed ID: 8589702
  • Sanyanusin P, Schimmenti LA, McNoe LA, Ward TA, Pierpont ME, Sullivan MJ, Dobyns WB, Eccles MR. 1995. Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux. Nat. Genet. 9: 358-364. PMID:  PubMed ID: 7795640
  • Thomas R, Sanna-Cherchi S, Warady BA, Furth SL, Kaskel FJ, Gharavi AG. 2011. HNF1B and PAX2 mutations are a common cause of renal hypodysplasia in the CKiD cohort. Pediatr. Nephrol. 26: 897-903. PMID:  PubMed ID: 21380624
  • Vivante A, Kohl S, Hwang D-Y, Dworschak GC, Hildebrandt F. 2014. Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans. Pediatr. Nephrol. PubMed ID: 24398540
  • Weber S, Moriniere V, Knüppel T, Charbit M, Dusek J, Ghiggeri GM, Jankauskiené A, Mir S, Montini G, Peco-Antic A, Wühl E, Zurowska AM, et al. 2006. Prevalence of mutations in renal developmental genes in children with renal hypodysplasia: results of the ESCAPE study. J. Am. Soc. Nephrol. 17: 2864-2870.  PubMed ID: 16971658


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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