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Rhizomelic Chondrodysplasia Punctata NGS Panel

Genes:
AGPS;
GNPAT;
PEX7

Syndrome Information

Clinical Description

Symptoms of Rhizomelic Chondroplasia Punctata (RCDP) include proximal shortening of the limbs, cataracts, severe mental retardation, seizures, and calcific stippling of cartilage.  About 50% of patients are clinically severe and do not survive beyond 5 years. RCDP is associated with deficient erythrocyte plasmalogens and elevated phytanic acid (phytanic acid is normal in the newborn period).  Measurement of plasmalogen synthesis and phytanic acid oxidation can be used to distinguish RCDP1 (caused by mutations in PEX7) from two single enzyme defects (RCDP2 caused by mutations in GNPAT and RCDP3 caused by mutations in AGPS) that are clinically indistinguishable from RCDP1.  All three genes are included in this panel.  Copies of the patient's biochemical analysis are extremely helpful in result interpretation.

Inheritance Pattern

Autosomal Recessive

Genotype-Phenotype Correlation

None known

Test Information

Test Method

Next Generation Sequencing (NGS) of the coding regions and intron-exon boundaries of the listed genesDeletion/Duplication: Dosage analysis by normalization of NGS read depth for the listed genes; Sanger sequencing for potential fill in / confirmation  

This test is also available as part of one or more NGS panels for peroxisomal disorders.

Clinical Utility

Identification of causative mutations in known or highly suspicious cases of RCDP based on clinical presentation and the blood biomarker profile; targeted carrier testing of relatives of proband; predictive prenatal testing when familial mutations are known.    

Clinical Sensitivity

Greater than 99% of patients will have at least one mutation identified by this panel; greater than 98% will have both mutations identified. There have been individual case reports of deletions/duplications in PEX7 and AGPS, but no published case series. 

Analytic Sensitivity

> 99% for inherited single nucleotide and small insertion/deletion variants for the nucleotides evaluated; >99% for multi-exon deletions and >98% for single exon deletions; >90% for multi-exon duplications and >75% for single exon duplications. Lower limit of detection for single nucleotide variants: 25% allele frequency (>99% sensitivity).

Sample Requirements

3-6ml whole blood in EDTA (purple topped) tubes. (see Pediatric or Adult blood sample algorithms for additional information)

We prefer whole blood for all tests.

Turn Around Time

Approximately 4 weeks

Fee and CPT Codes

$2601 for routine testing
CPT Code: 81479

Special Considerations

We request that copies of the patient's biochemical analysis be submitted with the sample.

This test is also available as part of one or more NGS panels for peroxisomal disorders.

INFORMED CONSENT from the patient is required prior to ordering a genetic test. The DNA Diagnostic Lab's consent is located on the second page of the requisition form. There is also a patient brochure, "Things Every Patient Should Know Before Consenting to a Genetic Test", available for download.