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Rhizomelic Chondrodysplasia Punctata Type 3 via the AGPS Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
AGPS 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4551AGPS81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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


  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

Rhizomelic Chondrodysplasia Punctata (RCDP) is neonatal onset and characterized by proximal shortening of the long bones (rhizomelia), multiple epiphyseal calcifications and joint contractures, cataracts, dysmorphic facies, and profound intellectual disability and growth deficiency. Most patients with RCDP die in the first or second year, and a few survive beyond the first decade of life (Braverman et al. 2012). RCDP has three subtypes which are indistinguishable based on clinical presentation. Type 1 accounts for ~ 90% of clincially diagnosed RCDP and is a peroxisome biogenesis disorder caused by PEX7 mutations. RCDP types 2 and 3 are due to defects in GNPAT and AGPS, respectively, which encode two peroxisomal single enzymes required for plasmalogen synthesis. Less than 10 patients with AGPS mutations have been reported so far. The characteristic biochemical findings are the same in both RCDP types 2 and 3 patients, including deficient plasmalogen synthesis and normal levels of plasma phytanic acid and VLCFAs (C24:0 and C26:0) (Thai et al. 2001; Itzkovitz et al. 2011). Diagnosis is confirmed by measuring enzyme activity in cultured skin fibroblasts and/or identifying disease causing mutations in the AGPS gene.


RCDP type 3 is an autosomal recessive disorder caused by AGPS defects. AGPS encodes the enzyme alkyl-dihydroxyacetone phosphate synthase which mediates the second step of plasmalogen synthesis in the peroxisomes. The reported AGPS mutations include missense mutations and a gross deletion of exon 11 (Thai et al. 2001; Itzkovitz et al. 2011).

Clinical Sensitivity - Sequencing with CNV PG-Select

PEX7 mutations account for over 90% of all individuals with RCDP. The remaining 10% are caused by defects in GNPAT and AGPS (Braverman et al. 2012). To date, only about 20 patients with RCDP type 2 and less than 10 patients with RCDP type 3 have been reported (Thai et al. 2001; Itzkovitz et al. 2011).

Only one gross deletion affecting AGPS exon 11 has been reported so far (Itzkovitz et al. 2011).

Testing Strategy

This test provides full coverage of all coding exons of the AGPS gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Individuals with clinical symptoms and biochemical findings consistent with RCDP, but without PEX7 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in AGPS.


Official Gene Symbol OMIM ID
AGPS 603051
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Rhizomelic Chondrodysplasia Punctata, Type 3 AR 600121


  • Braverman NE, Moser AB, Steinberg SJ. 2012. Rhizomelic Chondrodysplasia Punctata Type 1. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301447
  • Itzkovitz B, Jiralerspong S, Nimmo G, Loscalzo M, Horovitz DDG, Snowden A, Moser A, Steinberg S, Braverman N. 2012. Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. Hum. Mutat. 33: 189–197. PubMed ID: 21990100
  • Thai TP, Rodemer C, Jauch A, Hunziker A, Moser A, Gorgas K, Just WW. 2001. Impaired membrane traffic in defective ether lipid biosynthesis. Hum. Mol. Genet. 10: 127–136. PubMed ID: 11152660


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

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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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