Cutis Laxa via the PYCR1 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 8541 | PYCR1 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Cutis laxa type 2B is characterized by abnormal growth, developmental delay, and associated skeletal abnormalities. Cutis laxa type 3B is is characterized by aged facial features, sparse hair, eye abnormalities, intrauterine growth retardation and cutis laxa (Berk et al. 2012). The hallmarks of the PYCR1-related cuties laxa are wrinkled skin, joint hyperlaxity, triangular, progeroid facial appearance, psychomotor retardation, hypotonia, and osteopenia. Some other features include finger contractures, corneal opacity, cataract, and adduction of the thumbs (Reversade et al. 2009; Dimopoulou et al. 2013).
Genetics
Mutations in PYCR1 cause autosomal recessive Cutis laxa types 2B and 3B (also called De Barsy syndrome). PYCR1 protein (Pyrroline-5-carboxylate reductase) catalyzes the last step in proline biosynthesis and plays a role in cellular response to oxidative stress. To date, more than 30 unique pathogenic PYCR1 mutations have been identified. They are: missense (63%), splicing 18%, small deletion 12%, one nonsense and one large deletion (Kretz et al. 2011; Reversade et al. 2009; Dimopoulou et al. 2013; Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
Clinical sensitivity should be high. In one study, PYCR1 mutations were found in all 27 families tested (Dimopoulou et al. 2013). PYCR1 mutations explain ~25% of all autosomal recessive cutis laxa type II cases (Dimopoulou et al. 2013).
To date, only one large deletion involving PYCR1 has been reported (Kretz et al. 2011; Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the PYCR1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for this test are patients with symptoms consistent with autosomal recessive cutis laxa with progeroid facial appearance, psychomotor retardation, hypotonia and the family members of patients who have known PYCR1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PYCR1.
Candidates for this test are patients with symptoms consistent with autosomal recessive cutis laxa with progeroid facial appearance, psychomotor retardation, hypotonia and the family members of patients who have known PYCR1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PYCR1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| PYCR1 | 179035 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Cutis Laxa, Autosomal Recessive, Type IIB | AR | 612940 |
| Cutis Laxa, Autosomal Recessive, Type IIIB | AR | 614438 |
Related Tests
Citations
- Berk DR, Bentley DD, Bayliss SJ, Lind A, Urban Z. 2012. Cutis laxa: A review. Journal of the American Academy of Dermatology 66: 842.e1-17. PubMed ID: 22387031
- Dimopoulou A, Fischer B, Gardeitchik T, Schröter P, Kayserili H, Schlack C, Li Y, Brum JM, Barisic I, Castori M, Spaich C, Fletcher E, et al. 2013. Genotype-phenotype spectrum of PYCR1-related autosomal recessive cutis laxa. Mol. Genet. Metab. 110: 352-361. PubMed ID: 24035636
- Human Gene Mutation Database (Bio-base).
- Kretz R, Bozorgmehr B, Kariminejad MH, Rohrbach M, Hausser I, Baumer A, Baumgartner M, Giunta C, Kariminejad A, Häberle J. 2011. Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities. J. Inherit. Metab. Dis. 34: 731-739. PubMed ID: 21487760
- Reversade B, Escande-Beillard N, Dimopoulou A, Fischer B, Chng SC, Li Y, Shboul M, Tham P-Y, Kayserili H, Al-Gazali L, Shahwan M, Brancati F, et al. 2009. Mutations in PYCR1 cause cutis laxa with progeroid features. Nature Genetics 41: 1016-1021. PubMed ID: 19648921
Ordering/Specimens
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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ORDER OPTIONS
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