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Metaphyseal Chondrodysplasia, Schmid Type (MCDS) via the COL10A1 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
8771 COL10A1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8771COL10A181479 81479,81479 $890 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 backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Juan Dong, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Schmid-type metaphyseal chondrodysplasia (OMIM#156500) is characterized by short stature with relatively short limbs, bowed legs, and a waddling gait. Radiographic findings include shortening of the tubular bones, anterior cupping, sclerosis and splaying of the ribs, and diffuse metaphyseal flaring and irregularity that is most pronounced at the knees, coxa vara, and femoral bowing (Elliott et al. Am J Med Genet 132A: 191-193, 2005).

Genetics

MCDS is inherited in an autosomal dominant manner and is caused by variants in the COL10A1 gene. COL10A1 encodes collagen X α1-chain, which is comprised of a collagenous domain (COL1) flanked by a short N-terminal noncollagenous domain (NC2) and a C-terminal noncollagenous domain (NC1). Three identical α1(X)-chains form the homotrimer collagen X, which assembly is facilitated by the interaction of the NC1 domain. COL10A1 variants have been shown to cluster in the 3’ region of exon 3 (NC1 domain). They are about equally divided into two types, missense variants and variants that introduce premature termination signals (Bateman et al. Hum Mutat 25:525-534, 2005). Both haploinsufficiency and dominant-negative effects have been documented to be the molecular basis of MCDS (Chan et al. J Biol Chem 276: 7992-7997, 2001; Gregory et al. J Med Genet 37: 627-629, 2000). Variants in COL10A1 can also cause spondylometaphyseal dysplasia, Japanese type (Ikegawa et al. Am J Med Genet 63: 1659-1662, 1998), which has overlapping skeletal features with MCDS.

Clinical Sensitivity - Sequencing with CNV PGxome

This test is predicted to detect disease variants in more than half of individuals with a clinical diagnosis of MCDS (Bonaventure et al. Hum Genet 96: 58-64, 1995; Wallis et al. J Med Genet 33: 450-457, 1996; Bateman et al. Hum Mutat 23: 396, 2004; Makitie et al. Am J Med Genet 137A:241-248, 2005).

Testing Strategy

This test provides full coverage of all coding exons of the COL10A1 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 clinical and radiographic features consistent with Schmid-type metaphyseal chondrodysplasia and family members of patients who have a known COL10A1 variant. Patients suspected to have cartilage-hair hypoplasia but without extra-skeletal findings and who tested negative for RMRP gene are also candidates for this test.

Gene

Official Gene Symbol OMIM ID
COL10A1 120110
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Metaphyseal Chondrodysplasia, Schmid Type AD 156500

Citations

  • Bateman, J. F., et.al. (2004). "Identification of four novel COL10A1 missense mutations in schmid metaphyseal chondrodysplasia: further evidence that collagen X NC1 mutations impair trimer assembly." Hum Mutat 23(4): 396. PubMed ID: 15024737
  • Bateman, J. F., et.al. (2005). "Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia." Hum Mutat 25(6): 525-34. PubMed ID: 15880705
  • Bonaventure, J., et.al. (1995). "Mutations in three subdomains of the carboxy-terminal region of collagen type X account for most of the Schmid metaphyseal dysplasias." Hum Genet 96(1): 58-64. PubMed ID: 7607655
  • Chan, D., et.al. (2001). "Aberrant signal peptide cleavage of collagen X in Schmid metaphyseal chondrodysplasia. Implications for the molecular basis of the disease." J Biol Chem 276(11): 7992-7. PubMed ID: 11115494
  • Elliott, A. M., et.al. (2005). "Hand involvement in Schmid metaphyseal chondrodysplasia." Am J Med Genet A 132A(2): 191-3. PubMed ID: 15578582
  • Gregory, C. A., et.al. (2000). "Equal expression of typ X collagen mRNA fom mutant and wild type COL10A1 alleles in growth plate cartilage from a patient with metaphyseal chondrodysplasia type Schmid." J Med Genet 37(8): 627-9. PubMed ID: 10991694
  • Ikegawa, S., et.al. (1998). "Mutation of the type X collagen gene (COL10A1) causes spondylometaphyseal dysplasia." Am J Hum Genet 63(6): 1659-62. PubMed ID: 9837818
  • Makitie, O., et.al. (2005). "Schmid type of metaphyseal chondrodysplasia and COL10A1 mutations--findings in 10 patients." Am J Med Genet A 137A(3): 241-8. PubMed ID: 16088909
  • Wallis, G. A., et.al. (1996). "Mutations within the gene encoding the alpha 1 (X) chain of type X collagen (COL10A1) cause metaphyseal chondrodysplasia type Schmid but not several other forms of metaphyseal chondrodysplasia." J Med Genet 33(6): 450-7. PubMed ID: 8782043

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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