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Hypophosphatemia, X-Linked, via the PHEX 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
PHEX 81406 81406,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9855PHEX81406 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.

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


  • Juan Dong, PhD, FACMG

Clinical Features and Genetics

Clinical Features

X-linked hypophosphatemia (also called Hypophosphatemic rickets) is characterized by rickets with lower-extremity bone deformities, short stature, and recurrent spontaneous abscesses of the teeth. Biochemical findings include hypophosphatemia with low renal phosphate reabsorption, normal serum calcium level with hypocalciuria, normal or low serum level of vitamin D (1,25(OH)2D3), normal serum level of PTH, and increased activity of serum alkaline phosphatases (Gaucher et al. 2009; Ruppe 2014).


X-linked hypophosphatemia is inherited in an X-linked dominant manner with prevalence of 1 in 21,000 individuals. Both males and females can be affected. The PHEX protein coded by the PHEX gene is a phosphate regulating protein with homologies to endopeptidases, which regulate the balance of phosphate in the body. To date, ~370 unique pathogenic variants have been reported. They are: missense (22%), nonsense (16%), splicing (18%) and small deletion/insertion (35%), large deletion/duplication (9%) and four complex rearrangements (Morey et al. 2011; Pekkarinen et al. 2014; Rowe et al. 1997; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

In one study, PHEX pathogenic variants were identified 93 out of 118 probands (79%) (Gaucher et al.2009). In another study, PHEX pathogenic variants were identified in 20 out of 24 unrelated probands (83%), three of these probands carried a large deletion or duplication detected by MLPA method (Beck-Nielsen et al. 2012).

Testing Strategy

This test provides full coverage of all coding exons of the PHEX 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 male or female patients with symptoms and biochemical findings consistent with X-linked hypophosphatemia and the family members of patients who have known PHEX pathogenic variants.


Official Gene Symbol OMIM ID
PHEX 300550
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Hypophosphatemic Rickets, X-Linked Dominant 307800


  • Beck-Nielsen SS, Brixen K, Gram J, Brusgaard K. 2012. Mutational analysis of PHEX, FGF23, DMP1, SLC34A3 and CLCN5 in patients with hypophosphatemic rickets. Journal of Human Genetics 57: 453–458. PubMed ID: 22695891
  • Gaucher C, Walrant-Debray O, Nguyen T-M, Esterle L, Garabédian M, Jehan F. 2009. PHEX analysis in 118 pedigrees reveals new genetic clues in hypophosphatemic rickets. Hum Genet 125: 401–411. PubMed ID: 19219621
  • Gaucher C, Walrant-Debray O, Nguyen T-M, Esterle L, Garabédian M, Jehan F. 2009. PHEX analysis in 118 pedigrees reveals new genetic clues in hypophosphatemic rickets. Hum Genet 125: 401–411. PubMed ID: 19219621
  • Human Gene Mutation Database (Bio-base).
  • Morey M, Castro-Feijóo L, Barreiro J, Cabanas P, Pombo M, Gil M, Bernabeu I, Díaz-Grande JM, Rey-Cordo L, Ariceta G, Rica I, Nieto J, et al. 2011. Genetic diagnosis of X-linked dominant Hypophosphatemic Rickets in a cohort study: tubular reabsorption of phosphate and 1,25(OH)2D serum levels are associated with PHEX mutation type. BMC Med. Genet. 12: 116. PubMed ID: 21902834
  • Pekkarinen T, Lorenz-Depiereux B, Lohman M, Mäkitie O. 2014. Unusually severe hypophosphatemic rickets caused by a novel and complex re-arrangement of the PHEX gene. Am. J. Med. Genet. A 164A: 2931–2937. PubMed ID: 25124877
  • Rowe PSN, Oudet CL, Francis F, Sinding C, Pannetier S, Econs MJ, Strom TM, Meitinger T, Garabedian M, David A, Macher M-A, Questiaux E, et al. 1997. Distribution of Mutations in the PEX Gene in Families with X-linked Hypophosphataemic Rickets (HYP). Hum. Mol. Genet. 6: 539–549. PubMed ID: 9097956 [
  • Ruppe MD. 2014. X-Linked Hypophosphatemia. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJ, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 22319799


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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2) Select Additional Test Options

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